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https://f1000research.com/articles/12-921/v1	01 Aug 23	{ "type": "Research Article", "title": "Social bearing of laws and their implementation with reference to irretrievable breakdown of marriage: A comparative study of laws in India and Asian countries", "authors": [ "Raj Kumar Yadav", "Madhu Bala", "Priyanka Chaudhary", "Paramveer Singh", "Aarushi Mittal", "Mohd Kaif", "Akanksha Verma", "Mukesh Kumar Dudi", "Madhu Bala", "Priyanka Chaudhary", "Paramveer Singh", "Aarushi Mittal", "Mohd Kaif", "Akanksha Verma", "Mukesh Kumar Dudi" ], "abstract": "This research study explores the scope of introducing ‘irretrievable breakdown’ as a ground for divorce. Many developed countries have successfully introduced this ground and even removed the time limit with the passage of time for seeking a unilateral divorce. Some societies insist that if this ground is introduced, the number of divorces will increase, but it is not so. In India, a more than 10-years separation may be adopted as grounds for divorce to resolve this concern. This time period may be decreased if neither spouse has a child. The court can decide whether the marriage is ended. This is a comparative study of the laws on marriage in India and other Asian countries and their social effects. In this study, the researchers found that marriage was indissoluble in many countries a few decades ago and is now dissoluble. This paper discusses the concept of divorce and how it came into India with changes in social structure. The paper discusses the introduction of irretrievable breakdown as a ground for divorce in India. It explains the current situation of Asian countries with historical background to support the claim of this ground. Overburdened courts are not expected to look into the personal matter of the parties to the marriage. If parties to the marriage can live happily, they should choose to live peacefully, or amicable solutions can be found with their peer groups. If there is a deadlock, the parties to the marriage must restart their lives. There are certain precautions to remove the possibility of misuse of new grounds of divorce, e.g. ensuring a child's future, declaring the marriage dead by the court and not by the estranged spouses. Media can also play an essential role in saving marriages.", "keywords": [ "Irretrievable breakdown of marriage", "Indian Comparative study", "Divorce laws", "Social norms", "Gender equality", "Mediation", "Arbitration", "Legal reform" ], "content": "Introduction\n\nThe study explores the social bearing of laws and their implementation, focusing on the irretrievable breakdown of marriage in India and other Asian countries. The rationale for this investigation lies in the growing recognition of irretrievable breakdown as a ground for divorce, necessitating a deeper understanding of its implications on the legal and social landscapes.\n\nThis study will examine the laws regarding irretrievable breakdown of marriage in India and other Asian countries and analyse the social context and media’s role in shaping these laws. It will explore the impact of these laws, especially considering gender dynamics, finances, and child custody. The effectiveness of current legal provisions and their implementation will be assessed. Finally, recommendations will be provided for improvements to the legal framework and its implementation. The irretrievable breakdown of marriage is a complex legal and social matter that requires a thorough analysis of its legal framework and social implications. This comparative study examines the legal framework related to the irretrievable breakdown of marriage and its social bearing in India and other Asian countries.\n\nDivorce laws vary significantly from nation to nation. Some countries require a legal separation period before a divorce can be granted, while others have no such requirement. In addition, some nations require one party to demonstrate that the other party is at fault for the marriage breakdown, while others allow for “no-fault” divorce, which does not require either party to prove wrongdoing.\n\nDivorce related laws have changed in recent decades all over the world. Before the codification of laws, the position of women was not equal, and when it came into existence, equal status was being demanded. The authors are of the view after studying the pre-independence India that no law related to divorce was in existence and after the enactment women claimed and exercised their right to divorce. Previously, divorce was based on fault theory, and now there is the shift to the no fault theory. Now, globally many divorces are based on mutual consent. States that are more liberal and permissive in granting divorce have higher divorce rates independent of other factors, such as economic and social progress (Stetson and Wright, 1975). There is no evidence that the law shift from fault to no-fault divorce resulted in increased divorce rates. The existence of divorce laws eliminates support for norms of lifetime obligation (Weitzman, 1996). The quicker legal process and the weaker requirement to show fault or inconsistency have made divorce quicker and potentially less conflict-ridden. When we talk about the effects and determinants of divorce, one of the authors’ findings is refuted by the other. Ultimately one determinant must not be seen in isolation and having dependence on the other. For example, education, income, child, and age gap are not the sole criterion of divorce and no longer exist as these were conceived at the beginning of globalisation. A list of literature is provided in Table 1.\n\nIn divorce, parties start to dislike each other and change their ways. It is formally defined in the Encyclopedia Britannica; divorce is the turning away of partners from each other. Divorce is a complete turn from the couple’s way of life (1910).\n\nDivorce signifies the complete breakdown of the marital bond, and divorced persons return to their original status of being free to marry again. Divorce dissolves the marriage, and the parties return to their unmarried status and are free to marry again. Divorce is the legal dissolution of a socially and legally recognised matrimonial relationship that alters the obligations and privileges of the two persons involved, where all rights and mutual obligations of the marriage cease. In other words, after the decree of divorce, the marriage ends, and the parties cease to be spouses and are at liberty to go their way.\n\nDivorce is merely a process by which legal status is given to a relationship torn apart and can represent the end of two people’s relationship with each other. It is a testament that their relationship failed (Becker & Hill, 1955). Despite the universality of divorce, society tends to give negative values to divorce. It may appear as a simple phenomenon in legal parlance, but its implications in practical life are large. Divorce is also a significant life change with far-reaching social, pathological, legal, personal, economic, and parenting consequences. The reason for low divorce rates during economic recessions is the cost of obtaining a divorce in order to provide financial support for the children and maintain a separate household (Glick & Lin, 1986). Social situations such as social upheaval and war also tend to witness a dramatic increase in the divorce rate. Acocrding to Mckenry and Price (1988), divorce rates may have increased due to the possibility of extramarital affairs developing during wars.\n\nPeople who marry young have a higher probability of divorce (Thornton & Freedman, 1983; Rangarao & Sekhar, 2002). Divorce is high during the early years of marriage and declines rapidly and steadily with marital duration of the considerable time period of five or more years (Martin & Bumpass, 1989; Thornton & Rodgers, 1987). Statistically, it was discovered that individuals getting married before the age of 22 were more likely to be dissatisfied than those married between the ages of 22 and 29 (Hart & Shields, 1926). The biggest risk manifested in this research was when both husband and wife were under the age of 20, they were two to three times more likely to divorce than their counterparts who married in their twenties (Guttmacher, 1981; Norton & Moorman, 1987). The authors also believe that when a marriage does not last for a few days or months, the marriage may be dissolved as an irretrievable breakdown of the marriage.\n\nWhen spouses choose not to stay with each other after a short period, there is less chance of developing a sense of commitment and obligation. The separation period before the marriage’s dissolution may vary from several weeks to several years. This stage involves a series of emotional deaths, and the spouses are no longer interested in investing in their marriage (Mckenry & Price, 1988). Separation refers to couples living apart with the intention of getting divorced or who have been separated permanently or temporarily due to marital discord (Mckenry & Price, 1988). Divorce cannot be understood simply as a discrete legal event that occurs when the divorce papers are signed but as a process that occurs over time (Ganong & Coleman, 1994). Sexual incompatibility is a factor in marital unhappiness. For example, Baber (1953) insisted that sexual incompatibility is the root cause of marital fantasy. Satisfaction is a very complex phenomenon; it has physical, psychological and social contexts (Baber, 1953). Sexual morality issues may arise due to the long-awaited pendency of divorce cases, the parties to the marriage may lead an immoral life because of their desperate relationship and find other ways to satisfy their sexual covet. This is not a good sign of a healthy society (Wadlington, 1977).\n\nThe important factors in divorce are personal unhappiness and a desire to avoid a worst-case scenario. Not surprisingly, removing financial barriers for women and providing alternative sources of emotional and sexual satisfaction are important incentives for both men and women. Men are more likely to cite their children as a significant barrier to divorce. The presence of children in legal disputes, especially in divorces, adds complexity, necessitating careful proceedings to prioritize their needs and welfare. Issues such as custody, financial support, and emotional impacts must be addressed, which may prolong the case. Conversely, cases without children involved can theoretically be resolved faster. The disputing parties can negotiate directly, reducing complexity and potentially hastening resolution. However, it is crucial that speedy resolution does not compromise the justice quality, ensuring the rights of all parties are sufficiently protected and outcomes are equitable, regardless of the presence or absence of children. (Wallerstein & Kelly, 1979).\n\nPersonal religious beliefs are the second most cited barrier for both men and women (Moore & Waite, 1981). The divorce rates can reflect the inadequacies and deficiencies in the functional aspects of the institution of marriage (Moore & Waite, 1981).\n\nWhen problems persist, negative thoughts and suicidal tendencies can increase, and marriage can lack substance. Early resolution of divorce cases can lead to positive thinking for the parties involved, as time in prolonged court proceedings can be aimless and detrimental to the youth (Kposowa, 2003). Despite efforts to preserve the sanctity of marriage, divorce cases are rapidly increasing, indicating a need to recognize irretrievable breakdown as a legitimate ground for divorce (Kposowa, 2003).\n\nDivorce is an index of social change and has two sides. First as a negative and later seen as a positive event in life. During the divorce process, a person can be in pain, see nothing beyond the court date, and consider the court dates as hindrances. However, there have been reports of improved health status after the divorce process (Brown et al., 1980). For some divorced persons, the divorce is painless or result in only slight emotional disturbance. For these persons, divorce resolves a stressful situation and lead to a new sense of competence and development of better relationship and freedom to develop one’s interest (Brown et al., 1980). In contrast, divorce is painful for innocent parties who were not expecting the end of a relationship. Separation distress appears more significant when unexpected and the individual is opposed to the separation.\n\nCommunication difficulties, general incompatibility, not spending enough time at home, infidelity and disagreement over money matters can be reasons for divorce. Divorce is a response to an unsuccessful marriage in which the spouses reject each other, and not the rejection of the idea of marriage or the family. Physical separation is the last stage of divorce, and stages in the divorce process invariably include physical separation as one of the stages that prelude divorce. Separation may occur at any time in the process of dissolution of marriage. Research found that women are more likely to first suggest divorce or separation (Spanier & Thompson, 1984; Goode, 1963). Women may take a longer period to decide on separation. In the research by Spainer and Thompson, women spent an average of 22 months, whereas men spent an average of 12 months making the decision on separation; the average length of time was even longer when the divorce was mutually desired (1984). The strongest predictors of divorce are seen in the first five years of marriage. Higher divorce rates are found in nations where the average age of marriage is lower (Heaton et al., 2001; Morgan & Rindfuss, 1985).\n\nDivorce is allowed globally except in the Philippines and Vatican City. However, Muslims have the right to seek divorce in the Philippines. In 20 countries, namely, Argentina, Australia, Azerbaijan, Belgium, Botswana, Cuba, Germany, Luxembourg, Malta, Mongolia, Netherlands, New Zealand, Portugal, Slovakia, Spain, Sweden, Switzerland, Russia, United Kingdom (except Northern Ireland) and Vatican City there is no need to prove the fault of the other spouse. In other words, there is no existence of fault theory as a ground for divorce.\n\n\nMethods\n\nThis study employs a multifaceted approach, consisting of a doctrinal analysis of pertinent legal frameworks and a socio-legal examination of the law’s societal consequences. The research scrutinizes countries that have already incorporated the irretrievable breakdown as a basis for divorce. It compares them with nations, such as India and other Asian countries, that have yet to adopt this criterion. This is achieved through the review of books and research papers.\n\nThe legal structure and the social repercussions of introducing the irretrievable breakdown as grounds for divorce in Asian countries are briefly explored, revealing that this criterion is utilized for the amicable resolution of matrimonial disputes in all examined countries. We also delve into each country’s historical and cultural contexts to comprehend the social and legal factors influencing their perspectives on divorce.\n\nThe study’s presentation is clear and concise, delineating the research question, objectives, methodology, outcomes, and conclusions. Additionally, the researchers discuss the implications of their findings and offer recommendations for policymakers and other stakeholders.\n\nWe consulted JSTOR, Google Scholar and Scopus for the study. “Fault and no fault theory”, “irretrievable breakdown”, “unilateral divorce” and “determinants contributing in divorce” were search terms used to filter the consulting sources. 167 sources suitable for the research study on the irretrievable breakdown of marriage was used. The research focused on thematic and comparative analysis to gain comprehensive insights into our chosen topic. Each article was analyzed as per the focus of the research and listed out the major themes and sub-themes found in various literatures. For finalizing the themes and sub-themes, comparative analysis was used to differentiate similar or closely associated sub-themes. From December 2021 to April 2023, we conducted extensive research in the chosen field.\n\nImplementing laws related to the irretrievable breakdown of marriage is a topic of interest and importance in many Asian countries, including India. This area of study has been researched in order to compare and contrast the laws and policies of different countries regarding divorce and to identify the reasons behind any variations in implementation.\n\nOne of the main reasons for the study is to understand how the concept of irretrievable breakdown of marriage is defined and applied in different legal systems and to analyse the impact of these laws on the society and individuals involved in the process. This comparative analysis can help identify the strengths and weaknesses of the different approaches taken by various countries and explore the possible ways to improve the implementation of such laws.\n\nMoreover, this study can also provide insights into the social and cultural factors that influence the implementation of divorce laws in different countries. For example, the prevalence of arranged marriages in some Asian countries may affect how divorce is viewed and handled in those societies. Similarly, differences in the social and economic status of women in different countries may have an impact on how divorce laws are implemented.\n\nIn summary, the study of the irretrievable breakdown of marriage and its implementation in different Asian countries is important for understanding the legal, social, and cultural factors that influence the process of divorce. It can provide insights into the strengths and weaknesses of different approaches and help identify areas for improvement in implementing divorce laws. The study outcomes are listed below.\n\nIn Afghanistan, fault-based divorce remains the traditional method for dissolving a marriage, where one spouse can seek a divorce based on the other spouse’s serious fault or wrongdoing, such as adultery, cruelty, desertion, or imprisonment, which makes it impossible for the couple to continue their marriage (Roy, 1990). Unlike in many other countries, Afghanistan’s family law does not currently have provisions for no-fault divorce, meaning that divorce can only be granted based on fault-based grounds, and it necessitates the involvement of a court and a judge (Kamali, 1975).\n\nDivorce was first legalised in Afghanistan during the reign of King Amanullah Khan in 1921, who introduced a new civil code that permitted divorce and other significant social and political reforms (Roy, 1990). The divorce laws in Afghanistan, as outlined by the Civil Code and Sharia law, differ for men and women. Men possess the right to initiate divorce for any reason, while women can only seek divorce under specific grounds, such as abandonment, cruelty, impotence, or failure to provide financial support (Kamali, 1975).\n\nUnder Sharia law, a husband can divorce his wife by saying “I divorce you” three times, whereas women need the permission of their husbands or a court of law to initiate divorce proceedings (Kamali, 1975). Nevertheless, a new law introduced in 2009 offers greater protection for women, requiring men to provide financial support to their wives following a divorce and allowing women to seek divorce under certain conditions, such as abuse or abandonment (Rahmani, 2019).\n\nPethrus et al. (2019) conducted a matched cohort study on marriage and divorce among Swedish soldiers after military deployment to Afghanistan. The study highlights the complexities and unique circumstances surrounding divorce in the context of military deployment in Afghanistan.\n\nDivorce was first legalised in Armenia in 1918, but it was allowed only under limited circumstances, such as adultery, desertion, or abuse (Semerdjian, 2016). During Soviet rule, divorce laws were liberalised, giving both men and women the right to initiate divorce and permitting no-fault divorce in certain cases (Platz, 1995).\n\nArmenian law allows a spouse to file for divorce without the other spouse’s unilateral consent, provided they meet specific requirements like being separated for a certain period or having irreconcilable differences (Semerdjian, 2016). The no-fault theory of divorce, introduced in Armenia in 2004, simplified the process by removing the need for individuals to prove fault or wrongdoing by their spouse (Platz, 1995).\n\nAs per Article 19 of the Armenian Family Code, a divorce may be granted if one or both spouses file a joint or individual petition with a court (Semerdjian, 2016). The court can grant the divorce if it determines that the marriage has broken down and reconciliation is impossible. Additionally, the court may grant a divorce if one spouse is recognized as missing or has been absent for at least a year (Semerdjian, 2016).\n\nDivorce was first legalized in Azerbaijan after it gained independence from the Soviet Union in 1991 (Emami-Yeganeh, 1984). The first Family Code of Azerbaijan was adopted in 1999 to establish the country’s legal framework for marriage and divorce (Bayramov, 2021).\n\nIn Azerbaijan, divorce can be granted in cases of mutual agreement between spouses or on the grounds of irretrievable marriage breakdown, usually established through a court process. According to the Family Code of Azerbaijan, both parties must agree to a divorce for it to be granted. If one party does not agree to the divorce, the case can be taken to court, where the judge will consider the circumstances of the marriage and make a decision on whether to grant the divorce (Bayramov, 2021).\n\nCouples can obtain a divorce by mutual consent after a one-month waiting period without having to prove any fault. Suppose one party wishes to obtain a divorce unilaterally, they can do so after a three-month cooling-off period based on the no-fault theory. Under Azerbaijan’s Family Code, either spouse may file for divorce without stating any grounds for divorce through unilateral divorce provisions. The spouse who files for divorce must notify the other spouse and provide a copy of the divorce petition. If the other spouse does not object or the court rejects the objection, the divorce will be granted based on the petitioner’s request (Bayramov, 2021).\n\nHowever, in cases involving children, the court may require a joint custody agreement to be reached before granting the divorce (Bayramov, 2021).\n\nIn Bahrain, divorce laws have undergone various changes (Al Gharaibeh, 2011; Jones, 2007). The history of Bahrain’s divorce laws can be traced back to the country’s legal system, which is based on Islamic law. Traditionally, Islamic law required fault-based grounds for divorce, such as adultery or cruelty, and the husband had the unilateral right to initiate the divorce process (Jones, 2007).\n\nHowever, in recent years, Bahrain has modernised its divorce laws to provide more options for couples seeking to end their marriages (Al Gharaibeh, 2011). In 2009, the country passed a new Personal Status Law that introduced the concept of “irretrievable breakdown of marriage” as a new ground for divorce, which does not require fault to be established by either party (Jones, 2007).\n\nIn Bahrain, divorce by mutual consent is recognised under the Personal Status Law, which allows both spouses to request a divorce without specifying any grounds for divorce. To obtain a divorce by mutual consent, both spouses must request the divorce jointly in the presence of the court clerk, agree on the divorce terms, and ensure that the court verifies that all the conditions for the divorce have been met (Al Gharaibeh, 2011).\n\nIn Bahrain, the right to initiate divorce unilaterally is generally only available to men under Sharia law (Jones, 2007). However, women may obtain a divorce through court proceedings or through khula. Additionally, Bahraini law now allows women to initiate divorce proceedings, and the courts may also order reconciliation or counselling before granting a divorce (Al Gharaibeh, 2011). Khula is a term used in Islamic law to refer to a form of divorce initiated by the wife. It allows a Muslim woman to seek a divorce from her husband through a legal process. In khula, the wife initiates the divorce by offering financial compensation or relinquishing her financial rights to the husband in exchange for the dissolution of the marriage. This process is based on mutual consent and requires the involvement of a religious authority or a court, depending on the jurisdiction. The specific details and procedures for khula may vary across different countries and schools of Islamic law.\n\nIn Bangladesh, the divorce laws have undergone several changes since its independence in 1971 (Alam, Saha, & Van Ginneken, 2000; Parvez, 2011). Both men and women have the right to divorce unilaterally under Muslim law, while divorce can be obtained through court proceedings or by seeking khula. In 2011, Bangladesh introduced the “irretrievable breakdown of marriage” concept as a no-fault ground for divorce under its Muslim Family Laws Ordinance. The ordinance also provides for the dissolution of marriage through mutual consent and allows women to initiate divorce proceedings under certain conditions. Additionally, the ordinance allows for mediation and counselling before granting a divorce (Parvez, 2011).\n\nHowever, fault-based grounds for divorce, such as adultery or cruelty, still exist under Bangladesh’s family law (Alam, Saha, & Van Ginneken, 2000). The country’s legal system also recognizes the importance of reconciliation and encourages efforts to save the marriage before granting a divorce (Parvez, 2011).\n\nOverall, the divorce laws in Bangladesh have evolved to provide more rights and protection for women while still upholding traditional Islamic legal principles (Alam, Saha, & Van Ginneken, 2000; Parvez, 2011).\n\nIn Bhutan, divorce laws have changed significantly, reflecting the country’s unique cultural and legal traditions (Kaul, 2013; Lhamo, 2019). Before the Bhutanese Marriage Act of 1980, divorce in Bhutan was governed by traditional customary laws and practices, which varied widely across different regions and communities. The Bhutanese Marriage Act of 1980 introduced a fault-based system of divorce, which allowed parties to seek a divorce on the grounds of adultery, cruelty, or desertion, but also provided for the possibility of no-fault divorce. In 2005, the Bhutanese Parliament passed the Marriage (Amendment) Act, which introduced mutual consent divorce, requiring parties to undergo counselling before the divorce is granted. In 2011, the Marriage (Amendment) Act 2011 recognized the irretrievable breakdown of marriage as grounds for divorce, which also requires parties to undergo counselling before the divorce is granted (Kaul, 2013). Bhutan’s history of divorce laws reflects the country’s efforts to balance traditional values and cultural practices with modern legal principles and concepts (Kaul, 2013; Lhamo, 2019).\n\nIn Brunei, a predominantly Islamic country, family law matters, including divorce, are governed by Islamic law, or sharia (Minarrahmah, 2020; Ibrahim, 2015). Divorce in Brunei is typically fault-based, with grounds such as adultery, cruelty, desertion, or other specified faults (Ibrahim, 2015).\n\nIn addition to fault-based divorce, Brunei recognises the concept of khula, a form of no-fault divorce initiated by the wife (Ibrahim, 2015). Unilateral divorce is not recognised in Brunei, and a party seeking a divorce must typically obtain the consent of their spouse or go through a legal process to establish fault (Minarrahmah, 2020). The concept of irretrievable breakdown of marriage is not recognised in Brunei’s legal system, but parties may seek a divorce on the grounds that the marriage has become “untenable” (Ibrahim, 2015).\n\nIn Cambodia, current divorce laws are based on the Civil Code introduced in 2007, allowing for both fault-based and no-fault divorce (Brickell, 2014). In a fault-based divorce, one spouse must prove the other committed a severe offence, such as adultery, domestic violence, or abandonment, leading to the breakdown of the marriage (Brickell & Platt, 2015). In a no-fault divorce, both parties can agree to dissolve the marriage without assigning blame or fault. After one year of separation, either spouse can seek a divorce without proving fault based on the no-fault theory (Brickell, 2014). However, the law also requires couples to attempt mediation before seeking a divorce, providing for the division of property and child custody arrangements (Brickell & Platt, 2015). Cambodia does not recognise the “irretrievable breakdown of marriage” as grounds for divorce.\n\nIt is important to note that divorce is still a sensitive issue in Cambodia, particularly in rural areas where traditional values and beliefs about marriage and family remain strong (Brickell, 2014). Many couples prefer to resolve their marital issues through informal means, such as mediation or counselling, rather than pursuing a formal divorce (Brickell & Platt, 2015).\n\nIn China, the current divorce laws are governed by the Marriage Law of the People’s Republic of China, enacted in 1980 and amended in 2001 (Chen, Rizzi, & Yip, 2021). The law provides for both fault-based and no-fault divorce (Yi & Deqing, 2000).\n\nUnder the fault-based system, a divorce may be granted based on grounds such as adultery, domestic violence, desertion, separation due to irreconcilable differences, criminal conviction, and mental illness (Yi & Deqing, 2000). Additionally, parties may seek a divorce on the basis of mutual consent, which requires a one-month cooling-off period (Chen et al., 2021).\n\nChina allows for unilateral divorce under its Marriage Law, where either spouse can file for divorce with a local marriage registration office, but a 30-day cooling-off period is required (Chen et al., 2021). The Marriage Law recognises “irretrievable breakdown of marriage” as a ground for divorce, allowing both parties to file a joint application without having to prove fault or other grounds (Yi & Deqing, 2000).\n\nIt is important to note that the law applies equally to both men and women, with no gender bias in divorce proceedings (Chen et al., 2021). Additionally, the law requires that marital property be divided equally between the parties in the event of divorce (Yi & Deqing, 2000).\n\nIn Cyprus, the history of divorce laws reflects the country’s cultural and legal traditions and its changing social and political landscape (Jennings, 1993; Sampson, 2005). Until 1990, Cyprus had a fault-based system of divorce, influenced by the country’s Greek Orthodox Christian heritage (Sampson, 2005). The Cypriot Parliament passed the Family Law (Amendment) Law in 1990, introducing no-fault divorce, which required at least three years of separation (Sampson, 2005).\n\nThe Family Law (Amendment) Law 2003 introduced the concept of unilateral divorce, allowing parties to seek a divorce without their spouse’s consent after at least five years of separation but also allowed for contested divorce where fault had to be established (Sampson, 2005). In 2015, the Family Law (Amendment) Law 2015 recognised the irretrievable breakdown of marriage as grounds for divorce, requiring parties to undergo counselling before the divorce was granted (Sampson, 2005).\n\nOverall, Cyprus’s divorce laws reflect the country’s ongoing efforts to balance traditional cultural and religious values with modern legal principles and concepts (Jennings, 1993; Sampson, 2005).\n\nIn Egypt, the divorce laws have been shaped by a complex interplay of legal, religious, and cultural factors (Mashhour, 2005; Mendoza, Tolba, & Saleh, 2019). The country’s current legal system primarily relies on fault-based divorce, where grounds for divorce include adultery, cruelty, desertion, or other specified faults. These grounds must be proven in court for the divorce to be granted, often leading to lengthy and adversarial proceedings.\n\nEgypt also recognizes the concept of khula, a form of no-fault divorce initiated by the wife. Under khula, a wife can obtain a divorce by returning her husband’s dowry or providing financial compensation in exchange for ending the marriage. This practice allows women to dissolve their marriage without having to prove any misconduct by their spouse.\n\nIn addition to khula, Egypt acknowledges unilateral divorce, which enables a husband to divorce his wife without her consent under specific conditions. This practice is rooted in traditional Islamic law and can lead to unequal power dynamics in the divorce process.\n\nAlthough the concept of the irretrievable breakdown of marriage is not explicitly recognized in Egypt, some courts have interpreted khula as a form of irretrievable breakdown in certain cases (Mashhour, 2005). This interpretation allows for the dissolution of a marriage without establishing fault, thus providing a more accessible option for couples seeking to end their relationship.\n\nOverall, Egypt’s divorce laws reflect the country’s complex legal, religious, and cultural traditions (Mashhour, 2005; Mendoza, Tolba, & Saleh, 2019). While the legal system acknowledges both fault-based and no-fault divorce options, the process remains rooted in these traditions, which can create challenges for those seeking to navigate the system. As society continues to evolve, there may be opportunities for further reform and modernization of Egypt’s divorce laws to ensure a more equitable and accessible process for all individuals involved.\n\nIn Georgia, the country’s divorce laws have undergone significant transformations over time, influenced by various political, social, and cultural factors. Historically, Georgia’s divorce system was influenced by Marxist principles, which promoted a more accessible and simplified process. Over time, the legal system shifted towards a traditional, fault-based system, where one spouse had to prove the misconduct of the other for the divorce to be granted (Censer, 1981; Welch III & Price-Bonham, 1983).\n\nIn 2008, Georgia introduced a new family code that recognizes both fault-based and no-fault grounds for divorce. This reform allowed couples to dissolve their marriages without assigning blame, making the process more accessible and less adversarial. The new family code also permits unilateral divorce, enabling one spouse to initiate the divorce process without the consent of the other (Welch III & Price-Bonham, 1983).\n\nHowever, there are certain requirements and restrictions in place for unilateral divorce, such as a mandatory six-month cooling-off period and mandatory counselling sessions. These measures are designed to provide couples with the opportunity to reconsider their decision, resolve disputes, and potentially reconcile before finalizing the divorce.\n\nIn summary, Georgia’s divorce laws have evolved significantly over the years, transitioning from a Marxist-influenced system to a traditional, fault-based system, and ultimately to a system that recognizes both fault-based and no-fault grounds for divorce. The introduction of the new family code in 2008 has provided more options for couples seeking to end their marriages and has implemented safeguards to encourage reconciliation and amicable resolutions.\n\nIn India, divorce laws have evolved over time and are primarily governed by various personal laws based on religion (Dommaraju, 2016). Further, Dommaraju reported that fault-based grounds such as adultery, cruelty, or desertion were the main reasons for divorce before 1976. These fault-based grounds required one spouse to prove the misconduct of the other in order to obtain a divorce, often leading to lengthy and adversarial proceedings.\n\nThe Hindu Marriage Act of 1955 marked a significant shift in Indian divorce law by introducing the concept of irretrievable breakdown of marriage as grounds for divorce. This reform allowed couples to file for divorce by mutual consent after living separately for one year, without needing to assign blame to either party (Amato, 1994). The introduction of no-fault divorce made the process more accessible and less contentious for couples seeking to end their marriages.\n\nIn addition to the Hindu Marriage Act, other personal laws, such as the Muslim Personal Law and the Christian Marriage Act, also govern divorce proceedings in India. These laws allow for divorce on specific grounds, but the procedures and requirements may differ based on the couple’s religion (Dommaraju, 2016). This complex legal landscape can create challenges for couples navigating the divorce process, particularly when their religious beliefs or practices conflict with the available legal options.\n\nSocial and cultural attitudes continue to shape divorce laws and practices in India, often making the process complex and challenging, particularly for women (Amato, 1994). Traditional gender roles and societal expectations can create additional barriers to divorce, particularly for women seeking to end their marriages. In some cases, women may face social stigma, financial insecurity, or limited access to legal resources, which can make it difficult for them to obtain a divorce or protect their rights during the process.\n\nDespite the introduction of no-fault divorce and the recognition of irretrievable breakdown of marriage as grounds for divorce, the Indian legal system still grapples with challenges related to gender equality, social norms, and religious diversity. These challenges can create disparities in the divorce process and outcomes for different segments of the population, making it difficult for all individuals to access the same level of justice and support.\n\nIn recent years, there have been efforts to reform Indian divorce laws to address some of these challenges and promote greater equality and fairness in the process. For example, the Marriage Laws (Amendment) Bill seeks to introduce the concept of irretrievable breakdown of marriage as a universal ground for divorce, regardless of religion, and provide for equitable division of marital assets (Dommaraju, 2016).\n\nIn conclusion, India’s divorce laws have evolved over time, moving from a primarily fault-based system to one that recognizes both fault-based and no-fault grounds for divorce. However, the complex interplay of personal laws, social norms, and cultural attitudes continues to shape the divorce process in India, often making it challenging and complex for those seeking to end their marriages. Efforts to reform and modernize the legal system are ongoing, with the goal of creating a more equitable and accessible process for all citizens, regardless of religion or gender.\n\nIndian Supreme Court in a recent judgment (2023) of Shri Rakesh Raman v. Smt. Kavita has ruled that the irretrievable breakdown of a marriage can be considered as cruelty under Section 13(1)(ia) of the Hindu Marriage Act, allowing for the dissolution of the marriage. The decision was made in the case of a husband living separately from his wife for 25 years. In 2009, the Family Court granted the husband’s petition for divorce based on cruelty, but the High Court of Delhi reversed the decision in 2011. The Supreme Court’s recent ruling acknowledges that a marriage that has broken down irretrievably results in cruelty for both parties and can thus be a valid reason for dissolution. The court also directed the husband to pay the wife INR 3,000,000 as permanent alimony. The author also suggests that if there is a deadlock, the marriage may be declared as dead.\n\nThe 59th (1974), 71st (1978) and 217th (2009) Law Commission of India reports, quoting Indian and foreign Judgements have recommended the enactment of laws on irretrievable breakdown of marriage, but the Indian Parliament has yet to pass such legislation. This has created a situation where parties unable to obtain a divorce due to fault-based laws may be forced to remain in an unhappy marriage, leading to societal and personal implications.\n\nThe demand for an irretrievable breakdown as a new law and ground of divorce is driven by the changing social landscape, where traditional societal norms and values have given way to more modern attitudes towards marriage and relationships. The law must reflect these changes to remain relevant and practical, as the authors have concluded in the impugn research.\n\nOther countries have addressed the irretrievable breakdown of marriage through the enactment of no-fault divorce laws. These laws provide a more compassionate and equitable approach to divorce, focusing on the needs and rights of both parties.\n\nThe failure to enact laws on IBM in India highlights a disconnect between the law and society. It is essential to consider the social bearing of laws and their implementation, as it directly affects the lives of citizens.\n\nWhen divorce is allowed on the no-fault theory, it may be less likely for questions of maintenance to arise. In the modern scenario in India, both men and women are educated, and woman are not behind in any area; they are not deprived of education. The right to education in Article 21A, Constitution of India, has been inserted to ensure proper education dissemination, irrespective of sex. In the present time, a woman is less dependent on men, and are more likely to feel shy about taking help from her husband.\n\nSimply put, women may be more independent and less likely to perform her household job as it was considered decades back her essential job. They may be more likely to prefer servants to perform these household jobs and prefer servants for their childcare. This prevailing practice in society may put a financial burden on a person. It is the authors’ opinion that when a spouse has sufficient earnings, they must not be allowed to get any expenses from the other spouse, and the trial courts must strictly follow the law relating to the same as verbatim laid down in Section 24 in The Hindu Marriage Act, 1955. According to this law, if the wife has an independent income, then the husband does not have to pay the expenses to her. From the authors’ experiences, these expenses are often given to the wife by the husband, even if she has an independent income. This is a clear violation of the statute on divorce. The court may sometimes order a large sum of money to be paid to the husband. Nevertheless, the husband may be considered a criminal while the wife could refuse continuing the marriage by accompanying the husband for a month after their marriage and leaving soon after. The wrongdoer is liable to be punished by the court, and the innocent should be free because the law is enacted for this purpose.\n\nIn Indonesia, divorce laws have evolved from being primarily governed by Islamic law, which allowed divorce in cases of fault, to a more secular system introduced by the 1974 Marriage Law, which applies to both Muslims and non-Muslims (Heaton, Cammack, & Young, 2001). The Marriage Law recognizes several grounds for divorce, including adultery, desertion, cruelty, and a no-fault ground based on the irretrievable breakdown of the marriage (Heaton & Cammack, 2011). Despite these changes, access to divorce remains challenging for many women in Indonesia, particularly Muslim women who must often obtain their husband’s consent or go through a lengthy court process to obtain a divorce (Heaton et al., 2001).\n\nIn Iran, divorce laws have undergone significant changes, particularly since the Islamic Revolution of 1979, which led to the implementation of a new family law based on Islamic principles (Aghajanian & Thompson, 2013). This law allows for both fault-based and no-fault divorce, as well as unilateral divorce in cases of irretrievable breakdown of the marriage (Doherty, Kalantar, & Tarsafi, 2021). Fault-based divorce requires the spouse seeking divorce to prove fault on the other spouse’s part, with grounds including adultery, cruelty, drug addiction, and mental illness (Aghajanian & Thompson, 2013). No-fault divorce is possible through a process called khula, in which the wife can seek divorce without having to prove fault on the part of her husband, and unilateral divorce is possible through a process called talaq-e-tafwid (Doherty et al., 2021).\n\nIn Iraq, divorce laws have undergone significant changes, and the current legal system recognizes both fault-based and no-fault divorces (Odah, Bager, & Mohammed, 2018). Fault-based divorce requires the spouse seeking divorce to prove fault on the part of the other spouse, with grounds including adultery, cruelty, and abandonment (Anderson, 1960). No-fault divorce is possible in cases of irretrievable breakdown of the marriage, allowing either spouse to initiate divorce proceedings without having to prove fault on the other spouse’s part (Odah et al., 2018). Unilateral divorce is allowed in Iraq, but only under certain conditions, such as when a husband’s wife has committed a serious offense or is unable to perform marital duties due to a physical or mental disability (Anderson, 1960). Implementation of these laws may vary based on the interpretation of religious and cultural practices in different regions of the country (Odah et al., 2018).\n\nIn Israel, divorce laws have evolved since the state’s establishment in 1948, with the current legal system allowing for both fault-based and no-fault divorces, as well as unilateral divorce under certain conditions (Shiloh, 1970; Hacker, 2008). Fault-based divorce requires the spouse seeking divorce to prove fault on the other spouse’s part, with grounds including adultery, cruelty, and severe violence (Shiloh, 1970). No-fault divorce is possible through a process called “divorce by agreement,” in which couples can mutually agree to divorce without having to prove fault on the part of either spouse (Hacker, 2008). Unilateral divorce is possible under certain conditions, such as when a husband gives his wife a formal notice of divorce and pays her a sum of money known as a ketubah (Shiloh, 1970). In cases of irretrievable breakdown of marriage, either spouse can initiate divorce proceedings without having to prove fault, but the process may involve mediation and counseling sessions aimed at reconciliation before granting the divorce (Hacker, 2008).\n\nIn Japan, divorce laws have evolved over time, with the current legal system allowing for both fault-based and no-fault divorces, as well as unilateral divorce under certain conditions (Fuess, 2004; Ono, 2006). Fault-based divorce is possible but requires the spouse seeking divorce to prove fault on the other spouse’s part, with grounds including adultery, cruelty, and abandonment (Fuess, 2004). No-fault divorce is possible through “divorce by mutual consent,” which allows couples to divorce without proving fault as long as certain conditions are met (Ono, 2006). Unilateral divorce is allowed under certain circumstances, such as when a spouse has committed a serious offence or has a severe marital relationship breakdown (Fuess, 2004).\n\nThe concept of “irretrievable breakdown of marriage” was introduced in 1948 and allowed for divorce without requiring proof of fault as long as the marriage has broken down and there is no possibility of reconciliation (Fuess, 2004). However, the legal system in Japan still heavily relies on fault-based divorce, and there have been ongoing debates and efforts to reform the system to provide more options for no-fault and mutual consent divorce (Ono, 2006).\n\nIn Jordan, divorce laws have undergone changes over the years, with the legal system based on Islamic law that traditionally required fault-based grounds for divorce and gave the husband the unilateral right to initiate the divorce process (Kumaraswamy, 2001; Khataybeh, 2022). In 2001, Jordan introduced a new family law that expanded the grounds for divorce to include “irretrievable breakdown of marriage” as a no-fault ground for divorce, and allowed women to initiate divorce proceedings under certain conditions, such as if the husband had been absent for a specified period of time or if he had mistreated her. However, fault-based grounds for divorce, such as adultery or cruelty, still exist under Jordan’s family law. The law also requires a waiting period of up to three months before a divorce is granted, during which the couple may attempt to reconcile (Khataybeh, 2022).\n\nIn Kazakhstan, a former Soviet republic, significant changes in divorce laws have occurred since gaining independence in 1991 (Dall’Agnola & Thibault, 2021; Zhankubayev et al., 2021). Under the Soviet system, divorce was relatively easy to obtain, but after the collapse of the Soviet Union, Kazakhstan underwent a legal reform process to establish a more liberal, market-oriented legal system (Zhankubayev et al., 2021). Kazakhstan has since adopted a no-fault divorce system, allowing couples to divorce based on the irretrievable marriage breakdown without establishing fault, and divorce can be initiated unilaterally by either spouse. Despite the liberalization of divorce laws, there are still significant social and cultural barriers to divorce in Kazakhstan, particularly for women, as divorce is stigmatized in Kazakh society (Dall’Agnola & Thibault, 2021).\n\nIn North Korea, divorce is believed to be allowed, but the process and grounds for divorce are not well-defined. Divorce in North Korea is considered a rare occurrence and carries a significant social stigma, with societal pressure to maintain traditional gender roles and family structures. It is unclear whether North Korea recognizes fault-based or no-fault divorce, or whether there are provisions for unilateral divorce or the concept of irretrievable breakdown of marriage. However, given the highly controlled nature of the North Korean legal system, it is likely that divorce is subject to strict regulation and limited in scope (Kim, 1973).\n\nIn the Republic of Korea, the no-fault divorce system allows couples to obtain a divorce without establishing fault, and either spouse can initiate the process unilaterally (Lee, Seol, & Cho, 2006). The law includes provisions to protect vulnerable spouses, such as a mandatory conciliation process and the possibility of requesting spousal support. The Republic of Korea’s Family Law recognizes “irretrievable breakdown of marriage,” which allows for divorce even if fault cannot be proven. However, there are still social and cultural barriers to divorce in the Republic of Korea, particularly for women, and ongoing debates around the need for further reforms to address these issues (Lee et al., 2006).\n\nIn Kuwait, divorce laws are predominantly fault-based, requiring a party seeking a divorce to establish that their spouse committed a wrongful act justifying the dissolution of the marriage. No-fault divorce is recognized through the concept of khula, allowing women to seek a divorce without proving fault, but requiring them to offer to return their dowry or other property received from the husband. Unilateral divorce is recognized in Kuwait but with certain restrictions and requirements. Although the concept of irretrievable breakdown of marriage is not explicitly recognized in Kuwaiti law, some courts have interpreted khula as a form of irretrievable breakdown in certain circumstances (Al-Kazi, 2008; Tetreault & Al-Mughni, 1995).\n\nIn Kyrgyzstan, the history of divorce laws has been influenced by traditional Islamic and Soviet-era legal systems, with the country moving from a no-fault system during the Soviet era to a more flexible approach that recognizes both fault-based and no-fault grounds for divorce after gaining independence. The Family Code enacted in 1994 allowed for fault-based and no-fault divorce, with a requirement of a three-year separation for no-fault divorce. In 2003, unilateral divorce was introduced, requiring a two-year separation, but still necessitating fault in contested divorces. In 2019, the law on “irretrievable breakdown of marriage” was passed, allowing for divorce without establishing fault, but requiring counseling before the divorce is granted (Childress, 2018; Namazie & Sanfey, 2001).\n\nIn Laos, the history of divorce laws has been influenced by the country’s cultural and legal traditions and its socialist political system. The legal framework governing divorce in Laos is based on the 2006 Law on Family, which recognizes both fault-based and no-fault grounds for divorce. Under the current legal system, no-fault divorce can be granted after a one-year separation, enabling couples to end their marriages without assigning blame to either party. This approach aims to make the divorce process more accessible and less adversarial for those seeking to dissolve their unions. Unilateral divorce is also allowed in Laos, meaning that one spouse can initiate the divorce process without the consent of the other. However, in contested divorce cases, fault must be established in order for the divorce to be granted. This requirement can lead to prolonged and contentious proceedings as the parties attempt to prove the other’s misconduct. Although the concept of irretrievable breakdown of marriage is not currently recognized as grounds for divorce in Laos (Meredith & Rowe, 1986; Gordon, 2004), the availability of no-fault divorce based on a one-year separation offers a similar option for couples who wish to end their marriages without establishing fault.\n\nIn summary, Laos’ divorce laws have been shaped by its cultural and legal traditions, as well as its socialist political system. The current legal framework, based on the 2006 Law on Family, recognizes both fault-based and no-fault grounds for divorce, with unilateral divorce allowed under certain conditions. The country does not currently recognize the irretrievable breakdown of marriage as grounds for divorce, but no-fault divorce based on a one-year separation provides a comparable alternative.\n\nLebanon’s history of divorce laws has undergone several changes, including adopting fault and no-fault theories, unilateral and mutual consent divorce, and recognizing the irretrievable breakdown of marriage (Tarabey, 2013; Fournier, Malek-Bakouche, & Laoun, 2018). The transition from a fault-based system to a more flexible approach has been marked by the introduction of various laws, such as Law No. 542 (1983), Law No. 347 (1998), and Law No. 293 (2011) (Tarabey, 2013; Fournier, Malek-Bakouche, & Laoun, 2018). These laws have gradually broadened the grounds for divorce, allowing couples to seek divorce without establishing fault and requiring either mutual consent or a court order (Tarabey, 2013; Fournier et al., 2018).\n\nMalaysia’s legal system, influenced by Islamic law and English common law, provides for both fault-based and no-fault divorce, allowing both men and women the right to initiate divorce proceedings. The Islamic Family Law Act of 1984 expanded the grounds for divorce to include “irretrievable breakdown of marriage” as a no-fault ground, while civil laws also recognize no-fault divorce on the same grounds. Malaysian law requires a waiting period of up to three months before a divorce is granted, and mutual consent divorce is recognized for non-Muslims under the Law Reform (Marriage and Divorce) Act 1976 (Reddy, 1995; Jones, 1981).\n\nIn the Maldives, the legal system is based on Islamic law, which has traditionally required fault-based grounds for divorce and granted husbands the unilateral right to initiate the divorce process. However, in 2000, the family law was reformed to expand the grounds for divorce and improve gender equality in the divorce process (Shanoora et al., 2020; Rauf & Noman, 2021).\n\nThe 2000 family law introduced the “irretrievable breakdown of marriage” as a no-fault ground for divorce, allowing couples to end their marriage without assigning blame. Additionally, the law permitted women to initiate divorce proceedings under certain conditions, providing them with greater autonomy in the process (Shanoora et al., 2020).\n\nDespite these reforms, fault-based grounds for divorce and a waiting period of up to three months before a divorce is granted still exist in the Maldives. The waiting period is meant to allow for reconciliation efforts, but it can prolong the process and create additional challenges for couples seeking to end their marriage (Rauf & Noman, 2021).\n\nIn summary, the Maldives has made progress in modernizing its divorce laws, moving away from traditional fault-based grounds and providing women with more rights. However, aspects of the legal system still require further reform to ensure fairness and gender equality in divorce proceedings.\n\nIn Mongolia, the divorce process is guided by the Civil Code of Mongolia (2019), which does not require fault-based grounds for divorce. Couples can mutually consent to divorce after a one-month waiting period without the need to prove any wrongdoing by either party. This waiting period is intended to give couples the opportunity to reconsider their decision and potentially reconcile before finalizing the divorce.\n\nFor individuals seeking a unilateral divorce, there is a three-month waiting period and a mediation requirement in place. The mediation process aims to resolve disputes and facilitate an amicable agreement between the parties before the divorce is granted.\n\nMongolia does not have a specific legal provision for the irretrievable breakdown of marriages, but the no-fault divorce approach reflects a similar principle, allowing couples to end their marriages without establishing fault.\n\nThe country underwent significant legal changes in the 20th century, including revisions to family law and divorce procedures after the fall of the Soviet Union (Kim et al., 2017; Holmgren, 1986). These changes aimed to modernize the legal system and provide a more equitable and accessible divorce process for Mongolian citizens.\n\nIn summary, Mongolia’s divorce process is based on a no-fault approach, with waiting periods and mediation requirements in place to encourage reconciliation and amicable agreements. The country has undergone substantial legal reforms in recent decades to modernize its family law system and make the divorce process more equitable.\n\nIn Myanmar, the legal system recognizes both fault-based and no-fault divorce, with fault-based grounds including adultery, desertion, and cruelty under the Myanmar Buddhist Women’s Special Marriage and Succession Act of 1954 (Htoo, n.d.). No-fault divorce is allowed based on mutual consent, and the concept of “irretrievable breakdown of marriage” allows for unilateral divorce without proving fault after three years of separation (Molina & Tanaka, 2023). However, social and cultural factors may make it difficult for women to exercise their rights under these laws (Molina & Tanaka, 2023).\n\nIn Nepal, the legal system recognizes both fault-based and no-fault divorce. Under the Nepalese Marriage Registration Act of 2028 (1971), fault-based grounds for divorce include adultery, cruelty, and desertion (Bala, 2005). In addition to fault-based divorce, Nepal allows for divorce by mutual consent on a no-fault basis, with both parties required to agree to the divorce and wait at least one year from the date of marriage to file for divorce (Jennings, 2014). Nepal also recognizes the concept of “irretrievable breakdown of marriage,” which allows for unilateral divorce without proving fault on the other spouse’s part after three years of separation (Jennings, 2014).\n\nIn Oman, the legal system is based on Islamic law, which traditionally required fault-based grounds for divorce and gave the husband the unilateral right to initiate the divorce process (Al-Azri, 2011). The 2005 family law introduced the concept of “irretrievable breakdown of marriage” as a no-fault ground for divorce and allowed women to initiate divorce proceedings under certain conditions. Fault-based grounds for divorce, such as adultery or cruelty, still exist under Oman’s family law (Mansour et al., 2020). The Omani government has introduced reforms to the country’s family law to provide more excellent protection for women in divorce proceedings (Al-Azri, 2011). Oman’s family law also requires up to three months before a divorce is granted, during which the couple may attempt to reconcile (Mansour et al., 2020).\n\nIn Pakistan, the divorce process is regulated by the Muslim Family Laws Ordinance, which was enacted in 1961 to codify Islamic family law and standardize divorce procedures throughout the country (Cherry, 2001). This ordinance provides for both fault-based and no-fault divorce options, allowing couples to dissolve their marriages either by proving misconduct or by claiming the irretrievable breakdown of the marriage.\n\nUnder Pakistani law, men have the legal right to unilaterally divorce their wives without any grounds, a practice known as “talaq.” However, in 2018, the government took steps to curb the misuse of this practice by making “triple talaq” illegal and punishable by up to three years in prison (Yefet, 2011). Triple talaq is a controversial form of divorce in which a man can instantly end the marriage by pronouncing “talaq” three times in succession. The 2018 reform aimed to protect women’s rights and ensure fairer divorce proceedings.\n\nDespite these reforms, the divorce process in Pakistan still faces challenges related to gender inequality, cultural traditions, and religious interpretations. The Muslim Family Laws Ordinance was an important step toward standardizing divorce procedures and addressing some of these issues, but there is still room for improvement to ensure fairness and justice for all parties involved in a divorce.\n\nIn Palestine, divorce laws have undergone significant changes throughout history, particularly in the last century under British, Jordanian, and Israeli rule (Cohen & Savaya, 2003; Urbanik, 2005). Today, Palestine’s divorce laws remain complex and vary depending on the region and religious affiliation of the individuals involved, with Islamic law still playing a significant role in divorce proceedings. However, Palestinian civil law also allows for no-fault grounds for divorce, such as “irretrievable breakdown of marriage,” under certain circumstances (Cohen & Savaya, 2003).\n\nIn the Philippines, divorce has a complex history and is currently not legal, except for limited circumstances in which a marriage can be annulled, such as psychological incapacity, fraud, or lack of parental consent (Abalos, 2017; Reyes, 1953). Efforts to legalize divorce in the Philippines have faced resistance from religious groups and conservative politicians. There is no legal provision for no-fault divorce in the Philippines, with divorce only granted on specific grounds (Abalos, 2017).\n\nIn Qatar, the issue of unilateral divorce, particularly the practice of talaq, has been controversial and debated (Al-Ammari & Romanowski, 2016; Bahry & Marr, 2005). The Personal Status Law in Qatar provides for no-fault divorce based on mutual consent, and in 2020, Qatar passed Law No. 22 of 2020, which addresses unilateral divorce by not recognizing it and mandating counselling and mediation for couples seeking a divorce. While the irretrievable breakdown of marriage is not explicitly addressed in the Personal Status Law, a court could grant a divorce based on this ground if one of the parties can demonstrate it (Al-Ammari & Romanowski, 2016).\n\nIn Russia, both fault-based and no-fault divorce systems are available (Freeze, 1990; Keenan, Kenward, Grundy, & Leon, 2013). No-fault divorce, introduced in 2004, allows parties to divorce with mutual consent on the basis of no fault theory after a one-month waiting period. Unilateral divorce may be granted without proving fault after a three-month cool-down period, and the court may order a period of conciliation before granting the divorce (Keenan et al., 2013). Fault-based divorce is also available in cases such as adultery and cruel treatment, but it may involve longer waiting periods and more complex legal procedures (Freeze, 1990).\n\nIn Saudi Arabia, divorce laws are primarily governed by Islamic law based on the Quran and the Hadith (Saleh & Luppicini, 2017; Abdulrahman & Alamri, 2021). The divorce laws in Saudi Arabia are mainly fault-based, with men having the exclusive right to initiate divorce without having to prove fault on the part of their wives. Conversely, women generally need to provide grounds for divorce, such as abuse, neglect, or abandonment (Saleh & Luppicini, 2017).\n\nMen can unilaterally divorce their wives without any separation requirement and without having to provide proof of fault, a practice known as “talaq” (Saleh & Luppicini, 2017). However, there have been some reforms to the divorce laws in Saudi Arabia in recent years, particularly concerning women’s rights. In 2019, a new law was passed requiring courts to notify women when their husbands file for divorce, which was seen as a step forward in protecting women’s rights in divorce proceedings (Abdulrahman & Alamri, 2021).\n\nThe concept of “irretrievable breakdown” as a legal ground for divorce does not exist in Saudi Arabian law (Saleh & Luppicini, 2017; Abdulrahman & Alamri, 2021).\n\nIn Singapore, divorce is regulated by the Women’s Charter, which provides for both fault-based and no-fault divorce (Sun, Chong, & Lim, 2014; Quek Anderson, Chua, & Ning, 2022). According to Section 95 of the Women’s Charter (2009), a party can apply for divorce on the basis of the irretrievable breakdown of the marriage, which can be established through either three years of separation with the consent of both parties or four years of separation without the consent of one party. Additionally, fault-based divorce is available when one party can demonstrate that the other has committed adultery, behaved unreasonably, or deserted them for a continuous period of at least two years (Sun, Chong, & Lim, 2014).\n\nUnder the Women’s Charter, both parties to a divorce may also be entitled to maintenance. Spousal maintenance is available if one spouse is unable to support themselves and the other party has the financial means to provide support. Child maintenance is also provided for, and both parents have a legal obligation to provide financial support for their children after a divorce (Quek Anderson, Chua, & Ning, 2022).\n\nIn Sri Lanka, the history of divorce can be traced back to the country’s colonial past. Prior to British colonisation in the 19th century, there was no formal legal system governing divorce in Sri Lanka. Instead, marriages were typically dissolved through informal means, such as separation or abandonment (Wazeema & Jayathunga, 2017). Under British rule, Sri Lanka’s legal system was modernised, and laws governing divorce were introduced. Divorce was only permitted on fault-based grounds, such as adultery or cruelty. However, in 1959, the law was amended to allow for no-fault divorce in cases of irretrievable breakdown of the marriage (Amaratunga, 2018). Despite this change, mutual consent divorce is not recognised under Sri Lankan law. Instead, divorce can only be obtained through court proceedings, and the petitioner must provide evidence of fault on the other spouse’s part (Wazeema & Jayathunga, 2017). Additionally, there is no provision for unilateral divorce on the basis of no fault theory.\n\nThe process of obtaining a divorce in Sri Lanka can be complex and time-consuming, with several legal requirements that must be met before a divorce can be granted (Amaratunga, 2018). For example, the parties may be required to undergo counselling before the divorce can be finalised, and there may be a waiting period of up to two years before the divorce can be granted (Wazeema & Jayathunga, 2017).\n\nOverall, the history of divorce in Sri Lanka has been marked by a strong emphasis on fault-based grounds and a reluctance to recognise mutual consent as a basis for divorce (Amaratunga, 2018). While there have been some reforms in recent years to simplify the divorce process, divorce remains complex and often difficult for many couples in Sri Lanka (Wazeema & Jayathunga, 2017).\n\nDivorce in Syria is governed by the Personal Status Law, which was last amended in 2019 (Van Eijk, 2016). The law provides for both fault-based and no-fault divorce.\n\nUnder the Personal Status Law, a spouse may file for divorce on the grounds of harm, whether physical or psychological, or on the grounds of a severe defect in the other spouse, making the marriage’s continuation impossible (Van Eijk, 2012). Additionally, a spouse may file for divorce on the grounds of the other spouse’s abandonment for two years or more, or if the spouses have been separated for three years or more (Maktabi, 2010).\n\nThe law also allows for no-fault divorce based on the spouses’ mutual consent. If both parties agree to the divorce, they can submit a joint petition to the court (Van Eijk, 2016).\n\nUnilateral divorce is permitted for men under Islamic law. A husband may divorce his wife without her consent by pronouncing talaq, the Islamic form of divorce. However, the husband must provide financial support to his ex-wife for a period of three months following the divorce (Van Eijk, 2012). This is stated in the Personal Status Law of Syria, which governs divorce in the country.\n\nIn cases where children are involved, the Personal Status Law also addresses issues such as child custody, child support, and visitation rights (Maktabi, 2010).\n\nIn Tajikistan, the Family Code recognises both fault-based and no-fault divorce (Cleuziou, 2021). A spouse may file for divorce on the grounds of harm, whether physical or psychological or on the grounds of a serious defect in the other spouse, making the marriage’s continuation impossible (Cleuziou & Dufy, 2022). Additionally, a spouse may file for divorce on the grounds of the other spouse’s abandonment for a period of one year or more, or if the spouses have been living separately for a continuous period of two years or more (Cleuziou, 2021).\n\nThe Family Code also allows for no-fault divorce based on the mutual consent of the spouses (Cleuziou, 2021). If both parties agree to the divorce, they can submit a joint petition to the court (Cleuziou & Dufy, 2022).\n\nUnilateral divorce is permitted in Tajikistan, but it is subject to certain restrictions (Cleuziou, 2021). A husband may divorce his wife without her consent by pronouncing talaq, the Islamic divorce form (Cleuziou & Dufy, 2022). However, the husband must provide financial support to his ex-wife for a period of three months following the divorce (Cleuziou, 2021).\n\nIn cases involving children, the Family Code addresses issues such as child custody, child support, and visitation rights (Cleuziou & Dufy, 2022).\n\nIn Thailand, prior to 2019, fault-based divorce was the prevailing system (Teerawichitchainan, 2004). However, under the current Thai Civil and Commercial Code, both mutual consent divorce and no-fault divorce are recognised (Limanonda, 1995). Mutual consent divorce can be filed when both parties agree to end the marriage, while no-fault divorce can be filed by one party if the couple has been living separately for at least one year (Teerawichitchainan, 2004). The court may also require the couple to participate in mediation to resolve any property disputes (Limanonda, 1995). If no agreement is reached, the court will make a final decision on the division of property (Teerawichitchainan, 2004).\n\nIn Timor-Leste, divorce is regulated by the Family Code, which was enacted in 2009 and revised in 2016 (Niner, 2012). The Family Code provides for both fault-based and no-fault divorce (Grenfell, 2006). Under the Family Code, a spouse may file for divorce on the grounds of severe or repeated violation of marital duties, irretrievable breakdown of the marriage, or separation of the spouses for more than two years (Grenfell, 2006). The court may also grant a divorce if both spouses agree to it. In cases where children are involved, the Family Code addresses issues such as child custody, child support, and visitation rights (Niner, 2012).\n\nIn Turkey, the historical background of divorce can be traced back to the Ottoman Empire, where Islamic law governed family matters (Caarls & de Valk, 2018). However, during the modernisation period in the early 20th century, secular family law was introduced, recognizing the concept of civil marriage and divorce (Demir, 2013). In 1926, the Turkish Civil Code was enacted, establishing civil marriage and divorce procedures (Caarls & de Valk, 2018).\n\nToday, fault-based divorce is the default system in Turkey, but parties can opt for divorce based on mutual consent under the no-fault theory (Demir, 2013). In 2011, Turkey passed a law that introduced unilateral divorce without the need to prove fault on the basis of the no-fault theory (Caarls & de Valk, 2018). Under this law, if one party requests a divorce and the other party agrees, the court can grant a divorce without requiring proof of fault or a waiting period (Demir, 2013). If the other party contests the divorce, a two-year separation period must be established before a unilateral divorce can be granted on the basis of the no-fault theory (Caarls & de Valk, 2018).\n\nIn Turkmenistan, the Family Code governs divorce proceedings, allowing for divorce either by mutual consent or by a court decision (Khamidov, 2015; Liczek, 2005). In cases where one spouse seeks a divorce without the other’s consent, they must apply to the court and provide evidence of fault-based grounds, such as adultery, abandonment, or cruel treatment. There is no specific provision for no-fault divorce based on an irretrievable breakdown of the marriage, nor for unilateral divorce by one spouse without the other’s consent (Liczek, 2005). The Turkmenistan Family Code also addresses the division of property and custody of children in divorce cases (Khamidov, 2015; Liczek, 2005).\n\nIn the United Arab Emirates (UAE), divorce is governed by the Personal Status Law, which was last amended in 2005 (Al Gharaibeh & Bromfield, 2012; El-Alami & Hinchcliffe, 1996). The law provides several grounds for divorce, including mutual consent, harm caused by one spouse to the other, and failure to provide for the family (Al Gharaibeh & Bromfield, 2012). However, there is no specific provision for no-fault divorce based on the irretrievable breakdown of marriage (El-Alami & Hinchcliffe, 1996).\n\nIf both spouses agree to the divorce, they can apply to a court for an uncontested divorce (Al Gharaibeh & Bromfield, 2012). In cases where one spouse seeks a divorce without the consent of the other, they must demonstrate to a court that there are valid reasons for the divorce (El-Alami & Hinchcliffe, 1996).\n\nThe UAE courts have jurisdiction to hear divorce cases if one or both spouses are UAE nationals or residents (Al Gharaibeh & Bromfield, 2012). Additionally, Sharia law applies to all divorce cases in the UAE, regardless of the religion of the parties involved (El-Alami & Hinchcliffe, 1996).\n\nThe Uzbekistan Family Code governs the divorce process and allows for fault-based grounds for divorce, such as adultery, abuse, and abandonment. However, no-fault divorce is also available, which is based on the irretrievable breakdown of the marriage (Nazarovna, Azamkulovich, & Ziyadullayevich, 2020; Dedahonovich & Ferdinandovna, 2020).\n\nDuring divorce proceedings, the court addresses critical issues, including the division of property, spousal support, child custody, and child support. The court’s primary goal is to make decisions in the best interests of the children involved and ensure a fair division of marital property (Nazarovna et al., 2020). Factors such as the duration of the marriage, contributions of each spouse, and the needs of any dependent children are taken into account when dividing assets.\n\nIn conclusion, the Uzbekistan Family Code provides for both fault-based and no-fault divorce options. The court plays a central role in handling various aspects of the divorce process, ensuring that decisions are made in the best interests of the children and achieving a fair distribution of marital property.\n\nIn Viet Nam, the divorce process is governed by the Law on Marriage and Family, which addresses key aspects such as the division of property, child custody, and child support. The court plays a crucial role in overseeing these matters, with the aim of ensuring a fair division of marital assets and making decisions in the best interests of the children involved (Vu et al., 2014; Thi, 2021).\n\nThe division of property in Viet Nam typically involves an equitable distribution of marital assets, taking into consideration factors such as the duration of the marriage, the contributions of each spouse, and the needs of any dependent children. The court has the discretion to divide assets in a manner that it deems fair and just, which may not necessarily result in an equal split (Vu et al., 2014).\n\nChild custody arrangements in Viet Nam are determined based on the best interests of the child, with the court considering factors such as the child’s age, the parents’ capacity to care for the child, and the child’s preferences when making decisions about custody and visitation rights. Both parents have an obligation to provide financial support for their children, and the court can determine the appropriate level of child support based on each parent’s income and the needs of the child (Thi, 2021).\n\nDomestic violence is a significant issue in Viet Nam and is recognized by the law as grounds for divorce. When domestic violence is present in a relationship, it can have implications for the division of property and child custody arrangements. Courts may take into account the severity of the violence, the impact on the victim, and the safety of the children when making decisions about these matters (Vu et al., 2014).\n\nThe introduction of no-fault divorce in Viet Nam has provided more options for couples seeking to dissolve their marriages. This reform allows couples to obtain a divorce without having to prove any misconduct by either party, streamlining the process and reducing the potential for conflict. However, the divorce process still requires the involvement of the courts to address issues such as property division and child custody (Thi, 2021).\n\nAs social norms continue to evolve and the needs of the population change, the Vietnamese legal system is gradually adapting to better serve its citizens. Despite the progress made, there is still room for improvement in areas such as the protection of vulnerable parties during the divorce process and the promotion of gender equality within the legal framework.\n\nIn Yemen, the divorce process is primarily governed by Sharia law, which is the Islamic legal system derived from the Quran and the Hadith. The country’s legal framework is heavily influenced by traditional customs and Islamic jurisprudence (Gaimani, 2006; Würth, 2003). Consequently, the rights and responsibilities of spouses during and after a divorce are determined by these sources of law, reflecting the nation’s deeply rooted religious and cultural traditions.\n\nYemeni family law is a combination of tribal customs, Islamic legal principles, and state regulations. Although the Yemeni constitution guarantees gender equality, in practice, women often face discrimination, particularly in matters of marriage and divorce. Under the Yemeni Personal Status Law, a man can unilaterally divorce his wife by pronouncing the “talaq” (divorce declaration) three times, while a woman must seek a court’s permission for a divorce by proving her husband’s misconduct or inability to support her financially (Gaimani, 2006).\n\nIn addition to the unequal rights of men and women in initiating a divorce, Yemeni law does not recognize the concept of no-fault divorce, which allows couples to dissolve their marriage without proving any wrongdoing (Gaimani, 2006; Würth, 2003). This lack of legal progress reflects the challenges faced by the country in adopting more modern and egalitarian legal frameworks, which are often hindered by conservative social, cultural, and religious norms.\n\nChild custody, child support, and property division are also addressed within the framework of Sharia law in Yemen. In the case of child custody, mothers are generally granted custody of young children until they reach a certain age, at which point custody is typically transferred to the father. This age varies depending on the child’s gender and the specific school of Islamic jurisprudence followed in a particular region (Würth, 2003). Despite being granted custody, mothers often face challenges in obtaining and maintaining custody rights due to cultural and societal pressures.\n\nFathers, on the other hand, are responsible for providing financial support for their children, regardless of custody arrangements. Child support in Yemen is determined according to the father’s income and the children’s needs and is usually paid directly to the mother or her guardian (Würth, 2003).\n\nProperty division in Yemen is guided by Islamic inheritance laws, which allocate assets based on a fixed share system. Women are generally entitled to a smaller portion of the marital property than men. However, women can negotiate for better property rights through their marriage contract, which can include provisions for dowries, maintenance, and other forms of financial support (Gaimani, 2006).\n\nEfforts to reform family law in Yemen have been slow and challenging, as they must navigate the complexities of the country’s social, cultural, and religious norms. While some progress has been made, particularly in the areas of women’s rights and legal representation, there is still a long way to go to achieve gender equality and ensure that Yemeni citizens have access to fair and equitable divorce processes.\n\n\nKey findings and discussion\n\nSeveral key issues of the irretrievable breakdown of marriage are derived from the above study, particularly within the Indian and broader Asian context where such grounds for divorce are currently non-existent:\n\nLegal provisions: Laws related to irretrievable breakdown of marriage (IBM) vary across Asian countries. India lacks explicit provisions for IBM as a ground for divorce, unlike Singapore, China, and Sri Lanka, which have specific legislations. The authors assert that, as found by using observation techniques, the law has changed in Asian countries. The time required to obtain a divorce under Irretrievable Breakdown of Marriage (IBM) in India may be fixed ranging from six months to ten years in India, depending on various factors such as the existence of children, the likelihood of the marriage survival and the possibility of reunions. The 71st Report of the Law Commission of India in 1978 and the 217th Report in 2009 mention the time limits for declaring the marriage dead in New Zealand (three years) and Scotland (one year with consent and two years without consent) under the breakdown theory (Dommaraju, 2016).\n\nSocietal factors: Societal elements such as culture, religion, industrial, economics and globalization significantly shape the legal landscape of IBM. The societal stigma around divorce may contribute to some countries’ underutilization of IBM provisions. Society has changed due to new economies, and if divorces are criticized by the society, the divorce rate can decrease. However, society now accepts IBM as a need of the changing society. Change requires alignment with the law and society and is inevitable. Continuing obsolete laws result in disturbed families and society (Rangarao & Sekhar 2002).\n\nBurden of cases: The findings are that a law on irretrievable breakdown can reduce burden on courts, increasing social demand for justice delivery and timely resolution. Amicable resolution of matrimonial cases could be transferred from traditional courts to specialized family courts, saving time and requiring separation only for final nod decisions. Indian courts exhibit considerable discretion in granting divorce in IBM cases, despite the absence of explicit provisions. They rely on principles of justice, equity, and good conscience to safeguard the aggrieved party’s rights. The judiciary has emphasized the need for law interpretation over discretionary powers or inherent powers in granting divorce in IBM cases and has advocated for a new ground for divorce to ease disputes and ensure the smooth dissolution of nonviable marriages (Saigal & Gharpure, 2006).\n\nNeed for legal reforms: The study suggests incorporating IBM as a legal ground for divorce in Indian legislation, inspired by Asian countries’ examples. This could streamline the process and protect parties’ rights. The author also discusses incorporating the Muslim concept of dower (mahr) from Mohammedan law in instances of matrimonial discord, regardless of religion. Comparative studies of Indian and other countries emphasize the need to consider social, cultural, and economic factors that shape divorce laws, ensuring gender equality and protecting all parties involved (Sivaramayya,1989).\n\nGender inequality: Research shows gender inequality is a significant factor in implementing IBM-related laws. Women in India face challenges accessing legal resources, potentially leading to contentious divorce proceedings. In many Muslim countries, only men have the right to unilateral divorce as discussed earlier in Asian Muslim countries. The social bearing of divorce laws can impact women’s rights, gender equality, and broader social and cultural norms surrounding marriage and divorce (Sivaramayya,1989).\n\nAwareness and support: The study underlines the importance of augmenting the understanding of legal provisions and rights related to Irretrievable Breakdown of Marriage (IBM) among the public. It also underscores the significance of developing comprehensive support services for individuals navigating marital dissolution, to lessen its adverse societal ramifications in these countries (Cooper Sumner, 2013).\n\nThe media plays a crucial role in addressing irretrievable marriage breakdowns by disseminating information about healthy relationships, communication, conflict resolution strategies, and counseling and therapy benefits. It also presents real-life success stories, challenges misconceptions, advocates for policy modifications, and promotes open dialogues, creating a supportive environment for marital relationships. The government also plays a role in illuminating these issues, guiding parties to avoid costly outcomes like wasted time, financial loss, psychological distress, and impacts on children’s futures. These multifaceted efforts help mitigate the comprehensive losses linked to marital breakdowns.\n\nWhile the research paper provides valuable insights into the social bearing of laws and their implementation regarding the irretrievable breakdown of the marriage (IBM) in India and other Asian countries, it also has certain limitations that should be acknowledged:\n\nLimited scope: The study mainly focuses on Asian countries, which may not provide a comprehensive picture of the legal landscape of IBM in the world. Different countries and regions within may have unique legal frameworks and cultural contexts.\n\nCross-cultural comparison challenges: Comparing laws and their social implications across different countries can be challenging due to variations in legal systems, cultural norms, and societal expectations. The study may need to account for all the nuances and complexities involved in such comparisons.\n\nTemporal constraints: The study is based on the legal and social context at the time of its publication, which may not remain constant. Changes in legislation, social attitudes, and cultural practices can affect the relevance and accuracy of the findings over time.\n\n\nConclusion\n\nThe study on the irretrievable breakdown of marriage (IBM) in Asian countries, specifically focusing on India, reveals the significant variations in legal provisions, judicial discretion, societal factors, and gender inequality. The absence of explicit IBM provisions in Indian legislation highlights the need for legal reforms to align with changing social attitudes and promote gender equality. The research emphasises the importance of considering the social, cultural, and economic factors that shape divorce laws and their implementation to protect the rights of all parties involved. Furthermore, increasing awareness of IBM-related legal provisions and providing support services can help mitigate the negative social consequences of divorce. The law must be responsive to societal changes and create a harmonious and reciprocal environment for the smooth functioning of society.\n\nThe study suggests amendments to Indian divorce legislation to include irretrievable breakdown of marriage (IBM) as a ground for divorce, following the lead of other Asian countries. This measure aims to streamline the divorce process, better protect individual rights, and reduce the need for courts to investigate deeply personal or contentious issues that may have contributed to the breakdown of the marriage.\n\nComplementary efforts include public awareness through social media campaigns, education about IBM-related rights, and improved community support services like counselling, legal aid, and mediation. The study also recommends incorporating alternative dispute resolution methods and extra-judicial divorce, reducing the burden on the judicial system and potentially providing a more amicable speedy resolution.\n\nThe use of IBM as grounds for divorce also has implications when parties are unwilling or unable to disclose personal issues leading to the marriage breakdown. IBM, therefore, can facilitate divorce proceedings, avoiding the need for divulging personal or painful details.\n\nFinally, the study suggests that being non-specific to any religion or community, IBM can be uniformly applied to all citizens, contributing to the realization of a Uniform Civil Code in India.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAbalos JB: Divorce and separation in the Philippines: Trends and correlates. Demogr. Res. 2017; 36: 1515–1548. 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PubMed Abstract\n\nThornton A, Rodgers WL: The influence of individual and historical time on marital dissolution. Demography. 1987; 24: 1–22. PubMed Abstract \| Publisher Full Text\n\nTrent K, South SJ: Structural determinants of the divorce rate: A cross-societal analysis. J. Marriage Fam. 1989; 51: 391–404. Publisher Full Text\n\nUrbanik J: A Priestly Divorce in the Seventh Century Palestine. Marriage, Ideal–Law–Practice: Proceedings of a Conference Held in Memory of Henryk Kupiszewski. Warsaw: 2005; pp. 199–218.\n\nVan Eijk E: Divorce practices in Muslim and Christian courts in Syria. Family Law in Islam: Divorce, Marriage and Women in the Muslim World. 2012; pp. 147–170.\n\nVan Eijk E: Family law in Syria: Patriarchy, pluralism and personal status laws. Bloomsbury Publishing; 2016.\n\nVu HS, Schuler S, Hoang TA, et al.: Divorce in the context of domestic violence against women in Vietnam. Cult. Health Sex. 2014; 16(6): 634–647. 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Publisher Full Text" }	[ { "id": "226521", "date": "23 Dec 2023", "name": "Hiranmaya Nanda", "expertise": [ "Reviewer Expertise Family Laws", "Health Laws", "Business Laws" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThere are the intending variables to which the paper is conspicuous by its silence. IBM is a concept yet to find a place in statute book. It has been mentioned by the authors that in Pre Independence India has no law for divorce, however during that time laws relating to divorce were governed through Indian Divorce Act. In few Literatures the authors have categorically mentioned recognition of IBM as a ground for divorce in Indian Legal System. Later It has been denied by the authors. It seems Contradiction. India has not recognized IBM neither in its letter or spirit. The purpose of the law of divorce is not to provide the guilty party but to protect the innocent party. If the marriages has broken down to such an extent that it cant be improved then Should the Law insist on finding the party at fault? And to what extent would it help if one finds the defaulting party? And suppose no party is at fault or one party is at fault or both at fault, but the marriages has nonetheless broken down should the divorce be refused?\nThese Issues needs to be highlighted for IBM. Further the authors have discussed the Asian countries and the concept requires detailed analysis taking into account the facts of the each countries. Otherwise it amounts what it tends an ethnography study.\n\nMoreover the Title of the topic needs to be restructured focusing IBM instead Social bearing Laws. After having necessary corrections the paper merits publication.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "242503", "date": "09 Mar 2024", "name": "Gerrit Bauer", "expertise": [ "Reviewer Expertise sociology", "family", "inequality" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article examines divorce laws in Asian countries. It is based on a comprehensive literature review that provides a description of divorce laws in 50 countries. The authors have done valuable work on which further research in the fields of law, sociology, economics and demography can build.\nThe article is divided into three parts, each of which I will address in this review.\n1) Introduction: The authors contextualize divorce and divorce law within society. Table 1 presents selected studies on the determinants and consequences of divorce. The aim of this section seems to be primarily to demonstrate that divorce is a relevant phenomenon that has been extensively studied by various scientific disciplines. It should be noted, however, that these studies usually do not address legal issues. At this point, the table could be expanded to include a section of selected papers that examine the impact of divorce law on divorce rates. This would better connect Table 1 with the perspective of legal scholarship.\nIn addition, I suggest adding a section to the introduction to clarify terminology. Terms such as unilateral divorce, fault-based divorce vs. no-fault divorce, and irretrievable breakdown of marriage should be defined and the relationship between these concepts should be discussed.\n2) The major part of the article is devoted to the situation in 50 Asian countries. I cannot judge the accuracy of the presentation, but the literature review seems to be carefully researched.\n3) In my opinion, the last section \"Key Findings and Discussion\" could be improved, especially by a more in-depth discussion of the results. In the second part, the situation in each country is presented in a rather disconnected way, in alphabetical order of the countries. This leaves me with the question of comparison: What are the similarities, what are the differences in the regulations of the Asian countries? Where, for example, is still fault attribution in divorce, and where has it been replaced by unilateral divorce law? In which countries does Sharia law play a role, and where do religious norms have no influence on the legal system?\nThe authors would ideally create and publish a dataset for further research, coding the specific legal norms in each country. In combination with administrative and survey data, your coding of divorce laws could serve as a basis for studying a variety of questions in the field of law and social inequality: How do specific divorce regulations in Asia affect gender inequality? How do divorce rates differ across divorce law regimes? Do certain divorce laws promote women's labor force participation, etc.?\nI understand that creating such a dataset would require a lot of additional effort and time, but it would be a valuable resource for non-law scholars who want to analyze quantitative data from Asian Societies.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-921
https://f1000research.com/articles/10-1305/v1	22 Dec 21	{ "type": "Review", "title": "Continued dysregulation of the B cell lineage promotes multiple sclerosis activity despite disease modifying therapies", "authors": [ "Ana C. Londoño", "Carlos A. Mora", "Ana C. Londoño" ], "abstract": "A clear understanding of the origin and role of the different subtypes of the B cell lineage involved in the activity or remission of multiple sclerosis (MS) is important for the treatment and follow-up of patients living with this disease. B cells, however, are dynamic and can play an anti-inflammatory or pro-inflammatory role, depending on their milieu. Depletion of B cells has been effective in controlling the progression of MS, but it can have adverse side effects. A better understanding of the role of the B cell subtypes, through the use of surface biomarkers of cellular activity with special attention to the function of memory and regulatory B cells (Bregs), will be necessary in order to offer specific treatments without inducing undesirable effects.", "keywords": [ "Multiple sclerosis", "antibody secreting cell", "memory B cell", "naïve B cell", "B regulatory cell" ], "content": "Introduction\n\nMultiple sclerosis (MS) is a chronic, neuroinflammatory disease of autoimmune origin, which causes demyelination and neurodegeneration of the central nervous system (CNS). It is the leading cause of disability among young adults with neurological diseases.1 Current MS diagnosis methodologies are based on criteria that include clinical presentation, determination of oligoclonal bands (OCB) and other biomarkers in the cerebrospinal fluid (CSF), as well as presence of inflammatory and/or demyelinating lesions in the magnetic resonance imaging (MRI) analysis. Currently, the follow-up and response to treatment of patients with MS is based on the concept of “no evidence of disease activity” (NEDA) based on clinical presentation, imaging, and disability progression, without taking into account any other biomarkers of disease. Over the last three decades, the prognosis of disease has dramatically improved due to the availability of multiple disease modifying therapies (DMT).\n\nIt has been established that both T and B cells play a role in the pathogenesis of MS.2,3 The MS-promoting role of B cells can be carried out through the secretion of antibodies such as OCB, presentation of antigens, activation of T cells and/or production of cytokines.4 Perturbation of T cell homeostasis due to a reduction in cells of thymic origin, and reduction in the diversity of T cell repertoires, among others, has been documented in MS.5 Antibody secretion is the most studied function in the pathogenesis of MS and, in recent years, exploration of the role of cytokines in the regulation of immunity, for therapeutic purposes, has begun. In addition, the use of anti-CD20 therapies for MS, which do not affect plasmablasts (PB) and plasma cells (PC), has led to a better understanding of the role of B cells in the pathogenesis of the disease.4 Although DMT have the ability to slow down the progression of the disease, they are not a cure. In the present article, we show how the dysregulation of the B cell lineage could be strongly linked to the activity and progression of the disease and how selective therapy, guided by cell surface markers, could become key in controlling it.\n\nThe family of B cell subsets results from an evolutionary process of embryonic cells expressing different surface markers (especially CD19, CD20, and CD38) through their lifespan, in different organs, until they reach the state of antibody secreting cells (ASC), thus culminating the evolution process with the presence of effector B cells.6 The change of stage from membrane-linked antibody cell to ASC represents the terminal differentiation toward B cells that do not proliferate7,8 (Figure 1). The B cell lineage begins in fetal life from pluripotent hematopoietic stem cells (SC), located in the fetal liver and in the postnatal bone marrow (BM). Henceforth, they evolve into multipotent myeloid/lymphoid progenitors (MPP), which continue their evolution towards the common lymphoid progenitors (CLP).6 CLP from the BM evolve to a pro-B state in which they express the CD19 marker and then transform into pre-B cells; those, in addition to expressing CD19, begin to express CD20, and later progress to immature B cells that express IgM as a surface marker.6 While transiting from the BM to the secondary lymphoid organs (SLO), the B cells express the B cell receptor (BCR) surface markers IgM and IgD, thus evolving into transitional B cells; this step requires a checkpoint that entails clonal deletion and receptor editing before entering the SLO (spleen, lymphoid node, tonsils, and mucosa-associated lymphoid tissue [MALT]) where they become mature naïve B cells.6 The mature naïve B cells, at this point, can have three possible destinations: a) they enter the marginal zone of the spleen where they may become short-lived plasma cells (SLPC) that produce IgM and rapidly enter apoptosis (since these are B cells involved in rapid and transitory defense); b) move to the intestine and the pulmonary epithelium (B1 cells); c) migrate to splenic follicles and lymphoid nodules, becoming follicular B cells.9,10 Naïve B cells that carry the BCR IgD go through early class switch recombination (CSR) in the extrafollicular zone, with support from T cells, then enter the germinal center (GC) where they undergo somatic hypermutation (SHM), after which they express BCR IgG.11 Subsequently, the resulting memory B cells, PB and PC will have the ability to secret high-affinity antibodies for decades, or for the lifespan of an individual, and most of them will be able to migrate to the bone marrow to establish as long-lived plasma cells (LLPC).11,12,13 Dysregulation of the GC has been associated with autoimmune disease.14 Evidence suggests that the origin of B cell autoreactivity occurs in the GC due to dysfunction of thymus-derived follicular T helper cells and follicular regulatory T cells.15 PB may develop from any type of activated B cell (including naïve, marginal zone, follicular, and memory B cells), but it is not clear if PB that originated from these cells (except for memory B cells) are competent to mature to LLPC.6 PB will carry the CD19+CD20-CD27++CD38++IgG+/- markers, and will express the chemokine receptor CXCR4, which will help them get attracted to the chemokine CXCL12 in the BM niches. As an alternative, PB expressing the receptor CXCR3 will become LLPC in the spleen and lymph nodes (assisted by the chemokine CXCL12) or in inflamed tissue (assisted by the chemokines CXCL9-CXCL12), and subsequently undergo apoptosis upon resolution of inflammation.7 Hereafter, memory B cells access the CNS through the disrupted blood brain barrier (BBB). They are identified in perivascular spaces, demyelinating lesions in the brain and spinal cord, and disperse in the meninges where they can form aggregates known as tertiary lymphoid organs (TLO). These TLO emulate GC function, supporting the formation and persistence of cortical lesions.16,17,18,19 In addition, they are a local source of class-switch IgG that contribute to the immune process and are subsequently determined as OCB in the CSF of patients with MS.20 In the meninges, the inflammatory infiltrates are composed of CD3+ T cells, CD20+ B lymphocytes and PC.16 In the white matter lesions, the inflammatory infiltrates are localized in the perivascular spaces containing T and B lymphocytes and PC.16 In the diffuse infiltrates and normal-appearing white matter, CD8+ T lymphocytes predominate almost exclusively.16 The presence of PB in CSF has been reported.21,22 Despite the knowledge accumulated to this date, the complete understanding of the evolution of the B cell lineage is still in progress. Activated lymphocytes are able to access the CNS, both in health and disease, through the BBB, the blood meningeal barrier, and the blood-CSF barrier.12 In normal conditions the amount of B cells that access the CNS is very low.23 These cells primarily exit the CNS via lymphatic drainage through nasal blood vessels, or via meningeal lymphoid vessels to the lymphoid cervical nodules.24\n\nThe B cell lineage begins in fetal life from pluripotent hematopoietic stem cells (SC) in the fetal liver and in the postnatal bone marrow developing B cell receptors and migrating to different locations, including peripheral blood, and the secondary lymphoid organs (SLO) where they will acquire, in the germinal center (GC), the ability to recognize antigens and produce highly specific antibodies. In the pathogenesis of multiple sclerosis (MS), these cells may cross the BBB and may be found in the CSF, perivascular spaces (PVS), white matter (WM) demyelinating lesions and in the tertiary lymphoid organs (TLO). Abbreviations: SC: stem cell; SLO: secondary lymphoid organ; CSR: class switch recombination; SHM: somatic hypermutation; GC: germinal center; TLO: tertiary lymphoid organ; PVS: perivascular space; WM: white matter.\n\nNaïve and memory B cells are crucial within the B cell lineage and they have been shown to negatively correlate in their function: increased memory B cells and decreased naïve B cells have been linked with a worsening of the disease, and vice-versa.5 In fact, when the presence of memory B cells induce the auto-proliferation of CD4 T cells, which tend to home in the brain, naïve B cells are decreased.5 Memory B cells can be heterogeneous, i.e., originate from different cells or express different phenotypes, including class-switched (CD19+CD27+IgM-IgD-) and class-unswitched (CD19+CD27+IgM+IgD-).25 Inhibition of memory B cells prevents relapsing MS.25 In a study in naïve patients with relapsing remitting MS (RRMS), the interaction between T and B cells was documented, highlighting that B cells act as antigen presenting cells (APC) to auto proliferating CD4+ T cells.5 Increased amounts of T cell co-stimulatory proteins and major histocompatibility complex (MHC) class II molecules are expressed by B cells in the periphery (blood and SLO), and in the CSF and CNS of patients with MS.12 Patients in remission carrying the HLA-DR15+ marker showed an increase in auto-proliferative B and T cells and a decrease in naïve B cells.5 On the other hand, treatment with anti-CD20 was associated with a decrease in auto-proliferative memory T and B cells and increased presence of naïve B cells.5\n\nWithin the B cell lineage, the regulatory B cells subset (Bregs) stands out, since there is still no agreement on its origin and classification. Bregs are not a specific subtype of B cells, but represent a regulatory functional state resulting from inflammation.26 Although it has been assumed that interleukin 10 (IL10) is the hallmark of Bregs, other factors such as IL35, transforming growth factor (TGF) β, and direct cell-to-cell contact are also mechanisms of Bregs function.26 Immature B cells, mature B cells, PB and PC are believed to function as Bregs.26 The Bregs can express the following markers: IL10, CD27, CD5, CD25, CD86, CD24 and CD28.27 Based on the production of IL10, three important subtypes of regulatory Bregs have been identified, including the transitional (CD19+CD24highCD38high), naïve (CD19+CD24+CD38+), and memory (CD19+CD24highCD38-) subtypes, among which the transitional cells are the main producers of IL10.28 Transitional B cells are capable of suppressing differentiation of naïve T cells into Th1 and Th17, which are dependent on the co-stimulatory molecules CD80 and CD86.29 Survival of Bregs is linked to the B cell activating factor (BAFF) and to a proliferation inducing ligand (APRIL).20 Under normal conditions, the population of Bregs is kept low in order to maintain immune homeostasis.26 In newborns, 50% of umbilical cord blood B cells correspond to the transitional B cell subtype whereas, in adults, it represents only 4% of the cell population in peripheral blood.28 It is estimated that, in human peripheral blood, the Bregs subtype represents only 1-2% of all B cells.29 In an experimental allergic encephalitis (EAE) animal model, it was documented that IL10 contributed to the reduction of the inflammatory response mediated by microglia and astrocytes in the CNS.30 Bregs transfer reversed the increase in Th1 and Th17 cells in an arthritis model lacking IL10.31 In mice with low expression of the IL35 subunit p35, or EBi3 in B cells, an inability to recover from EAE was detected, with evidence of activation of macrophages and inflammatory T cells, and an increased activity of B cells such as APC.32 IL10 regulates the differentiation of the lineage from IL10-secreting B cells to PB that secrete IgG or IgM.33 In a post-mortem analysis of MS patients with high levels of meningeal inflammation and cortical demyelination, Magliozzi et al., reported an increase in IL10 expression, among other proinflammatory cytokines and molecules related to B cell activity and lymphogenesis in meninges and CSF. Additionally, an increase in IL10 was found in the CSF of MS patients with high cortical involvement at the time of diagnosis.34 Early development of MS in individuals with the clinically isolated syndrome (CIS), or radiologically isolated syndrome (RIS), seems to correlate with a reduced production of IL10 by B cells.35 In a cohort of MS patients followed for 10 years, Farian et al. found that patients with positive OCB at diagnosis advanced, more frequently and earlier in the course of the disease, to a progressive phase.36 This can be explained by the presence of a greater intrathecal inflammatory component that causes greater cortical involvement.36 Besides, the authors reported an over-expression of inflammatory molecules, including IL10.36 PB and PC inside the MS lesions presented a high IL10 expression.37\n\nAnother subset of CD19+ B cells that could be relevant to MS pathogenesis are the double negative (DN) B cells (IgD-CD27-) and the CD21low cells, which have been associated with aging and autoreactivity.38 These cells are believed to develop outside the GC, are independent from T-cells, and display a pro-inflammatory cytokine profile.38 These cells have been found in healthy subjects, and have also been found at higher levels in the CSF of MS patients younger than 60 years when they were compared to age-matched healthy donors (DN B cells 19.5% against 3.03%, and CD21low 21.95% against 6.06%, respectively).38 Most DN B cells display an IgG+ phenotype while CD21low B cells originate from a heterogeneous population that includes CD27- naïve, CD27+ memory, and IgG+ and IgM+ B cells.38 Both DN and CD21low B cell frequencies were higher in the CSF compared to blood levels for these patients.38 Fraussen et al. have suggested that the DN B cells may have multiple origins, considering IgG+ cells better linked to the class-switched memory B cells, while IgM+ cells share more similarity with the naïve and the non-class-switched IgD+CD27+ memory B cells.39\n\nInflammation of the CNS is reflected in the presence of B cells in the CSF.21 Cepok et al. evaluated the B cell subtype in CSF in MS patients, finding that the majority of detectable cells were memory B cells (CD19+CD27+), whereas a minority were naïve B cells (CD19+CD27-); those were different from naïve B cells that predominated in peripheral blood.21 In addition, they detected PB (CD19+ CD27++CD138+CD38+) subtypes representing between 30-50% of cells in CSF, and were present in the course of the disease, without correlation with the level of PB present in peripheral blood, while short lived PB (CD19+CD27++CD138+CD38++HLADR++) and PC (CD19+/- CD27++CD138+CD38+HLADR-) were absent from CSF.21 In contrast, Corcione et al. reported the predominance of both memory B cells and PC in the CSF of MS patients without treatment.18 In patients with RRMS and primary progressive MS (PPMS) with positive B cells for G1m1 (IgG1 heavy chain gene), Lossius et al. detected IgG1 ASC with a phenotype compatible with highly proliferating PB (CD19dimCD27hiCD38+) and with high expression of CD138+, HLA-DR+ and KI67+ in CSF.40 In pediatric MS, an increase in memory B cells in CSF, with a predominance of non-switched memory B cells and PB, was found, while in adults with MS, class-switched memory B cells and PC predominated in CSF during relapses of MS.25,41 Using a deep repertoire sequencing of IgG heavy chain variable genes (IgG-Vh) in paired CSF and peripheral blood from patients with MS, VonBudinghen et al. found that there was a cluster of clonally related B cells involved in a bidirectional cell exchange across the BBB, with some of them being present primarily in the CNS while others were present in the periphery or in both compartments.42 Additionally, using the same protocol, they found evidence of clonally related B cell receptors in a patient’s blood and CSF, after seven years of therapy with rituximab, indicating a prolonged presence in this compartment during the disease span due to recirculating memory B cells or LLPC.43 Greenfield et al. found that clonally related B cells were present as class-switched IgG and CD27+ in the CSF of patients with MS, leading to the conclusion that, despite having been on DMT, there were complex patterns of persistence of clonal B cells in CSF and blood.22 A significant depletion of CD20+ B cells has been detected in the blood, CSF and perivascular spaces in the CNS after therapy with rituximab and ocrelizumab.44,45 Table 1 presents a summary of the different surface markers that characterize the B cell lineage through its lifespan.\n\nUp-to-date reported B-cell subtypes with reference to the B cell lineage in MS. Sub-types from other inflammatory conditions are also mentioned.88 Abbreviations: SLO: secondary lymphoid organ; GC: germinal center; BM: bone marrow; ASC: antibody secreting cells; LLPC: long lived plasma cells.\n\nAdvances in immunotherapy have made it possible to limit the presence and expansion of B cells, thus reducing relapses and the progression of disability. However, the determination of which cells from the lineage could be responsible for clinical deterioration, or improvement, is still to be investigated. In the treatment of other autoimmune diseases, such as pemphigus, the mapping of cell markers has been used to evaluate the response to treatment, finding alterations in the function of CD19+CD24hiCD38hi Bregs cells, which are present in significantly higher numbers in patients in an active state compared to patients in the remitting state of RRMS.46 Late antibody-mediated rejection continues to be a problem for patients undergoing kidney transplantation and, for many years, it was believed that tolerance and rejection of transplantation were mediated by T cells.47 However, it was recently shown that a population of Bregs may be playing a deleterious role in transplant immunity, and be responsible for the production of alloantibodies.48,49,50 Recently, B cells (CD19+CD24hiCD38hi) dysfunction has been reported in peripheral blood, with decreased production of IL10 in patients with RRMS compared to healthy subjects.28 In turn, these cells have a less stimulatory effect on naïve CD4+ T cells, which produce IFNγ and tumor necrosis factor α (TNFα).28 Additionally, anti-CD19 monoclonal antibody has no effect on Bregs, which are regulators of EAE extension/expression through the secretion of immunosuppressive cytokines.51 In addition, Chen et al. determined the presence of autoreactive CD19+CD20- plasma cells in the CSF of patients with RRMS (20.18%), SPMS (29.58%) and PPMS (31.73%), including patients exposed to DMT.51\n\n\n\na. Interferon B (IFNβ) acts in the periphery, inducing apoptosis of CD27+ memory B cells through a mechanism that requires FAS receptor/transmembrane activator and calcium-modulating cyclophilin ligand interactor (TACI) signaling, leading to a specific depletion of these memory B cells (which carry the ability to harbor EBV) and an increase in the CD27- cell subtype that contains naïve B cells secreting IL10.52 Furthermore, it was observed that memory B cell depletion was accompanied by a reduction in EBV markers.52 IFNβ leads to the inhibition of leukocyte proliferation and antigen presentation.53 It also changes the cytokine profile towards an anti-inflammatory profile in both peripheral blood and the CNS, and reduces T cell migration by inhibiting the activity of the T cell matrix proteinase.53 IFNβ increases naïve B cells and decreases memory B cells in peripheral blood.54 Ersoy et al. showed that IFNβ induces the production of high amounts of IL10 compared to therapy with azathioprine in patients with RRMS.55 A meta-analysis study in patients with MS who received IFNβ showed that there was a lower proportion of Th17 cells in the peripheral CD4+ T cell pool and a reduction of IL17 and IL23 levels in serum.56\n\nb. Fingolimod is a sphingosine-1-phosphate (S1P) modulator that binds to the S1P receptor on lymphocytes, and retains naïve B cells and central memory B cells in lymphoid nodes.57 B cell subsets in the periphery are susceptible to being modified by fingolimod, thus leading to a reduction of memory B cells and an increase in the number of transitional B cells and Bregs in the periphery,58 with an associated increase in the production of IL10.32 Treatment with fingolimod has also been associated with a reduction in the lymphocyte count in peripheral blood and with an increase in the percentage of naïve B cells.59 Fingolimod also causes an increase in DN B cells.54 Fingolimod does not affect the exchange of B cells through the BBB, but it affects the intrathecal clonal expansion, thus inhibiting the activity of the GC.60\n\nc. Dimethyl fumarate (DMF) causes long-term lymphopenia through its effect on two genes: it induces NFrf2 (antioxidant effect) and inhibits NFkB which, in turn, induces a change from the Th1 to the Th2 subtype.57 DMF increases the ratio of naïve B cells to memory B cells and increases the number of transitional and IL10 producing B cells.32 DMF increases the percentage of naïve B cells, with a relative reduction in memory B cells and DN B cells.54\n\nd. Teriflunomide is a drug that inhibits the dihydroorotate dehydrogenase, thus interfering with the biosynthesis of pyrimidines and leading to a reduced cell proliferation. It can significantly reduce Bregs (CD24+CD38high), mature B cells (CD24+CD38low) and, to a lesser extent, memory B cells (CD24+CD38-) in the peripheral blood of patients with RRMS.61 Yilmaz et al. reported a reduction of PC in the peripheral blood of patients with RRMS, who were treated with teriflunomide.62\n\ne. Natalizumab blocks the entry of T cells (mainly CD4) into the CNS by neutralizing VLD4 or α4β1 integrins (57). Natalizumab in peripheral blood lowers PB and increases memory B cells.54 Kemmerer et al. reported an insignificant increase in the number of B cells and memory B cells in patients treated with natalizumab. In addition, PB were reduced due to a mechanism of natalizumab that alters their traffic through the BBB. Natalizumab decreases the exchange of peripheral and intrathecal B cells, but does not modify their intrathecal clonal expansion and can induce a reduction of OCB production in some cases.60,63 Traub et al. found that natalizumab promotes the activation and proinflammatory differentiation of peripheral B cells in MS.64\n\nf. Although glatiramer acetate (GA) is a compound affecting T cells, no effect in the maturation and differentiation of B cells has been detected.64 GA interferes with antigen presentation and promotes switching from the pro-inflammatory Th1 state to an anti-inflammatory Th2 state, on top of inducing CD8+ T regs cell production.57 The pro-inflammatory pattern, mediated by the secretion of IL6 by peripheral B cells, has been shown to abate and switch to a pattern mediated by IL10-secreting Bregs in MS patients treated with GA.65 However, other studies on the efficacy of GA on B cells in patients with RRMS have reported a reduction in the total numbers of B cells, PB and memory B cells in peripheral blood.54,65,66 By reducing the expression of intracellular adhesion molecule (ICAM-3), GA contributes to reducing the migration of B cells to the CNS.20\n\ng. Rituximab blocks the CD20 receptor, thus removing pathogenic B cells.57 Although rituximab depletes naïve and memory B cells in the circulation and is not as effective in depleting B cells in tissues, effector and regulatory cells are balanced during cell repopulation after therapy.32 Palanichamy et al. found that rituximab induced depletion of memory B cells in blood for up to 12 months.67 A depletion of T cells by more than 50% and B cells by 95%, in CSF, has also been reported after treatment with rituximab in patients with RRMS.68 Using the surface B cell marker CD21 in patients with secondary progressive MS, who received IV rituximab on days 0 and 15, and intrathecal rituximab on day 0, six weeks and twelve months later, Komori et al. found a significative reduction in CD21 expression in the serum of patients, suggesting a complete and lasting depletion of B cells, as opposed to an insignificant change in CSF corresponding to an incomplete and transitory depletion of B cells in the CNS compartment.69 In patients with neuromyelitis optica (NMO) seropositive for aquaporin-4, treatment with rituximab was followed by no relapse while their memory B cells were below 0.05% in peripheral blood.70 Hausler et al., working on a model of EAE induced by myelin oligodendrocyte glycoprotein (MOG) and another model in naïve mice observed, after treatment with the murine subrogate of rituximab, a persistence of mature B cells in the spleen; an early reconstitution of B cells in the bone marrow and in the spleen before being released into the periphery; and a presence of reactive B cells against myelin when the model included activation of B cells.71 Altogether, these findings suggest that pathogenic B cells were able to persist despite an anti CD20 treatment.71 In addition, they reported a fast depletion of B cells in the peripheral blood, which upon discontinuation of treatment, began to repopulate, proving that cells have different sensitivities to therapy with anti CD20.71\n\nh. Ocrelizumab is a humanized monoclonal antibody version of rituximab capable of causing more severe CD19+ cell depletion than rituximab in patients with rheumatoid arthritis.72 Ocrelizumab is also associated with a very long therapeutic effect, up to 22 months, after the last dose as demonstrated by the RRMS clinical trials OPERA I and OPERA II.73 Recent studies have shown that patients who received treatment with rituximab, or ocrelizumab, for RRMS and NMO for several years, developed hypogammaglobulinemia or a defective recovery of B cells, which could be asymptomatic or could present with bacterial infections or recurrent viral diseases.74,75 The duration of hypogammaglobulinemia fluctuated between one month and eleven years.75 Marcinno et al. recommended that, in patients who receive anti CD20 therapy, the serum levels of IgA, IgG, and IgM should be determined before initiation of treatment, and repeated yearly with special attention to patients who present a drop in IgG and IgM early in the course of therapy, and who should receive protection against tetanus.76\n\ni. Alemtuzumab depletes the CD52 marker in B and T cells with very long periods of CD4 T cell depletion.57 Alemtuzumab is able to deplete 70 to 95% of CD4 T cells in active relapsing MS.25 During the reconstitution of B cells after treatment with alemtuzumab, there is a predominance of immature transitional cells, which is followed by a predominance of mature naïve B cells, accompanied by an increase in BAFF, while the reappearance of memory B cells is slow.32,77 Mohn et al. reported a change in the distribution of B cells toward a B cell-naïve phenotype in MS patients treated with alemtuzumab, observing negativization of OCB in two patients.78 The adverse effect of alemtuzumab, including autoimmune disease of the thyroid gland, kidney, platelets and lungs, are well known and correlate with the early recovery of the B cell population with persistence of CD4 T cell depletion, especially during the first year of therapy.79\n\nj. Atacicept binds to BAFF and to APRIL, blocking the maturation, differentiation and survival of B lymphocytes.57,80 Atacicept depletes transitional and naive B cells, PB and PC, and IL10-producing B regs.32,81 Atacicept causes B cell depletion without affecting progenitor cells (pre- and pro-B cells) and memory B cells.54 Treatment of MS patients with atacicept, unexpectedly, induced more relapses in the ATAMS trial.80,81\n\nk. Cladribine is a chlorinated deoxyadenosine analog, partially resistant to adenosine deaminase.34 The role of cladribine as an immune reconstitution therapy (IRT) has been proven by its prolonged depleting effect on CD4+ T and B lymphocytes in the periphery.82,83 Cladribine has the ability to reduce class-switched and unswitched memory B cells to a level comparable to that seen in therapy with alemtuzumab.82\n\nl. Inebilizumab is an anti-CD19+ B cell drug with the ability to deplete the B cell lineage from pro-B cell to PC stage, which was recently reported to induce rapid depletion of B cells and PC in MS patients in a phase I study.84 A new generation of anti-CD20 therapies capable of depleting B cells in the resident organ is under development, including obinutuzumab,85 although it has not been tested in the treatment of MS yet.\n\nm. Human immunoglobulin G (IVIg) acts on steady-state B cells, inhibiting the homeostatic proliferation of B cells accompanied by an induction of cell aggregation.86\n\nn. Autologous haematopoietic stem cell transplantation (AHSCT) is another alternative treatment that achieves a therapeutic effect by depleting all lymphocytic cell population involved in MS; however, its efficacy depends on the type of cell ablation used, since, as described by Hausler et al. while reporting an animal model of EAE, the reconstitution of B cells after anti-CD20 therapy stems from the B cell population that has survived in the bone marrow and spleen.71 An analysis of peripheral blood lymphocyte reconstitution after AHSCT, with high-dose immunosuppressive therapy in patients with RRMS followed for two years, disclosed a greater progressive expansion of the population of naïve B cells in the first and second year post-transplant.87 At one month, patients with systemic sclerosis who underwent AHSCT had a transient increase in transitional B cells and PB with an increase in the percentage of naïve B cells up to 14 months; their cytokine profile also changed in the long term, increasing IL10 secretion.88 The B cell compartment also showed decreased percentages of pre- and post-switch memory, as well as DN B cells.88\n\nBurton tyrosine kinase (BTK) inhibitors appear promising as potential therapeutic agents, since evobrutinib has previously been shown to prevent the activation of B cells and improves the clinical course in EAE.89\n\n\nDiscussion\n\nThe origin of MS still remains enigmatic, although different animal models of EAE have been developed, emulating a peripheral attack compromising the CNS, or an intrinsic CNS pathology process with effect in the peripheral blood.90 Sabatino et al. have suggested that the paradigm of autoimmune reaction occurring within the CNS may coexist with the outside-in paradigm.12 Either way, B and T cells are interdependent in the pathogenesis of MS. Inside the brain, the TLO found in the meninges are the driving force of the autoimmune pathogenic process.91 It has been proposed that previous EBV infection, vitamin D deficiency, and/or a genetic substrate may be the initiators or determinants of the disease process in MS. The B cell lineage plays a crucial role in the pathogenesis of MS and remains active during the course of the disease, in the periphery and CNS, and an aggressive depletion with current therapies can only control the clinical activity and slow down the progression toward disability. Deciphering the intricate variety of phenotypes and the role of the different B cell subsets in MS would be paramount for a complete understanding of this disease.\n\nThe acknowledgement of the role of B cell subsets in the presentation of several inflammatory diseases has stemmed from observations in autoimmune conditions such as rheumatoid arthritis, end-stage renal disease secondary to nephritis, bullous pemphigus, and granulomatosis with polyangiitis.92,93 Patients with end-stage kidney disease, who have an increase in transitional B cells and Bregs in the blood before transplant, and who present a significant reduction in post-transplant Bregs, are more likely to suffer acute and chronic rejection.92 Although Bregs appear as anti-inflammatory cells, there is evidence that they may play a pro-inflammatory role in certain pathologies. In another study in patients with bullous pemphigus, Liu et al. confirmed that identifying the role of each cell subtype in the pathophysiology of the disease is crucial.94 In the same study, a dysfunction of Bregs exhibiting a pro-inflammatory phenotype was observed to contribute to the production of autoantibodies.94\n\nIn MS, it has been documented that memory B cells can lead to an exacerbation of RRMS through the activation of T cells in the periphery.5 Furthermore, the fact that memory B cell numbers are decreased under the action of various DMT, and the fact that they were not found to be eliminated by atacicept, confirms their pathogenic role. Most of the immunomodulatory therapies currently available generally induce a reduction in memory B cells and an increase in naïve B cells in peripheral blood, which translates into clinical improvement. In contrast, natalizumab blocks the passage of B cells, mainly memory B cells, through the BBB, increasing their number in peripheral blood. The effect of B cell intrathecally depleting agents is not fully understood.\n\nIn relation to Bregs, Matsushita et al. observed that depletion of B cells, before the induction of an EAE model, exacerbated the severity of the pathology, due to the depletion of the Bregs population and its suppressive capacity; in contrast, depletion during the acute phase decreased symptoms by affecting the effector cells, which prevented the activation of CD4+ T cells.95 Identifying the subtypes of B cells which may be responsible for the inflammatory process in MS, in the periphery and in the CNS, is essential to achieve a selective and timely intervention in order to modulate or neutralize their function and to avoid disease progression, without interfering with the functions of immune surveillance and decreasing the anti-inflammatory response of Bregs.85,96 The ability of some cells of the B lineage to transform into Bregs, counteracting inflammation through the production of IL10, is remarkable and warrants to be considered for the development of better therapeutic strategies. Several studies conducted on patients who received kidney transplantation and patients with other autoimmune diseases, have shown that treatment with anti-CD20 is effective in the restoration of the balance between effector B cell and Bregs, and that the repopulation of B cells might predict a clinical relapse.97\n\nCurrent consensus dictates that early initiation of therapy in patients with MS leads to a better prognosis. However, a common dilemma in the MS clinics entails deciding when patients with CIS should start treatment. It is usually considered that CIS patients with high risk factors such as presence of OCB, uptake lesions on MRI, and marked severity of the clinical episode are most likely to evolve to clinically definitive MS or RRMS. Another dilemma is observed in patients with CIS who have been started on DMT, based on risk factors, but who, after four or five years of follow up, do not display evidence of disease activity yet.98 Mapping B cell subtypes in peripheral blood and CSF could be considered as an additional tool to determine alterations in the B cell lineage, which could be suggestive of disease activity in these subjects.\n\nThe main goal of this review entailed the summary of the B cell lineage diversity, following the transformation that cells undergo in each specialization stage allowing them to fulfill distinct roles in their attack on the CNS. Simultaneously, it raises the need to give a directed treatment that could improve drug delivery in the CNS, and a more ingenious monitoring of individual responses to therapies, in order to personalize treatment protocols. Finally, the complexity of the function of LLPC and the extraordinary role that they play in the B cell lineage require further investigation, as well as a deeper review of the contemporary medical literature.99\n\n\nConclusion\n\nIt is becoming evident that the identification of the role of different B cell subsets, in the periphery and CNS during the lifespan of MS, has been of paramount significance for the understanding of the pathogenesis of the disease. Specifically, a careful evaluation of the expression of surface markers of transitional, naïve, memory B cells and Bregs, in blood and/or CSF, could contribute to a prompt identification of patients who are not responding to therapy and who may be susceptible to undergo relapses and disease progression. A better understanding of the role of these cell subsets would be useful for engineering intelligent cell therapies that, hopefully, may permit a better control of the disease in the future. This approach would encourage us to rethink the current therapeutic strategy in order to improve the prognosis and quality of life of patients with MS.", "appendix": "Acknowledgements\n\nThe authors especially thank Ms. Luisa Munévar Mora for her contribution with the artistic design of Figure 1.\n\n\nReferences\n\nKlineova S, Lublin FD: Clinical course of multiple sclerosis. Cold Spring Harbor Perspectives in Medicine. 2018; 8: a028928. PubMed Abstract \| Publisher Full Text\n\nSospedra M: B cells in multiple sclerosis. Current Opinion in Neurology. 2018; 31: 256–262. Publisher Full Text\n\nHohlfeld R, Dornmair K, Meinl E, et al.: The search for the target antigens of multiple sclerosis, part 2: CD8+ T cells, B cells, and antibodies in the focus of reverse-translational research. Lancet Neurology. 2016; 15: 317–331. PubMed Abstract \| Publisher Full Text\n\nLi R, Patterson KR, Bar-Or A: Reassessing B cell contributions in multiple sclerosis. Nature Immunology. 2018; 19: 696–707. 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Oral presentation plenary section PS06.05 11 sept 2020. 8th joined Actrims-Ectrims meeting. MS virtual 2020.PubMed Abstract\n\nCarter NA, Vasconcellos R, Rosser EC, et al.: Mice lacking endogenous Il-10-producing regulatory B cells develop exarcebated disease and present with an increased frequency of Th1/Th17 but a decrease in regulatory T cells. Journal of Immunology. 2011; 186: 5569–5579. PubMed Abstract \| Publisher Full Text\n\nStaun-Ram E, Miller A: Effector and regulatory B cells in multiple sclerosis. Clinical Immunology. 2017; 184: 11–25. PubMed Abstract \| Publisher Full Text\n\nHeine G, Drozdenko G, Grün JR, et al.: Autocrine IL-10 promotes human B-cell differentiation into IgM- or IgG- secreting plasmablasts. European Journal of Immunology. 2014; 44: 1615–1621. PubMed Abstract \| Publisher Full Text\n\nMagliozzi R, Howell OW, Nicholas R, et al.: Inflammatory intrathecal profiles and cortical damage in multiple sclerosis. Annals of Neurology. 2018; 83: 739–755. 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PubMed Abstract \| Publisher Full Text\n\nUccelli A, Aloisi F, Pistoia V: Unveiling the enigma of the CNS as a B cell fostering environment. Trends in Immunology. 2005; 26: 254–259. PubMed Abstract \| Publisher Full Text\n\nOleinika K, Mauri C, Salama AD: Effector and regulatory B cells in immune-mediated kidney disease. Nature Reviews. Nephrology. 2019; 15: 11–26. PubMed Abstract \| Publisher Full Text\n\nMonschein T, Salhofer-Polanyi S, Altmann P, et al.: Should I stop or should I go on? Disease modifying therapy after the first clinical episode of multiple sclerosis. Journal of Neurology. 2021; 268: 1247–1253. PubMed Abstract \| Publisher Full Text\n\nHalliley JL, Tipton C, Liesveld J, et al.: Long lived plasma cells are contained within the CD19-CD38hiCD138+ subset in human bone marrow. Immunity. 2015; 43: 132–145. PubMed Abstract \| Publisher Full Text" }	[ { "id": "135362", "date": "09 Jun 2022", "name": "Mickaël Bonnan", "expertise": [ "Reviewer Expertise MS", "NMOSD" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis review article deals with the variety and roles of B cells subtypes in MS pathology. Authors tried to engulf diverse data concerning B cell lineage, in general and throughout compartments and MS stages. They finally examined how B cell lineages are affected by disease-modifying treatments (DMT).\nAlthough this review provides a general overview of the literature concerning B cell lineage in MS, important points were not expanded. Tertiary lymphoid organs (TLO), which drive cortical pathology and prognosis are shortly described. Mutual exchange of cells across the BBB, local heterogeneity of B cell clusters in the brain, location of affinity maturation are too shortly described.\nOur main criticism is nested in figure 2: how consistent and reproducible are data obtained concerning B cell lineages according to the variety of definitions used to qualify each state of maturation?\nFigure 1: plasmablasts and plasmocytes are only depicted in CSF. Homing of these cells was also described in brain and TLO (i.e. ref 16). Moreover it is easy to evaluate that rare floating ASC (cf ref 21) cannot account of the amount of intrathecal IgG synthesis (they account in a range of ~1%). CSR may also occur in brain TLO. Lastly, bidirectional exchange of B cells, which is major process (e.g. ref 42), was not emphasized in the figure.\nSentence: ‘They are identified in perivascular spaces, demyelinating lesions in the brain and spinal cord, and disperse in the meninges where they can form aggregates known as tertiary lymphoid organs (TLO)’. TLO are real and complete lymphoid organs, lacking a conjunctive external capsule and occurring in a non-genetically driven location. Memory B cells are only part of TLO, which are mostly driven by CD3−CD4+CD45+ lymphoid tissue inducer (LTi) cells then stromal cells.\nSentence: ‘A significant depletion of CD20+ B cells has been detected in the blood, CSF and perivascular spaces in the CNS after therapy with rituximab and ocrelizumab’. Indeed, B-cells are totally depleted from blood after antiCD20 infusion, whereas CSF compartment remains partly and transiently depleted. This is the point: antiCD20 fails to deplete intrathecal compartment from CD20+ cells, possibly due to the lack of effectors (low complement concentration in CSF, rare NK cells). Intrathecal infusion, although increasing bioavailability in CSF, does not add any efficacy.\nTable 2. We did not understood the importance of Table 2, except giving example that stringent definition of cell classes is not as stringent as it could be among authors and papers. This table may suggest that surface markers of B cells in MS could be specific. We do not understand the column 'compartment': does it mean that the lineage was found in this compartment? If so, it is worth to also indicate which lineage was NOT found in each compartment.\n*In Conclusion. Sentence: ‘Specifically, a careful evaluation of the expression of surface markers of transitional, naïve, memory B cells and Bregs, in blood and/or CSF, could contribute to a prompt identification of patients who are not responding to therapy and who may be susceptible to undergo relapses and disease progression.‘ Although a real improvement of CSF FACS availability remains possible, we do not believe that the study of B cells will drive therapeutic opportunities or help to monitor the disease. CSF is especially difficult to obtain and is probably not a target for scheduled biological tests. Moreover, as the authors demonstrated throughout the text, the precise role of each B cell subtype is far from being understood in MS.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [ { "c_id": "8597", "date": "03 Aug 2022", "name": "Carlos Mora", "role": "Author Response", "response": "We thank Dr. Bonnan (article reviewer) for his thorough comments to the first version of our manuscript. We have reviewed and modified Figure 1 to remark that the natural exchange of B-cells across the BBB is bidirectional, that class switch recombination (CSR) may also occur in the brain TLO, and that plasmablasts and plasma cells figure out in the brain (including the TLO), CSF and peripheral blood. We also labelled the T-cells present in the white matter lesion and in the secondary lymphoid organ (SLO). In the section titled ‘B cells in the CSF compartment in MS’ the sentence remarked by the reviewer has been modified as follows: ‘A significant depletion of CD20+ B cells has been detected in the blood, with a partial and transient depletion in the CSF and the CNS perivascular spaces, after therapy with rituximab.’ In the penultimate paragraph of the ‘Discussion’ section, we have added two new references to the manuscript, which give more detailed information about the relevance of the tertiary lymph organ (TLO [Londoño AC and Mora CA. Role of CXCL13 in the formation of the meningeal tertiary lymphoid organ in multiple sclerosis. F1000Research 2018, 7:514 https://doi.org/10.12688/f1000research.14556.3] now reference 99) and about the controversial poor response to therapy with rituximab in the CSF compartment with persistence of B cells (Bonnan M, Ferrari S, Courtade H, Money P, Desblache P, Barroso B, Debeugny S. No Early Effect of Intrathecal Rituximab in Progressive Multiple Sclerosis (EFFRITE Clinical Trial). Mult. Scler. Int. 2021, 2021, 8813498 -now reference 100). This paragraph reads as follows: ‘We still believe that the meningeal TLO works as an operation center with the ability to magnify an auto-immune response by maintaining antibody diversity, B cell differentiation isotype switching, oligoclonal expansion and local production of autoreactive PC.99 However, recent studies with intrathecal rituximab have shown an inadequate effect in progressive MS and failed to show an early effect, with persistence of markers of inflammation in CSF and leptomeningeal enhancement, in PPMS.69,100 Factors involved in a decrement of CNS efficacy of intrathecal rituximab include a decreased complement-dependent cytotoxicity (due to a low complement concentration in the CSF), a decreased antibody-dependent cytotoxicity (due to a lower proportion of CD56dimNK cells) and a poor bioavailability of rituximab for the B cells embedded in the CNS due to the dynamics of the CSF flow from the lumbar cistern to the arachnoid granulations.69’ The first sentence of the ‘Conclusion’ section has been modified as follows: ‘It is becoming evident that a better identification of the role of different B cell subsets, in the periphery and CNS during the lifespan of MS, will be of paramount significance for the understanding of the pathogenesis of the disease.’ With reference to the comments to Table 1, titled ‘B cell subsets surface markers’, the reviewer is right in his assertion that the motivation for the presentation of this table was the recognition of the significant diversity in the terminology and nomenclature used for the identification of the B cell subtypes in different organs (we used the term ‘compartment’ in the table) described by at least nine different articles cited in our review (references 12, 20, 21, 27, 40, 85,88, 96 and 101). According to the data presented in the table, we also believe that surface markers of B-cells in MS could be specific. Minor changes were introduced to the table including the meaning of the ‘compartment’ heading and a clarification in the ‘compartment’ column for the ‘centroblast’ and ‘centrocyte’ cell markers (the abbreviation ‘GC’ was replaced by ‘CSF’ in both [reference 96])." } ] } ]	1	https://f1000research.com/articles/10-1305
https://f1000research.com/articles/12-33/v1	09 Jan 23	{ "type": "Review", "title": "Dance/movement therapy as a holistic approach to diminish health discrepancies and promote wellness for people with schizophrenia: a review of the literature", "authors": [ "Jacelyn Biondo" ], "abstract": "Individuals with a diagnosis of schizophrenia face a myriad of obstacles to wellness, beginning with diagnostic discrepancies including over- and misdiagnoses on the schizophrenia spectrum. People with schizophrenia experience profound amounts of stigmatization from the general population, their healthcare providers, and even themselves. Such stigmatization creates a barrier for wellness, poorer prognoses, and often limits adherence to physical and mental healthcare. Moreover, it can exacerbate the already stifling symptomatology of their diagnoses, including specific bodily-related symptomatology. Oftentimes, a diagnosis of schizophrenia disrupts one’s relationship with their body including a diminished mind-body connection, decreased interoceptive awareness, and thus unsuccessful intra- and interpersonal relationships. Some recent research suggests the use of mind-body therapies, however, if these practices are internalizing, they may not be appropriate for people with schizophrenia experiencing more acute symptomatology excluding them from treatment. Dance/movement therapy (DMT) is an embodied psychotherapeutic treatment option that can support participants in improving mind-body connection, social relationships, and self-regulatory skill development. Research on DMT has shown promising results for people with schizophrenia, however such research is limited and would benefit from increased studies that particularly measure the effects of DMT on mind-body connection and increased interoception for people with schizophrenia. Moreover, integrative and collaborative treatment models that couple DMT and biofeedback may further our understanding of the physiological and neurological effects of DMT interventions for people with schizophrenia and beyond. This review will examine the recent literature on health inequities for people with schizophrenia, their specific body-based disruptions and needs, and DMT as a promising treatment model, particularly when coupled with biofeedback.", "keywords": [ "dance/movement therapy", "schizophrenia", "mind-body connection", "interoception", "healthcare disparities", "embodiment", "neurobiology" ], "content": "Introduction\n\nIndividuals diagnosed with schizophrenia face discrepancies regarding health care services at a rate much higher than the general population (Moore et al., 2015; Oud & Jong, 2017; Tan et al., 2021). The inequities they face include both physical (Moore et al., 2015; Sølvhøj et al., 2021) and mental health care (Ivanova, 2021; Metzl & Roberts, 2014; Rössler, 2016), and contribute to a decrease in general wellbeing and thus quality of life. People with schizophrenia have specific and additional needs due to their complicated symptomatology inclusive of body-based dysregulations (Biondo et al., 2021; Davis, 2019; Klaver & Dijkerman, 2016). Dance/movement therapists have foundational knowledge rooted in embodied, trauma-informed, nonverbal psychotherapeutic practices (Homann, 2020; Koch, 2017). Through a strengths- and body-based approach, dance/movement therapy (DMT) surpasses traditional verbal communication, establishing inclusion for many forms of preferred communication styles (Biondo et al., 2021). Joining through movement facilitates increased attunement, which is a necessary component to foster self-regulation and encourage healthy interpersonal skills. Additionally, DMT provides the framework to access embodiment and neurophysiological theories, which supports the multifaceted needs of individuals diagnosed with schizophrenia. One of the primary tenets of DMT is that the mind and body are interrelated and thus have a relationship that inform wellness. DMT is an active and embodied treatment option to increase mind-body connection. This paper will review the current literature on physical and mental health care inequities for people with schizophrenia, bodily disturbances associated with the diagnosis, and ways in which DMT, possibly coupled with biofeedback, can be a holistic approach to treatment.\n\n\nDiscussion\n\nMental health disparities for people begin with diagnostics. This is largely due to the structural racism that occurs within mental health facilities. Systemically racist underpinnings of mental health care facilities cause undue stress for People of Color (POC), particularly Black and African American men (Metzl & Roberts, 2014). Pre-Civil Rights era, a diagnosis of schizophrenia was largely associated with middle-class, white housewives experiencing symptoms of regressive behaviors, disrupted moods, and an inability to care for the home (Metzl & Roberts, 2014). However, Metzl and Roberts (2014) noted that this shifted dramatically in the mid-1950s in parallel with the Civil Rights movement. At that point in time, schizophrenia became a diagnosis largely relegated to Black and African American men at rates of 65% more frequently than white men. By the 1970s and 1980s, Black and African American men were five to seven times more likely to receive a diagnosis of paranoid schizophrenia than their white male counterparts (Metzl & Roberts, 2014). The authors asserted that both historically and presently, Black men are more likely to receive a diagnosis of schizophrenia than white men with the same presenting symptoms. This research identified an over–diagnosis of schizophrenia and an under–diagnosis of mood disorders for Black and African American men. This is partially attributed to the mistrust and stigmatization psychiatrists and other mental health care workers have towards POC and people with severe mental illnesses (Metzl & Roberts, 2014).\n\nIndividuals with schizophrenia experience stigmatization at rates higher than other individuals with mental health diagnoses (Rössler, 2016). Ivanova (2021) defined stigmatization as “a mark of shame, disgrace or disapproval which results in an individual being rejected, discriminated against, and excluded from participating in a number of different areas of society” (p. 47). Historically, people who experienced mental illness were treated extremely poorly with consequences of being held against their will, tortured, or even killed (Rössler, 2016). Although these practices have ceased, the fear of people with mental illness, particularly those with a diagnosis of schizophrenia, remains. The association of violence or aggression with individuals with schizophrenia is incorrect (Ivanova, 2021; Rössler, 2016). Research shows that people with schizophrenia are 75-120% more likely to be a victim of violence than the general population (Ivanova, 2021).\n\nStigmatization also affects people with schizophrenia on personal and social levels. In a survey inclusive of 27 countries, people with schizophrenia reported discriminatory behaviors in their personal relationships at a rate of 50% and in job related relationships at a rate of 67% (Rössler, 2016). This stigmatization traverses into the relationship between people with schizophrenia and their health care providers, who have a higher rate of negative beliefs about people with schizophrenia than the general population (Rössler, 2016). Stigmatizating behaviors extend to psychiatrists, making them less likely to meet in a clinical context with individuals diagnosed with schizophrenia (Rössler, 2016). Consistent stigmatizing behaviors from others can lead to self–stigmatization behaviors for individuals with schizophrenia —compounding a diminished sense of self-esteem and self–efficacy (Rössler, 2016). This ultimately inhibits and limits the care that people with schizophrenia are seeking and receiving, and contributes to negative effects on their overall prognosis (Ivanova, 2021).\n\nIn events where people with schizophrenia have sought mental health services, some reported feeling “devalued, dismissed, and dehumanized by healthcare professionals” (Ivanova, 2021, p. 49). This speaks to the level of exclusion people with schizophrenia experience, deeply rooted in stigmatization (Lincoln et al., 2021). Individuals with schizophrenia are often excluded from medical decision making and feel coerced by medical care practitioners (Ivanova, 2021). Both medical decision making and social exclusion can have detrimental effects on mental and physical wellness, leading to an increase in symptomatology (Lincoln et al., 2021). Research has shown a direct relationship between feelings of social exclusion with negative neurobiological responses (Lincoln et al., 2021; Metzl & Roberts, 2014). Beyond medical care, researchers have often excluded individuals with schizophrenia from their studies due to the presence of positive symptomatology or an exacerbation of symptomatology indicating they may be unable to manage the intervention or treatment (Biondo et al., 2021). This prevents people with schizophrenia from informing, testing, and responding to possible treatment protocols that could provide them with more effective care. A less medical and more psychosocial approach to support could mediate some of this stigmatization, and resultant exclusion, exhibited by health care providers (Ivanova, 2021). Unfortunately, these undesirable behaviors of medical professionals traverse beyond mental health care and into the realm of physical health care as well (Kohn et al., 2022; Oud & Jong, 2017; Sølvhøj et al., 2021; Swildens et al., 2016).\n\nPeople with a diagnosis of schizophrenia have a lifespan 10-20 years shorter than the general population and have a 2.5 times higher risk of death compared to the general population (Moore et al., 2015; Oud & Jong, 2017). The co-morbidity rate for schizophrenia and somatic disorders—including diabetes mellitus, cardiovascular diseases, and respiratory diseases—is the highest level of physical health co-morbidity as compared to other people diagnosed with severe mental illness (Tan et al., 2021). There are many factors that contribute to inequities in health care for people with schizophrenia, including disparities in access, use, and provision of services (Kohn et al., 2022) and general limited use of somatic health care practitioners (Swildens et al., 2016). In addition to the poor medical treatment adherence rate (Kohn et al., 2022; Laursen, 2019), people with schizophrenia also received poorer care, less preventative and curative screening processes, and less prescriptions (Laursen, 2019). Somatic diseases are often underdiagnosed and under-treated amongst people with severe mental illness, particularly schizophrenia (Kohn et al., 2022; Laursen, 2019; Oud & Jong, 2017).\n\nOne of the causes of poorer quality of care is the ongoing stigmatization of people with schizophrenia (Kohn et al., 2022; Oud & Jong, 2017; Sølvhøj et al., 2021; Swildens et al., 2016). Individuals diagnosed with schizophrenia feel that they are spoken down to or even patronized by doctors when they are seeking treatment. Furthermore, due to differences in communication styles and preferences, people with schizophrenia have reported feeling uncomfortable expressing their concerns to doctors for fear of being physically or emotionally hurt or becoming recipients of other forms of stigmatization (Kohn et al., 2022).\n\nStigmatizing behaviors compound communication difficulties, reducing the ability for people with schizophrenia to express their physical concerns readily (Kohn et al., 2022). This surge in stress may also result in the emergence of or contribution to somatic diseases (Oud & Jong, 2017; Vancampfort et al., 2017). Oftentimes, such communication difficulties heighten isolative behaviors. Negative symptomatology of schizophrenia, including social withdrawal and lack of spontaneity, can interfere with appropriate physical health care. These symptoms encourage a sedentary lifestyle, which typically decreases one’s ability to report physical health symptoms accurately and readily (Moore et al., 2015; Oud & Jong, 2017; Vancampfort et al., 2017). Moreover, a sedentary lifestyle coupled with metabolic effects of antipsychotic medications contribute to people with schizophrenia being overweight, furthering their propensity towards developing a somatic disease (Laursen, 2019; Moore et al., 2015; Oud & Jong, 2017). Both the negative symptomatology and the negative side effects of antipsychotics trigger poor self-esteem (Vancampfort et al., 2017) and a loss of hope for people with schizophrenia (Oud & Jong, 2017). The added complication of having a limited social support in addition to the aforementioned complications all act as barriers to accessible, quality health care of people with schizophrenia (Vancampfort et al., 2017).\n\nPeople with schizophrenia often have specific care needs due to movement dysregulations that are associated with their diagnosis (Biondo et al., 2021; Davis, 2019). The Diagnostic and Statistical Manual of Mental Disorders, Fifth edition (DSM-5) notes macro-level movement dysregulations such as holding bizarre postures or grossly disorganized movements (American Psychological Association [APA], 2013); however, there are many more subtle and disruptive bodily disturbances associated with schizophrenia including movement fragmentation, unsynchronized movement, subtle and bizarre facial expressions, or limited ability for spontaneous movements or gestures (Biondo et al., 2021; Davis, 2019).\n\nDiminished body awareness often correlates with higher symptomatology, which thus contributes to further bodily disruptions (Costantini et al., 2020). This cycle of symptomatology and body disturbances disallows healthy mind-body connectivity for people with schizophrenia. Typically, bodies and brains communicate with one another in order to maintain a homeostatic relationship within one’s self. This reciprocal communication pathway allows for self-regulatory actions as needed (Yao & Thakkar, 2022). These and other body disruptions for people with schizophrenia contribute to a significant decrease in mind-body connection, which interfere with wellness on multiple levels.\n\nIndividuals diagnosed with schizophrenia may experience difficulty with interpreting their own body signals as well as those of others (Oud & Jong, 2017). This also attributes to the disruption of body boundaries (Benson et al., 2019; Costantini et al., 2020); at times they do not understand where their bodies end and others begin. A diminished sense of boundaries can have both intra– (Ardizzi et al., 2016; Benson et al., 2019; Costantini et al., 2020; Torregrossa et al., 2022) and inter–personal (Torregrossa et al., 2022) difficulties. On an intrapersonal level, individuals may experience a disruption of their body in shape, size, location, ownership (Costantini et al., 2020), and pain levels (Kohn et al., 2022; Yao & Thakkar, 2022) — they may even have difficulty recognizing their own voice or face (Benson et al., 2019). Moreover, without a grounded sense of bodily self, people with schizophrenia often experience a diminished ego or sense of self (Benson et al., 2019; Biondo et al., 2021; Costantini et al., 2020; Torregrossa et al., 2022; Yao & Thakkar, 2022).\n\nFurther compounding a limited sense of self for people with schizophrenia is their often disrupted interoceptive awareness. Healthy interoceptive awareness is associated with brain functioning and can be affected by a diagnosis of schizophrenia. Interoception is the internal and physiological awareness of one’s bodily sensations (Ardizzi et al., 2016; Torregrossa et al., 2022; Yao & Thakkar, 2022), that supports an integrative processes of internal body cues (Yao & Thakkar, 2022). Thus, without interoceptive awareness, people with schizophrenia often experience increased positive symptomatology (Torregrossa et al., 2022). Inhibited interoception alters one’s ability to appropriately regulate the autonomic nervous system, which is essential to survival. It similarly affects the response rate of receiving external sensory signals—exteroception—and the ability to process cognition and emotion (Ardizzi et al., 2016; Yao & Thakkar, 2022). Ardizzi et al. (2016) noted that “interoceptive accuracy … also appears to be involved in the autonomic regulation during social interactions and individual resilience ability,” (p. 2) further compounding interpersonal relationships.\n\nIn order to fully understand and relieve symptomatology of the body for people with schizophrenia, it is argued we need to use the body as a tool for exploration and healing (Klaver & Dijkerman, 2016). Yao and Thakkar (2022) noted that “exploring how persons with schizophrenia experience their bodies and interpret their bodily signals is potentially key to understanding illness mechanisms” (p. 758).\n\nMind-body treatment interventions have proven effective for people with schizophrenia; however, one caveat to inclusion into these practices is stabilization of acute symptomatology of schizophrenia. Therefore, mind-body connection interventions for people with schizophrenia often focus on the diminishment of negative symptomatology (Behere et al., 2019; Sabe et al., 2019; Vogel et al., 2019). This is due, in part, to the internalization that accompanies some of the more meditative practices of mind-body connectivity, which may increase positive symptomatology. In their review, Behere et al. (2019) suggested that yoga may be effective in improving negative symptomatology, however, there was no mention of whether the interventions had an effect on mind-body connectivity. In their systematic review (K = 15; N = 1081), Sabe et al. (2019) noted that that mind-body therapies, such as tai chi, yoga, and qigong, support increased self-efficacy and agency, and decrease stress for people experiencing negative symptoms of schizophrenia.\n\nVogel et al. (2019) reviewed mind-body and aerobic exercises in their meta–analysis (K = 22; N = 1249), noting that typically psychopharmacological and some psychological interventions are ineffective at treating negative symptomatology of schizophrenia. They further posited that physical exercise can have beneficial effects on neural pathways as these neural pathways relate to the internal reward system. Moreover, physical exercise was shown to be effective at decreasing negative symptoms and feelings of depression, while increasing working memory, social cognition, attention, cardiorespiratory fitness, and improving Positive and Negative Symptom Scale (a medical scale used for measuring symptom severity of patients with schizophrenia) scores (Vogel et al., 2019). The authors concluded that activation is an important component of wellness for people with schizophrenia and that mind-body exercise shows promise as an intervention for this population.\n\nDance/movement therapy (DMT), rooted in nonverbal communication and dance as a healing factor, is an under-researched approach to increasing mind-body connectivity. Dance/movement therapy is defined by the American Dance Therapy Association (2016) as “the psychotherapeutic use of movement to promote emotional, social, cognitive, and physical integration of the individual for the purpose of improving health and well-being” (https://www.adta.org). Koch et al. (2019) conducted a meta-analysis which indicated that DMT has proven to be an effective psychosocial treatment option for a number of psychological and health related outcomes.\n\nThe effects of DMT on symptom management for people with schizophrenia has shown promising results for people with both acute (Biondo et al., 2021) and chronic (Bryl et al., 2020) presentations of the diagnosis. Recent research has shown DMT to be effective in reducing positive (Biondo et al., 2021) and negative symptoms of schizophrenia (Biondo et al., 2021; Bryl et al., 2020; Gökcen et al., 2020; Savill et al., 2017). Of particular interest for this review are the following additional results yielded from the research studies: increased social connectivity (Biondo et al., 2021; Bryl et al., 2020; Gökcen et al., 2020); mind-body awareness, and self-awareness (Biondo et al., 2021; Bryl et al., 2020).\n\nIn our previous work, we examined the effects of a single-session DMT intervention for people with schizophrenia who were currently in an inpatient psychiatric facility due to symptom exacerbation (Biondo et al., 2021). This mixed methods feasibility study (N = 28) showed promising results in the diminishment of psychological discomfort and positive and negative symptoms of schizophrenia, as measured by the Brief Psychiatric Rating Scale, for participants randomized to a DMT intervention versus those in a treatment as usual control group. The qualitative findings substantiated the quantitative findings and provided complementary data in which participants reported increased interpersonal skills and feeling a sense of belonging. This is particularly pertinent based on the aforementioned stigmatization people with schizophrenia are faced with, contributing to disrupted interpersonal relationships. Both Biondo et al. (2021) and Bryl et al. (2020) reported an increase in self-awareness inclusive of mind-body awareness in these studies.\n\nBryl et al. (2020) conducted a mixed methods randomized controlled trial (N = 31) providing 20 group DMT sessions over 10 weeks. Although the quantitative results of this study did not show significant findings, the qualitative data provided rich accounts of participant experiences in the DMT sessions. Participants articulated a greater awareness of self-integration including an increase in mind-body connectivity, and an increase in awareness of body boundaries (Bryl et al., 2020). A similar theme was noted in our 2021 research, as participants shared feelings of increased self-awareness, particularly as it related to a positive change in their symptomatology. Increased self-awareness often led to reports of an increase in self-confidence and self-efficacy (Biondo et al., 2021; Bryl et al., 2020).\n\nFollowing their respective study interventions, participants expressed an increase in motivation to engage in more activities (Bryl et al., 2020) and further treatment (Biondo et al., 2021). A desire to continue activation may have been inspired by increased insight around felt changes from the sessions (Biondo et al., 2021), and a connection participants made between physical and mental health (Bryl et al., 2020).\n\nTenets of the embodied aesthetics framework (Koch, 2017), affective and embodied neurobiology (Homann, 2010, 2020), and the embodied–enactive–interactive brain (Vaisvaser, 2021) underlie the foundations of DMT that may support wellness for people with schizophrenia. For many years of practice in the creative arts therapies—dance/movement, music, and art therapy—there have been notable gaps in theoretical frameworks that explained the active factors that contributed to wellness (Koch, 2017). In response to this, Koch (2017) focused her research on developing the embodied aesthetics framework in which “the body is seen as a living organism (organismic metaphor), a unity with multiple interfaces to the environment and other persons, constituting emergent superordinate units beyond the person” (p. 86).\n\nThe embodied aesthetics framework situates and overlaps the following components: bodily consciousness; environmental interactions, and an active body as a center for knowledge. Rooted in this theory, Koch (2017) identified five groupings of identified active factors that contribute to wellness: (1) hedonism; (2) aesthetics; (3) (nonverbal) meaning making; (4) enactive transitional support; and (5) generativity. Within each of these active factors, further detail is provided to encapsulate the contributors to wellness more fully.\n\nImprovisation and playfulness are highlighted as significant components of hedonism, lending to creativity, strength, self-efficacy, and interpersonal connectivity. The role of aesthetics is not only to produce beauty, but also to feel confident that one creates beauty. Authenticity of movement provides self-efficacy for the mover, while allowing someone to truly be seen and fostering mind-body connection. Such nonverbal communication is a premise of DMT. In Koch’s (2017) framework, this can be sectioned into cognitive, affective, and transpersonal symbolizing. In the former, participants of DMT are able to cognitively organize and integrate symbols that emerged from the dance. In affective symbolizing, the dance becomes a vehicle for processing and expressing emotions. In the latter, the dance becomes a spiritual bridge connecting the mover to the understanding of universal cohesion and a place for ritual to form. Through these processes, the movement creates and maintains containment for the participant(s) providing safety in expression and a trajectory towards wellness. With this enactive transitional support, movers can develop agency, re-establish self-safety, and encourage activation. The final category of generativity serves the mover in being a creator, which fosters self-efficacy, agency, continued activation, and resilience (Koch, 2017). Together, the components of the embodied aesthetics provide support for increased mind-body connection and physical and mental wellness.\n\nThe experiential nature of DMT lends towards an embodied neurological approach that connects the mind and body through movement experiences and nonverbal psychological processing. The collaborative creation of in-the-moment intervention choices made between participant and therapist allow agency and therapeutic rapport to be at the forefront of DMT sessions. Homann (2020) theorized five components to the embodied neurological approach to DMT: (1) polyvagal and biochemical regulation; (2) interoception; (3) empathy and attunement; (4) memory and affective systems and (5) brain lateralization. Priority is placed on the mind-body connection as a contributing factor to accessing one’s emotional intelligence and defining a healthy sense of self. Furthermore, Homann (2020) found:\n\nDMT’s unique emphasis on experiential engagement of the body has significant therapeutic implications, engaging the mind from the inside out. Movement engages deep systems of biochemical regulation, facilitates arousal and rest, and stimulates the core of self–perception at the neurological intersections of emotional, sensory, and cognitive processes. (p. 298)\n\nDance/movement therapy informed by Polyvagal theory promotes the simultaneity of activation and rest and is often fostered by safe social engagement. Such safety is developed through attunement and can be experienced through touch and gaze (Homann, 2010). Gray (2017) referred to the “safety–trust–relationship continuum” in her framework for Polyvagal–informed DMT as a foundational component to shifting physiological, and thus psychological states in the therapeutic process (p. 44). Early ruptures in attachment can manifest though affective, cognitive, and physical reactions. With this in mind, it is imperative that the repair processes access each of those manifestations, which is possible through DMT (Gray, 2017; Homann, 2020). Through the DMT process, participants develop an increase in body awareness while cultivating feelings of relaxation, self-regulation, and agency. Moreover, as individuals receiving treatment create a space of relative safety, they are provided with greater access to a healthy relationship with their body. The therapeutic process of dance and movement within a DMT session can improve interoception, thus providing functional access to body and neurological activation, resulting in greater understanding of physical and emotional needs (Homann, 2020).\n\nThis process of developing greater awareness of self can then transfer to fostering healthier and more productive interpersonal relationships. Attachment is developed through empathic connections, and nonverbal communication is a pathway through which mirror neurons are activated (Homann, 2010). Kinesthetic attunement or embodied empathy is experienced when a dance/movement therapist and client engage in mirroring one another’s movements, a common technique of DMT. Imparting a sense of being seen in this way for people with schizophrenia validates their authentic selves and instills a sense of pride and feelings of belonging (Biondo et al., 2021).\n\nA relationship substantiated by attunement, empathy, and authenticity allows for depth of processing through nonverbal experiences including intersubjectivity and integration of implicit and explicit memory. The nonverbal attunement and neuronal matching experienced collectively by dance/movement therapists and clients creates safety and the capacity for sharing unconscious material through intersubjective processes (Homann, 2010). This intersubjective experience “activates the mirror neuron system, and, through consequential neuronal, hormonal, and chemical cascades connecting the limbic system, the autonomous nervous system and the right hemisphere’s orbitofrontal cortex, facilitates the experience of being with another, in a conscious manner” (Homann, 2010, p. 90). This integrative process happens on emotional, sensorial, and cognitive levels.\n\nIntegration expands to that of memory as implicit memory can be stored in the body and elicited through the embodied processes of DMT and become explicit. This process not only allows recollection of memory, but it also provides an environment for emotional processing and re–narration to create a place of safety for deeper exploration and healing (Homann, 2020). Furthermore, integration goes beyond that of implicit and explicit memory and extends to lateralization of the brain. Movements, particularly those which crosses the midline and engage the whole body, support an integration of brain hemispheres providing lateralization, whole brain connectivity, and thus integration of self (Homann, 2020).\n\nThe embodied–enactive–interactive brain framework is an integrative approach of the creative arts therapies with fundamentals of neuroscience that takes similar approaches to the two aforementioned frameworks. Vaisvaser (2021) theorized that the mind, body, and environment intersect which creates a space for integration and thus wellness. Furthermore, exploration of brain functions as they relate to therapeutic factors are presented in five sections: (1) embodiment through a neuroscientific lens; (2) “predictive nature of the mind and the formation and reformation of internal models”; (3) “predictive processing mechanisms in the context of psychic apparatus”; (4) “developmental and therapeutic implications of the brain’s predictive mechanisms”; and (5) “the relational account of neural functioning and the underpinnings of empathy” (Vaisvaser, 2021, p. 2). Underlying the embodied–enactive–interactive brain is the premise that mind, body, and interpersonal relationships are the root of healing processes for which the creative arts therapies are a vehicle.\n\nThe concept of an embodied brain suggests that the body—and particularly interoceptive and proprioceptive awareness—plays an active role in cognitive processes. Sensory experiences of the body are not only a receptive vessel for informational absorption, but also activators for neural indicators of sensory, motor, emotional, and linguistic information (Vaisvaser, 2021). The environmental component of this framework aligns with social engagement in Polyvagal theory, placing value on the relational component of cognitive and emotional processes. With that, the intersectionality of our mind–body–relational being provides a platform for perception of self and other through creative processing. The predictive brain has a complex and multisensory relationship with the body and environment. Brain prediction, or the “embodied brain,” in which the brain reflects on past experiences in order to determine probable outcomes, incorporates interoceptive knowledge to predict movement, intention, and emotion, and to further agency, self–efficacy, and self–awareness (Vaisvaser, 2021).\n\nVaisvaser (2021) theorized that an embodied or predictive brain encourages and supports advancement or progress within the therapeutic realm. Therefore, individuals engaged in the creative arts therapies connect with interoceptive and exteroceptive sensory information, which, through processing, increases emotional awareness and expression. Per Vaisvaser (2021) this then contributes to activation, disrupting the potential for returning to a homeostatic place of stagnancy. The creative arts therapies provide a structure for positive disruption of that which is familiar and lead to the creation of new opportunities. Dance/movement therapy can thus be an opportunity for emotional expressivity, externalization, and therapeutic meaning–making (Biondo et al., 2021; Vaisvaser, 2021). Furthermore, re–narration of past traumatic events can provide an opportunity for integration and insight. This forward movement is further cultivated by a safe environment and therapeutic rapport (Vaisvaser, 2021).\n\nVaisvaser’s (2021) review suggests that these introspective and intrapsychic experiences are deepened through relational encounters both overt and intersubjective. Neurologically, our brains are wired to seek out social engagement. Verbal and nonverbal interactions are instrumental in healthy and adaptive brain functioning though activation of mirror neurons and neuronal synchronization (Vaisvaser, 2021). These processes aide in an increase in intra– and interpersonal emotional awareness, as well as the release of oxytocin, supportive of adaptive attunement. Empathy, kinesthetic and otherwise, creates pathways for intersubjective processes and mentalization. “Importantly, mentalization during empathic engagement refers to the attribution of emotions, wishes, desires, and needs … suggesting that distinct neural networks are involved in self–knowing and knowing others…” (Vaisvaser, 2021, p. 6–7). Moreover, shared moments of synchrony through kinesthetic empathy establish foundational tools for rapport building, co–regulation, healthy attachment, and resilience, particularly when rooted in arts and artistic experiences. Vaisvaser (2021) suggested the field of neuroimaging to better understand the distinct processes of neural activity.\n\nBiofeedback is an underutilized therapeutic tool that affirms mind-body connectivity while giving recipients and clinicians in–the–moment health related information. This further substantiates the notion that physical health can directly affect mental and emotional aspects and vice versa (Austad & Gendron, 2018). Although there is some consideration for the mind-body connection and how it affects wellness, many forms of traditional psychotherapy do not enter into the therapeutic process with the body at the forefront (Austad & Gendron, 2018; Fiskum, 2019).\n\nAs self–regulation is deeply rooted in the body and neurophysiology, biofeedback may be a functional approach to physiological regulation. This can elevate awareness of the mind-body connection while providing adaptive tools for self–regulation. Provision of such regulation tools can further self–awareness and improve physical and mental health (Austad & Gendron, 2018). Measurements of high Heart Rate Variability (HRV), and signals of lower cardiac complexity, can provide data suggestive of an increased capacity for emotion regulation and overall psychological wellbeing (Fiskum, 2019). HRV biofeedback may have a positive effect on “synchronized blood-flow oscillations … further strengthening the functional connectivity between brain areas” (Fiskum, 2019, p. 418).\n\nKing and Parada (2020) suggested using mobile brain/body imaging (MoBI) as a more pragmatic way of measuring neuroscientific activation resulting from an intervention within the creative arts therapies (CATs). Mobile brain/body imaging could be a process through which we gain a greater understanding of the relationship between neuroaesthetics and the CATs, the framework of which adopts the “4E” approach to cognition: embodied, extended, embedded, and enactive (King & Parada, 2020). Although the authors speak primarily in regard to art therapy, they proposed that research using MoBI with other CATs, such as dance/movement therapy could be beneficial in further understanding the underpinnings of mind-body connection as it relates to active art (or dance) making. The use of MoBI supports examination of the mind, body, behavior connection in a more natural setting of artistic practice; furthermore, the therapeutic processes and active factors of therapy have proven to be difficult to capture and can be explored with MoBI. “Importantly, the brain autonomously and continuously senses the body (i.e. interoception). MoBI, allowing the acquisition of brain/body physiological signals during a natural therapeutic encounter, opens the door for studying interoception in the wild” (King & Parada, 2020, p. 8367). Furthermore, such research could bring greater awareness to the cognitive processes that inform artistic or aesthetic experiences as they relate to one’s sense of self, agency, and efficacy.\n\n\nConclusions\n\nIndividuals with schizophrenia face disproportionately high barriers to health and wellness. Discrepancies in health care for this population begin with diagnostics (Metzl & Roberts, 2014; Oud & Jong, 2017) and extend through the duration of the illness, affecting symptomatology, intra- and interpersonal skills, quality of life, self–efficacy, and overall prognosis (Kohn et al., 2022; Rössler, 2016; Vancampfort et al., 2017). People of color, particularly Black men, have historically been most affected by diagnostic inequities and biases (Metzl & Roberts, 2014). Furthermore, people with schizophrenia face high rates of stigmatization, not only by the general population, but also by the health care providers by whom they are seeking services (Ivanova, 2021; Rössler, 2016). These stigmatizing behaviors, coupled with communication differences that people with schizophrenia may experience, deter people with schizophrenia from seeking and receiving quality health care (Kohn et al., 2022). Moreover, their propensity towards a dissociative relationship with their bodies and additional bodily dysregulations places this population at a proportionately higher risk for medical illness (Moore et al., 2015; Oud & Jong, 2017; Tan et al., 2021) resulting in a significantly shorter life span than the general population (Kohn et al., 2022; Swildens et al., 2016; Tan et al., 2021).\n\nThe cyclical nature of physical and mental symptomatology triggering one another indicates that improved mind-body awareness could be a supportive option for people with schizophrenia (Costantini et al., 2020). Recent research has shown that this population is particularly vulnerable to experience diminished understanding of their mind-body connection (Kohn et al., 2022; Yao & Thakkar, 2022) and a decrease in interoceptive knowledge (Ardizzi et al., 2016; Torregrossa et al., 2022; Yao & Thakkar, 2022). This limits the ability to process internal and bodily signals and information that could provide insight around physical health needs. Much of the body–mind connection research focuses on externalization and could benefit from an inside-out perspective initiating interventions from the body and making cognitive connections after participants have a bodily, felt experience. This process would support both physical and mental aspects of care benefitting both general and mental health care, both of which are needed for people with schizophrenia.\n\nDance/movement therapy is a treatment option that addresses physical, mental, and social aspects of participant wellness (Bryl & Biondo, 2022). More recently, DMT frameworks have been explored and expanded to be inclusive of embodied, neurophysiological theories. Of note is the inclusion of neurophysiological theories which incorporate concepts of attunement and self–regulation both of which play a significant role in DMT (Homann, 2010, 2020). Due to the direct relationship between the vagus nerve and interoception (Homann, 2020), DMT would be an apparent intervention choice. As an active and embodied intervention, the research discussed demonstrates that DMT has the capacity to address multi–layered needs of people with schizophrenia including raising interoceptive awareness. As research has shown, DMT for people with schizophrenia can help participants become activated through movement (Bryl et al., 2020), improve interpersonal relationships, process and express emotions, improve self–efficacy, and increase mind-body connection (Biondo et al., 2021; Bryl et al., 2020). Dance/movement therapy is an active intervention in which people experiencing all levels of acuity can participate (Biondo et al., 2021). Moreover, the nonverbal relationships possible through DMT can allow for increased joining with those who may have communication differences. These components of invitation for people with schizophrenia truly meet each participant where they are in their wellness process and destigmatize the diagnosis, allowing an authentic development of healthy ego, self-efficacy, and relationship (Biondo et al., 2021; Bryl & Biondo, 2022).\n\nSimilarly to DMT, biofeedback is an option for further mind-body integration that provides participants with an active role in their wellness (Austad & Gendron, 2018). Both treatment interventions provide participants with immediate data regarding the effects the body can have on the mind and vice versa. Additionally, both provide in-the-moment information to provide active skills participants can integrate into their daily lives. Collaborative healthcare teams could provide a more holistic approach to treatment for people with schizophrenia, as this could partner complementary areas of expertise, bridge inter–healthcare provider relationships as well as communication between providers and clients, and expand the healthcare continuum for people who have historically been resistant to seeking treatment and stigmatized when they do. Furthermore, applications such as MoBI can expand our current knowledge regarding if and how interoception can positively impact people with schizophrenia and inform future treatment implications (King & Parada, 2020).\n\nThis review seeks to highlight the disparities people with schizophrenia face regarding lack of accessible (Swildens et al., 2016) and quality health care (Moore et al., 2015; Sølvhøj et al., 2021), multifaceted forms of stigmatization they encounter (Ivanova, 2021; Kohn et al., 2022; Sølvhøj et al., 2021), and specific barriers they face regarding the bodily disruptions and dysregulations associated with their symptomatology (Biondo et al., 2021; Costantini et al., 2020; Torregrossa et al., 2022). Dance/movement therapy is an intervention that can provide individuals diagnosed with schizophrenia an opportunity to participate in an embodied psychosocial treatment intervention that addresses these precise body-based needs, while simultaneously providing physical activation, emotional processing, mind-body connection, interpersonal relationships, and self–regulation. These are components that not only support increased personal and interpersonal wellness, but also provide self–efficacy to encourage physical and mental health care adherence, and embodied treatment experiences placing mind-body wellness at the forefront of care (Biondo et al., 2021). The addition of biofeedback to DMT could provide further physiological (Austad & Gendron, 2018; Fiskum, 2019) and neurological data (King & Parada, 2020). A treatment protocol inclusive of DMT can provide a foundation for the rehumanization process that people with schizophrenia certainly deserve.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAmerican Psychiatric Association: Diagnostic and statistical manual of mental disorders: DSM–5. American Psychiatric Association;2013.\n\nArdizzi M, Ambrosecchia M, Buratta L, et al.: Interoception and positive symptoms in schizophrenia. Front. Hum. Neurosci. 2016; 10: 379. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAustad CS, Gendron MS: Biofeedback: Using the power of mind–body connection, technology, and business in psychotherapies of the future. Prof. Psychol. Res. Pract. 2018; 49(4): 264–273. Publisher Full Text\n\nBehere RV, Thirthalli J, Varambally SS, et al.: Mind–body practices in schizophrenia—Opportunities and challenges. Schizophr. Res. 2019; 212: 4–5. PubMed Abstract \| Publisher Full Text\n\nBenson TL, Brugger P, Park S: Body self–disturbance in schizophrenia–spectrum populations: Introducing the Benson et al. Body Disturbances Inventory (B–BODI). PsyCh J. 2019; 8: 110–121. PubMed Abstract \| Publisher Full Text\n\nBiondo J, Gerber N, Bradt J, et al.: Single–session dance/movement therapy for thought and behavioral dysfunction associated with schizophrenia: A mixed methods feasibility study. J. Nerv. Ment. Dis. 2021; 209(2): 114–122. PubMed Abstract \| Publisher Full Text\n\nBryl K, Biondo J: Dance/movement therapy and schizophrenia spectrum disorders: A reflection of clinical practices and history. OBM Integr. Compliment. Med. 2022; 6(4). Publisher Full Text\n\nBryl K, Bradt J, Cechnicki A, et al.: The role of dance/movement therapy in the treatment of negative symptoms in schizophrenia: A mixed methods pilot study. J. Ment. Health. 2020; 13(1): 1–11. Publisher Full Text\n\nCostantini M, Salone A, Martinotti G, et al.: Body representations and basic symptoms in schizophrenia. Schizophr. Res. 2020; 222: 267–273. PubMed Abstract \| Publisher Full Text\n\nDavis M: 2018 Guide to the Movement Psychodiagnostic Inventory (MPI).2019. Reference Source\n\nFiskum C: Psychotherapy beyond all the words: Dyadic expansion, vagal regulation, and biofeedback in psychotherapy. J. Psychother. Integr. 2019; 29(4): 412–425. Publisher Full Text\n\nGökcen A, Ekici G, Abaoglu H, et al.: The healing effect of goal–oriented dance and movement therapy in schizophrenia: A rater–blinded randomized controlled trial. Arts Psychother. 2020; 71: 101702. Publisher Full Text\n\nGray AEL: Polyvagal–informed dance/movement therapy for trauma: A global perspective. Am. J. Dance Ther. 2017; 39: 43–46. Publisher Full Text\n\nHomann KB: Embodied concepts of neurobiology in dance/movement therapy practice. Am. J. Dance Ther. 2010; 32: 80–99. Publisher Full Text\n\nHomann KB: Dynamic equilibrium: Engaging and supporting neurophysiological intelligence through dance/movement therapy. Am. J. Dance Ther. 2020; 42: 296–310. Publisher Full Text\n\nIvanova M: The stigmatization of schizophrenia. The University of Ottawa Journal of Medicine. 2021; 11(2): 47–51. Publisher Full Text\n\nKing JL, Parada FJ: Using mobile brain/body imaging to advance research in arts, health, and related therapeutics. Eur. J. Neurosci. 2020; 54: 8364–8380. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKlaver M, Dijkerman HC: Bodily experience in schizophrenia: Factors underlying a disturbed sense of body ownership. Front. Hum. Neurosci. 2016; 10: 305. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKoch SC: Arts and health: Active factory and a theory framework of embodied aesthetics. Arts Psychother. 2017; 54: 85–91. Publisher Full Text\n\nKoch S, Riege R, Tisborn K, et al.: Effects of dance movement therapy and dance on health–related psychological outcomes. A meta–analysis update. Front. Psychol. 2019; 10(1806): 1–28. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKohn L, Christiaens W, Detraus J, et al.: Barriers to somatic health care for persons with severe mental illness in Belgium: A qualitative study of patients’ and healthcare professionals’ perspectives. Front. Psych. 2022; 12: 798530. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLaursen TM: Causes of premature mortality in schizophrenia: A review of literature published in 2018. Curr. Opin. Psychiatry. 2019; 32(5): 388–393. Publisher Full Text\n\nLincoln SH, Johnson T, Winters A, et al.: Social exclusion and rejection across the psychosis spectrum: A systematic review of empirical research. Schizophr. Res. 2021; 228: 43–50. PubMed Abstract \| Publisher Full Text\n\nMetzl JM, Roberts DE: Structural competency meets structural racism: Race, politics, and the structure of medical knowledge. Virtual Mentor. 2014; 16(9): 674–690. PubMed Abstract \| Publisher Full Text\n\nMoore S, Shiers D, Daly B, et al.: Promoting physical health for people with schizophrenia by reducing disparities in medical and dental care. Acta Psychiatr. Scand. 2015; 132: 109–121. PubMed Abstract \| Publisher Full Text\n\nOud MJT, Jong BM: Somatic diseases in patients with schizophrenia in general practice: Their prevalence and health care. BMC Family. 2017; 10(32). Publisher Full Text\n\nRössler W: The stigma of mental disorders: A millennia–long history of social exclusion and prejudices. EMBO Rep. 2016; 17(9): 1250–1253. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSabe M, Sentissi O, Kaiser S: Meditation–based mind–body therapies for negative symptoms of schizophrenia: Systematic review of randomized controlled trials and meta–analysis. Schizophr. Res. 2019; 212: 15–25. PubMed Abstract \| Publisher Full Text\n\nSavill M, Orfanos S, Bentall R, et al.: The impact of gender on treatment effectiveness of body psychotherapy for negative symptoms of schizophrenia: A secondary analysis of the NESS trial data. Psychiatry Res. 2017; 247: 73–78. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSølvhøj ID, Kusier AO, Pederson PV, et al.: Somatic health care professionals’ stigmatization of patients with mental disorder: A scoping review. BMC Psychiatry. 2021; 21(443): 443. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSwildens W, Termorshuizen F, de Ridder A , et al.: Somatic care with a psychotic disorder. Lower somatic health care utilization of patient with a psychotic disorder compared to other patient groups and to controls without a psychiatric diagnosis. Admin. Pol. Ment. Health. 2016; 43: 650–662. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTan XW, Lee ES, Toh MPH, et al.: Comparison of mental–physical comorbidity, risk of death and mortality among patients with mental disorders—A retrospective cohort study. J. Psychiatr. Res. 2021; 142: 48–53. PubMed Abstract \| Publisher Full Text\n\nTorregrossa LJ, Snodgress MA, Hong SJ, et al.: Anomalous bodily maps of emotions in schizophrenia. Schizophr. Bull. 2022; 45(5): 1060–1067. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVaisvaser S: The embodied–enactive–interactive brain: Bridging neuroscience and creative arts therapies. Front. Psychol. 2021; 12: 634079. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVancampfort D, Firth J, Schuch FB, et al.: Sedentary behavior and physical activity levels in people with schizophrenia, bipolar disorder and major depressive disorder: A global systematic review and meta–analysis. World Psychiatry. 2017; 16: 308–315. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVogel JS, van der Gaag M , Slofstra C, et al.: The effect of mind–body and aerobic exercise on negative symptoms in schizophrenia: A meta–analysis. Psychiatry Res. 2019; 279: 295–305. PubMed Abstract \| Publisher Full Text\n\nYao B, Thakkar K: Interoception abnormalities in schizophrenia: A review of preliminary evidence and an integration with Bayesian accounts of psychosis. Neurosci. Biobehav. Rev. 2022; 132: 757–773. PubMed Abstract \| Publisher Full Text" }	[ { "id": "160297", "date": "31 Jan 2023", "name": "Robyn Cruz", "expertise": [ "Reviewer Expertise Dance/movement therapy", "movement disorders", "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\nThe scope of this paper is impressive and the arguments for providing care for individuals with schizophrenia that is aligned with care for the whole person continues to be a worthy topic for research and practice. The decades-long focus of pharmacotherapy as the primary treatment for schizophrenia continues to show progress, but the need for other treatment modalities such as dance/movement therapy (DMT) to address social and psychological components of the illness such as trauma are still required. This review will combine comments with a focus on strengthening the content to help achieve the worthy goals of the paper.\nIntroduction – I am not completely clear about the meaning of the sentence “Through a strengths- and body-based approach, dance/movement therapy (DMT) surpasses traditional verbal communication, establishing inclusion for many forms of preferred communication styles (Biondo et al., 2021).” especially for readers who may not have an understanding of DMT. I think here in the introduction – an introduction to the field of DMT is warranted. The section that is on page 5 (of the pdf version of the article) could be moved to the introduction and I believe it would be very useful in tying together other sections of the paper for the reader new to DMT. The sections on body symptomatology, interoception, and mind-body treatments could be helped by setting the context early on with what DMT is and the fact that it has been used for decades with seriously mentally ill patients as well as others.\nDiscussion – I feel that there needs to be more research cited, and more diversity of sources for the important discussion of mental health disparities. Currently there is sole dependence on Metzl & Roberts (2014). In addition the mention of the changes in rates of diagnosis over time fails to mention the important fact that diagnostic criteria have changed quite drastically over time as well. To cite myself (Cruz, 1995, p. 38), “Yet a narrowing of diagnostic criteria for schizophrenia has taken place during the last 50 years, changing the determination of who is diagnosed schizophrenic. The DSM-III (1980) represented the sharpest break with previous editions in the definition and diagnostic criteria for schizophrenia (Andreasen & Flaum, 1991). Many forms of the disorder were removed and included in other categories, most notably psychosis not elsewhere classified, affective disorders, and related personality disorders. In spite of this narrowing, research on movement disorders has not regularly included the removed disorders.”\nIn 1952 DMS I was published and the criteria for schizophrenia as noted above included other disorders that later were winnowed out. DSM II was published in 1968 and DSM III in 1980 – in spite of these changes, it would be good to note if disparities in diagnosis by race continued across the changing symptom criteria.\nAlso the discussion on stigmatization – other sources should be cited as there is dependence on Rossler (2016). It could be helpful also to make a connection between the discussion on stigmatization and stigmatizing behaviors – it is possible combining the paragraph that begins “Stigmatization also affects people with schizophrenia on personal and social levels.” with the section located under the heading “physical health disparities” could be helpful for the reader.\nThink about the sections in “Mental Health Disparities” and “Physical Health Disparities” as setting up the reader for better understanding of why DMT has the potential to promote wellness for this group. I think it is necessary to distinguish better between “Body symptomatology” and “Bodily disturbances…” as what is described under body symptomatology are abnormal involuntary movements which can be naturally occurring or side effects of pharmacology but are related to dysfunction of neurotransmitters of the extrapyramidal system (Cruz, 1995; 2009). I also think that the text in the “Bodily disturbances section could more meaningfully be combined with the “Interoception” section of the paper – they cross-over in ways that might be confusing to the reader not familiar with these terms.\nI am curious what the real purpose of the “Mind-body treatments” section is and if the author thinks of DMT as a mind-body treatment? If so this needs to be clarified for the reader so that the DMT research section (which is brief and does not include any meta-analyses that have been conducted) is clear and then clearly separated from the theoretical sections that follow. These theoretical areas “embodied aesthetics framework and embodied neurology need better framing as theoretical frameworks. How those frameworks might directly impact work with schizophrenic patients needs more obvious connection for the reader.\nI am also curious about the inclusion of biofeedback which is a bonafide technique and neurofeedback with seems to be theoretical – what could be learned or achieved with it? They don’t seem to “fit” very well with this paper.\nConclusion – may serve as a good guide for the reorganizing that I’ve suggested in this review. It is comprehensive of the major points in a very clear manner that serves the paper well.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] }, { "id": "169980", "date": "28 Apr 2023", "name": "Hod Orkibi", "expertise": [ "Reviewer Expertise Psychodrama and drama therapy", "arts therapies", "community mental health", "process and outcome research", "systematic reviews." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, the article focuses on a timely issue of offering DMT to clients with schizophrenia, which is generally an under-investigated field.\n\nIn the Discussion, address clearly the unique contribution of DMT to this population, and how modality-specific change factors are reasoned to lead to outcome. In other words, based on the literature reviewed, it will be meaningful if you specify your own theory of change with respect to DMT for this population.\n\nAlso, the polyvagal theory has been criticized in the literature, and this has to be mentioned.\n\nThe abbreviation CATs should appear in the first time the term \"creative arts therapies\" - it appears under: \"Contributing factors\". This should be followed by CATs.\n\nThe Conclusion section can be more concise in highlighting the take home message of this review to strengthen the impact of the paper.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-33
https://f1000research.com/articles/12-61/v1	16 Jan 23	{ "type": "Systematic Review", "title": "Polymorphism studies and candidate genes associated with litter size traits in Indonesian goats. a systematic review", "authors": [ "Mutasem Abuzahra", "Loay Abu Eid", "Mustofa Helmi Effendi", "Imam Mustofa", "Mirni Lamid", "Saifur Rehman", "Mutasem Abuzahra", "Loay Abu Eid", "Imam Mustofa", "Mirni Lamid", "Saifur Rehman" ], "abstract": "Background: Litter size (LS) is a significant, challenging, and economical aspect of the goat industry in Indonesia. It is influenced by several different factors and genes; consequently, identifying potential genes and loci associated with litter size has become a genetic problem. Several genetic indicators have been found to be associated with litter size in goats. This has prompted the need to discuss candidate genes associated with litter size in goats in Indonesia. Methods: A systematic review was conducted using critical databases including ResearchGate, Google Scholar, PubMed, Google search engine and Science direct. There were any exclusion criteria, they were as follows: articles published in languages other than English, Conference papers, short communication papers and papers not related to animals. After reviewing the abstracts of 42 publications, the remaining 17 investigations were chosen for full paper evaluation. A further eight studies were removed after a comprehensive evaluation of the publications because they did not match our inclusion criteria. Results: These markers include growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15), bone morphogenetic protein receptor type IB (BMPR1B), and kisspeptin (KISS1). Single nucleotide polymorphisms in these genes contribute to the development of novel genetic markers that helps in the selection of goats with the most favorable genotypes for litter size. This type of genetic selection is more successful than the traditional way of selecting animals for reproductive traits, particularly litter size. Conclusions: As a result, this study summarizes the genetic impacts of polymorphisms in candidate genes associated with litter size features in Indonesian goats.", "keywords": [ "BMP15", "BMPR1B", "GDF9", "Goat", "KISS1", "Litter size" ], "content": "Introduction\n\nThe prolific trait in goats refers to the ability to have multiple kids at the same time. Genetic variations that increase the rate of ovulation and the number of offspring per birth affect the prolific trait of each goat differently.1 Indonesia has a goat population of nearly 19 million, producing 72.553 tons of meat per year from 7,144,010 heads (FAOSTAT, 2019). According to the Indonesian Ministry of Agriculture (2020), goat meat accounts for 1.8% of total national meat production. The import of goat meat products reached 1.49%, with a total of 387,663 heads imported. This condition demonstrated that increasing the goat population is critical to meeting national needs.2 The genetics of prolificacy emphasizes the importance of three major fecundity genes in sheep, bone morphogenetic protein 15 (BMP15), Bone morphogenetic protein receptor type IB (BMPR1B) and growth differentiation factor 9 (GDF9). All three genes are members of the TGF superfamily.3 First identified as a fecundity gene in sheep was the booroola gene (BMPR1B). There was no change in the expression level of this gene, but the ovulation rate increased due to the cumulative impact of this substitution mutation.4 The FecB locus is autosomal with codominant expression and is characterized by “precocious” ovarian follicle differentiation, resulting in the production of a large number of ovulatory follicles that are smaller in diameter than wild-type follicles. In sheep, mouse, and rat granulosa cells, BMPR1B has been identified as one of the type 1 receptors downstream of BMP15.5\n\nBone morphogenetic protein 15 (BMP15), also known as FecX (fecundity chromosome X), is a gene that regulates the prolific properties of different sheep types1 paracrine factor that promotes follicle growth, granulosa cell proliferation, and cell-survival signaling, and an X-linked gene (FecX locus) of sheep belonging to the TGF family,6 BMP15 plays a role in the booroola phenotype and is additionally usually known as the GDF-9B genetic code for protein synthesis in oocytes, which further improves follicle formation and fecundity in sheep and goats. It is unknown what role BMP15 genes play in granulose cell management.7 The GDF9 gene encodes a transforming growth factor that oocytes secrete during folliculogenesis. GDF9 regulates female sexual reproduction, gonad development, gamete generation, and the ovulation cycle by modulating the signaling pathways of the transforming growth factor-β receptor and transmembrane receptor protein serine/threonine kinase.8 So far, research on the kisspeptin (KISS1) gene as a candidate gene for reproductive characteristics in animals has demonstrated that this gene plays a vital function in animal reproduction.9 Kisspeptins directly promoted the release of gonadotropin-releasing hormone (GnRH) via KiSS1R, which in turn stimulates the production of leutenizing hormone (LH) and follicle stimulating hormone (FSH). Additionally, research has shown that kisspeptin plays a part in the formation of the placenta.10 Because KISS1 is important as a regulator of puberty initiation, variations in this gene are anticipated to be associated with reproductive features in goats such as high prolificacy, sexual precocity, and year-round estrus phenotypes. Kisspeptins may have a role in photoperiodic reproductive regulation in hamsters.9 SNPs in the goat KISS1 gene were consequently found to be significantly associated with litter size.11\n\nThe current review discusses the outcomes provided in numerous research and offers data by pooling these studies' research findings. To the best of knowledge, no review studies have been carried out on the relationship of candidate genes with litter size in Indonesian goats. The purpose of this review paper was to investigate the influence of genetic variants on litter size in Indonesian goats, specifically focusing on the four genes that have received the most attention in the scientific community: BMPR1B, BMP15, GDF9, and KISS1. The review paper was constructed by combining the results of all research that had been previously published in scientific papers (Table 1).\n\n\nMethods\n\nA detailed and comprehensive search was conducted to find related research and data published between 2011 and September 2022 using critical databases including ResearchGate, Google Scholar, PubMed, Google search engine and Science direct. One reviewer (M.A) independently searched for relevant studies using the following search terms: “BMPR1B”, “BMP15”, “GDF9”, “KISS1” “goat”, “litter size”, “prolificacy”, “Indonesian goat litter size” “SNP” “polymorphism” and “fecundity”. Furthermore, the reference lists of the papers that were found were examined to identify qualified studies that might not have been found through the journal and database search processes.\n\nOnly papers reporting associations between candidate genes and litter size, sample sizes per genotype, Chi-squared means for each genotype, genotype and allele frequencies, and descriptions of statistical methods used to collect these results were included in this analysis. When there were any exclusion criteria, they were as follows: articles published in languages other than English, Conference papers, short communication papers and papers not related to animals.\n\nEventually, 5545 titles of publications and papers were analyzed, with 83 being chosen for additional review. Following the removal of duplicates, the abstracts of 59 articles were chosen for screening. After reviewing the abstracts of 42 publications, the remaining 17 investigations were chosen for full paper evaluation. A further eight studies were removed after a comprehensive evaluation of the publications because they did not match our inclusion criteria. The study incorporated the remaining nine publications to guarantee high-quality data (Figure 1).\n\n\nResult\n\nDNA polymorphism analysis can be used for a variety of purposes, including sex determination, individual paternity testing, species identification, disease detection, phylogenetic analysis, and marker-assisted selection. In comparison with conventional breeding practices, the understanding and use of DNA polymorphisms has led to the identification of unique genetic markers that may be used to precisely select animals for improved output.12 The selection of high-potential parents is critical for improving the next generation by using genetic markers associated with litter size.13 Nevertheless, due to the low selection accuracy, improving this feature is difficult. This is related to a combination of low-to-moderate heredity and the predominant effect of the environment. The utilization of molecular genetics to identify gene loci and chromosomal areas containing single nucleotide polymorphisms (SNPs) impacting commercially relevant livestock characteristics has increased at an unparalleled rate over the last decade. Marker-assisted selection technology enables the precise selection of favourable sequence variants that have been shown to improve performance, eliminating much of the guesswork associated with traditional phenotypic selection.14\n\nGoats are known to have a number of genes that influence reproductive traits and the characteristics of their offspring, including litter size. Among these are the BMP15, KISS1, and BMPR1B genes, as well as the GDF9 gene, and all four of these genes are potential candidates for genetic marker screening of goat litter size. Through the use of genetic marker screening, a number of different polymorphisms within these genes have been identified as being associated to the performance of the reproductive system and the litter size. As a consequence of this, these SNPs have the potential to serve as novel molecular markers for determining the litter size of goat (Table 1).12–22\n\nThe SNPs of GDF9 genes were identified, and litter size traits were analyzed in four Indonesian goats (Saanen, Bligon Kacang and Kejebong). The results of the PCR restriction fragment length polymorphism (RFLP) analysis revealed four new polymorphisms in all three GDF9 genes. PCR-RFLP analysis revealed the SNP V397I with accession number XM_013965446.2,15 and three SNPs in (g.3615T>C g.3760T>C g.3855A>C) with accession numbers EF446168, EU883989 and KY780296.20 In the 60 Saanen goats tested, SNP V397I revealed only one genotype GA, showing that this SNP is monomorphic. One of the two most well-known SNPs in the GDF9 gene is G1189A, also known as p.Val397Ile/V397I. This SNP is related with varying levels of prolificacy in goats all over the world.23 To this day, the V397I SNP has been the subject of a significant amount of research in a variety of goat breeds.24 Similar to the results presented in this study, a previous investigation found that the V397I SNP was nonpolymorphic in Black Bengal Indian goats, and that study genotyped the V397I SNP.15 In contrast to the results of this investigation, the V397I SNP was discovered to exhibit polymorphism in a number of different breeds. Because the frequency of the G1189A mutant allele was 0.06 in Jamunapari goats and 0.15 in crossbred goats, this indicates that the mutation is stable in the population.24\n\nOnly the SNP g.3855A>C was analyzed in the second investigation to determine genotype frequencies, which discovered only two genotypes AA and AC, with the genotype CC not detected in these three goats (Bligon, Kacang, and Kejebong). Because the SNPs found in goats in those studies exhibited low polymorphism, no further research was undertaken to investigate whether it relates to litter size in goats.\n\nThere has been an evaluation of polymorphism of the BMP15 gene in the litter size and there was the detection of SNPs associated with litter size traits of c.38A>G and c.49G>A,19 746A>G,1 g.735A>G16 and g.135G>C17 with accession numbers EU743938.1, JQ350891.1, JQ320890 and AF236078 respectively, out of Boer, Kacang, Boerka, Kosta, Samsoir an Etawah breed. These SNPs of the BMP15 gene were identified using DNA pool sequencing and PCR-RFLP methods. The findings of the BMP15 gene sequence with GenBank (access code EU74393.1) revealed that the genotype frequency of the BMP15 gene based on Boer goat, Kacang of samples was found by two SNP, c.38A>G and c.49G>A.\n\nThe outcome of the genotype frequency on SNP c.49G>A, the genotype frequency of the BMP15 gene based on samples of Boer, Kacang, and Boerka goats used in this study presented the following genotypes: GG, GA, and AA (Table 2).19 Boer goat genotypes found in BMP15 SNP c.49G>A genes were GG, GA, and AA, with genotype frequencies of 0.471, 0.235, and 0.294. Kacang goat genotypes reported in BMP15 SNP c.49G>A genes have been GG, GA, and AA, with genotype frequencies of 0.125, 0.438, and 0.438, respectively. Boer goat genotypes found in the BMP15 SNP c.49G>A gene were GG, GA, and AA, with genotype frequencies of 0.235, 0.235, and 0.529, respectively. Additionally, the heterozygosis (Ho) and heterozygosity (He) tests demonstrated that the observed Ho in Boer, Kacang, and Boerka goats was not significantly different from the expected He. The difference between the observed heterozygosis value and heterozygosis may be utilized to detect a genetic inequality in the observed Boer goat, Kacang, and Boerka populations, showing that selection activity has already happened, and that random marriage has not occurred. The detected heterozygosis value (Ho) of the BMP15 gene in Boer, Kacang and Boerka goats was 0.235, 0.438, and 0.235, respectively. On SNP c.49G>A, the greatest heterozygosis value in Kacang goats is 0.438. The population balance is presented in Table 2 by the Hardy–Weinberg equilibrium (HWE). The results demonstrate that the BMP15 gene on SNP c.49G>A is in a balanced state.\n\na The different letter in the same column means differ significantly (P<0.05), D=disequilibrium in HWE if χ2 value more than 3.841.\n\nThe analysis of the diversity of the BMP15 SNP 746A>G gene1 produced + and G alleles which had ++ and G+ genotypes, table 2 shows that the GG genotype was not found in local goats. Table 2 also shows that the frequency of the + allele in the BMP15 gene is higher compared with the G allele. The + allele frequency is 0.965 and the G allele frequency is 0.035, indicating that the + allele frequency is greater than the G allele frequency in the BMP15 gene. This indicates that the candidate gene BMP15, which was discovered in various types of sheep, was also discovered in local goats, with a value of more than 1%. Thus, the gene BMP15 in local goats is polymorphic because the allele frequency value is greater than 1%. The Chi-squared (χ2) test analysis against the BMP15 gene revealed that the genotype and allele frequencies are homogeneous. These findings show that the local goat population is still healthy and balanced HWE, and that the goat population has never been selected. The observed heterozygosity value (He) in Table 2 is 0.070 greater than the expected heterozygosity value (He) of 0.068. This finding indicates that the observed and expected heterozygosity values in local goats do not differ significantly in the BMP15 gene fragment.\n\nThe result of SNP 735A>G16 (Table 2) reveals allele and genotype frequencies. Gembrong goats come in all three genotypes. The GG genotype, on the other hand, was missing in Kosta, Samosir, and Kacang goats. This result showed that allele A is higher than allele G in all goats. The Kosta goat had only homozygous AA, the Samosir goat had two genotypes AA (0.88) and AG (0.12), and three genotypes were found in Gembrong as the following AA (0.40), GG (0.20), and AG (0.40). Meanwhile, in the Kacang goat two genotypes were detected in the study24 AA and AG were 0.58 for A allele and G allele was 0.42, in contrary Das et al.25 reported that allele G had higher frequency than allele A as the following 0.762 and 0.238 respectively. PCR-RFLP analysis in SNP (g. 135G>C)17 showed only the GG genotype. The DNA observed was monomorphic for the BMP15 gene (exon 1) with GG genotype (Table 2).\n\nThere has been an evaluation of polymorphism of the BMPR1B gene in the litter size and there was the detection of SNPs associated with litter size traits of c.85A<G, c.742C<T, c.743T<C, c.744C<T and c.225 G<C with accession number KC142198.1.17 the study samples were collected from the Etawah breed. These SNPs of the BMPR1B gene were identified using PCR-RFLP methods. The frequency of the C allele in the gene BMPR1B (exon 1), was found to be higher than G (Table 2). The genotype frequencies found in the BMPR1B SNP c.225 G<C gene were GG and CC with genotype frequencies of 0.038 and 0.962. Meanwhile, allele frequencies were 0.038 and 0.962 for G and C, respectively. In this study, a heterozygous genotype was not found, while both C and G genes were not fixed. The condition of the BMPR1B gene (exon 1) in research causes the Hardy–Weinberg balance is not met (P<0.05). By contrast, after researching the FecB mutation in six distinct breeds of productive goats (Black Bengal, Beetal, Barbari, Malabari, and Sikkim), the researchers found that none of the goats were homozygous carriers of the trait.26\n\nThe polymorphism of the KISS1 gene in the litter size was evaluated, and it was discovered of 14 SNPs in Kacang, Kejobong and Senduro as the following (g.2064T>A, g.250G>A, Ng.2540C>T, g.2196G>C, g.2270C>T, g.2425C>G, g.2436A>G, g.2360A>G, g.2459G>A, g.1978C>T, g.2055A>C, g.2489T>C, g.2601T>A),2 For the polymorphism research analysis, only two SNPs, g.2425C>G and g.2459G>A, were explored utilizing PCR sequencing from three population groups in Kejobong Senduro and Kacang. Polymorphisms could not be detected in Senduro goats, whilst Kacang and Kejobong were polymorphic, with genotype frequencies in Kacang CC 0.71, CG0.14, and GG 0.14, and allele frequencies of C 0.79, G 0.21, and 0.50, respectively, with the allele frequencies for allele C, were 0.44 and 0.56, respectively. In the case of SNP g.2459G>A, polymorphism was found in all breeds, with genotypes GG (0.29, 0.75, and 0.38), and GA (0.43, 0.12, and 0.62) in the three breeds, while genotype AA was only found in two breeds (Kacang and Kejobong), with genotypes AA (0.43, 0.12, and 0.62). (0.29 and 0.13). In the Damascene and Zarabi goat breed, those with the TT genotype at intron 1 had a greater progesterone level compared to those with the TA genotype.9 In the meanwhile, it was discovered that there was an SNP known as T125A in the intron 1 region of the KISS1 gene. The allelic frequency of alleles A and B was measured at 0.43 and 0.57, respectively.27\n\nIn both SNPs, Kacang goats were in HWE. Kejobong and Senduro goats were not subjected to HWE at g.2425C>G, but rather at g.2459G>A (χ2>3.841). SNP T125A was identified in 48 Kaligesing goats aged 3 years old using PCR-RFLP and DNA sequencing, and the results revealed that The KISS1 gene was polymorphic in the studied population, having one single nucleotide variation. (SNP T125A). SNP was then used to study the genotype of all individuals using the PCR-RFLP method. There were three genotypes identified (TT, TA, and AA). The genotype frequency of TA was 0.60, AA was 0.40, and TT was not included in the genetic diversity calculation. T and A allele frequencies were 0.30 and 0.70, respectively. The SNP genotype distribution differed from the HWE (χ2=8.10; P=0.025).\n\nMulyono et al.17 had investigated KISS1 gene in goats using PCR-RFLP, four SNPs were found in exon 1 and intron 1 of the KISS1 gene (c.585A>C, c.50G>A, c.82A>T, c.114C>A, c.116C>A, and c.57T>C). In this review study, only the genotype and allele frequency of the SNP in intron 1 was examined. In the Eatawah goat, there have been three genotypes (AA, AT, and TT), the genotype frequencies for the A and T alleles were 0.11 and 0.89, respectively, whereas the genotype frequencies for the AT and TT genotypes were 0.179 and 0.802.16 Indicated that if a polymorphic locus has 0.05, it is classified as an SNP. The allele and genotype frequencies will maintain unchanged as long as there will be no selection, mutation, non-random mating, migration, or genetic drift in the population.\n\nIn Table 2, a summary of the litter sizes of a few breeds of Indonesian goats was provided. In the study conducted by Mulyono et al.,17 it was revealed that combinations of alleles in the BMP15 gene produced two genotypes: genotype ++ with a frequency of 0.93 and the average of litter size of 1.59±0.58, and genotype G + with a frequency of 0.07 and an average litter size of 1.65±0.2 similar outcomes shown in SNPs of 818C>T, and 959A>C.5 However, research investigating how BMP15 mutations affect litter size is limited. Used PCR-SSCP and DNA sequencing to analyze exon 2 of the BMP15 gene in two Chinese local goat breeds. According to the findings of the research, Funiu white goats had three genotypes (AA, BB, and AB), whereas Taihang black goats only had two genotypes (AB and BB). Those Funiu white goats carrying the genotype BB had either 0.91 or 0.82 more kids than those carrying the AB or AA genotypes, correspondingly, indicated that the BMP15 gene would be a significant contributor to the fertility of Funiu white goats.28\n\nThe result of the KISS1 gene with SNP (g.2459C>G) showed that the litter size of the same genotype varied between the two studies with different flocks of Kacang, Kejobong and Senduro2,18 The first study showed the same result of litter size 3.00±0.0 among the three breeds, whereas the second study found a larger litter size (4.01±0.96) in KISS1 (g.2459C>G) with the same breeds. This could be due to the small number of samples used in the second study, but it was also discovered that the associated SNP g.2425C>G had a significant effect on litter size in the KISS1 gene among the Kacang and Kejobong breeds, with values of 2.67±0.13 and 2.33±0.25, respectively. Febriana2 found four unique SNPs in the KISS1 gene intron 1, of which two are prominently associated with reproductive traits in local goat breeds native to Indonesia. Both the AA genotype at g.2436A>G and the GA genotype at g.2436A>G had a significant influence on litter size across all Indonesian native goat breeds. On the other hand, the genotypes g.2360A>G, g.2425C>G, and g.2510G>A did not exhibit the same link with LS in various breeds of goats. It's interesting to note that the Kacang and Kejobong breeds are the only ones where the AG genotype at g.2360A>G, CC genotype at g.2425C>G, and AA genotype at g.2510G>A showed greater LS. In addition, the CC genotype at the g.2425C>G locus in SD goats has nearly the same LS average as Kacang (2.67±0.23) and is higher than Kejobong (2.33±0.25). However, g.2425C>G and g.2459G>A both expressed that the genotype at these loci has a substantial impact on the LS at the first and the third parities, in contrast to the second parity. Nonetheless, the GA genotype at g.2459G>A was only significant in the first parity. In addition, the CC genotype at g.2425C>G and the AA genotype at g.2436A>G revealed a relationship with LS at the third parity. This association was substantially higher than the association with LS at the second parity and the first parity. At the third and last parity, we were, however, lacking in samples. In general, the CC genotype at locus g.2425C>G, the AA genotype at locus g.2436A>G, and the GA genotype at locus g.2459G>A were good genotypes related with LS and parity substantially (p>0.05) in local goat breeds from Indonesia.2 In contrast, there was no interaction impact between parity and genotype. on litter size in Black Bengal goats.29 On the other side, in the fourth parity, the TT genotype was connected to greater litter size in Chinese goat breeds than the CC genotype was. This was revealed by evaluating the litter size values between the two genotypes.11 It was discovered that there is a substantial correlation between the genotypes of Gaddi goats and the number of kids born to each litter. The results of the research indicate, on the other hand, that there is a connection between the allele T found in the KISS1 gene and the size of the litter.27 The polymorphism in the goat KISS1 gene was found to have a substantial influence on the reproductive features in a prior study.9 Additionally, in Guangzhong, Saneen, and Xinong goats, a discernible link was found to exist between the KISS1 gene polymorphism and the litter size,11 a further SNP in the KISS1 gene was discovered in the Guanzhong breed of goat that was associated with litter size.30–32 Research conducted on Egyptian goat breeds (Zaraibi, Baladi, and Barki) indicated that two SNPs in the KISS1 promoter region were substantially linked with litter size. These SNPs were T2124A and C2270T. According to the findings of 29, there are three polymorphisms in Black Bengal goats that are related to larger litter sizes. These are G296C, G2510A, and C2540T. In the promoter region of the KISS1 gene, a new polymorphism called G231C was discovered. This polymorphism was found to have a statistically significant connection with the litter size in goats (P<0.05).10\n\nStudy of Exon 1 in gene BMPR1B with SNP c.225 G>C showed that genotype GG had a higher litter size than the other genotypes, the study had found no association among genotypes of BMPR1B (exon 1) gene and litter size.17 Relevant to the results that obtained, the surveyed BMPR1B mutation did not have a major links with litter size in Markhoz goats. Additionally, goat breeds from India, Iran, China, Egypt, and Malaysia were examined for the FecB mutation, and all of these goats were determined to be homozygous non-carriers of the mutation.5 There is no evidence to suggest that the BMPR1B gene is linked to any reproductive traits in goats,33 in a sample of nine Indian goat breeds, researchers discovered two unique SNPs in the promoter region of the BMPR1B gene, 242T>C and 623G>A, but also no association with prolificacy traits.34\n\nOne of the few studies to identify a correlation between GDF9/V397I and litter size in goats35 indicated that V397I has a substantial influence on litter size; furthermore, it found related findings in Chinese dairy goats.36 Contrastingly, neither Q320P nor V397I were associated with litter size in seven native Indian goat breeds investigated.35 Wang et al.23 found that V397I had a significant impact on litter size until sample size exceeds 1300. We didn't find any places in the GDF9 gene that were strongly linked to the size of a Black Bengal goat's litter. According to Ahlawat et al.,3 the impact of parity on litter size in Indian Black Bengal goats is significant (P<0.01). Das et al.37 also noticed a highly significant (P<0.001) influence of parity on litter size in this investigation. Ahlawat et al.5 investigated the relationship with new SNPs in the BMP15, BMPR1B and GDF9 genes and litter size in seven Indian goat breeds. No SNPs including 1189G>A and 959A>C in GDF9 and 242T>C in BMPR1B were found to be linked with litter size. According to the findings in Indonesian goats with the GDF9/V397I and all over the world, it was concluded that there is not likely to be a substantial association between the SNPs in goats as there is in sheep. Additional research with larger samples may provide additional light on the connection between this SNP and goats.\n\n\nConclusion\n\nThe discovery of polymorphisms in fecundity genes has aided in the selection of goats with superior reproductive performance, as a result of which goat litter size has increased. In this review, 36 SNP loci from the goat BMP15, KISS1, BMPR1B, and GDF9 genes were gathered and sorted, the relationship between part-potential SNPs and the trait of goat litter size was analyzed and discussed. Among these mutations, four were monomorphic: GDF9/V397I in Saanen, KISS1/g.2425C>G in Senduro, BMP15/g.135G>C in Etawah, and BMP15/g.735A>G in Kosta. Meanwhile, these six SNPs were studied for their association with litter size traits in the Indonesian goat breeds (Table 2). In Indonesian goats, only four of the six SNPs were shown to be substantially associated with litter size traits (Table 2). The goats used in this study were reared or raised on institutions' farms and were chosen for their high performance of desirable traits such as productivity. As a result, there is a good chance that the SNPs were already selected for the genotype associated with high reproduction performance expression. As a result, additional research should be conducted with larger sample size and with different small and large farms from different regions and areas.\n\nOverall, the findings in the Indonesian goat support the notion that the BMP15, KISS1, BMPR1B, and GDF9 genes increase litter size. These outcomes are critical for developing molecular breeding strategies for goats as well as improving goat reproduction and production performance.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare. PRISMA checklist for Polymorphism studies and candidate genes associated with litter size traits in Indonesian goats. A systematic review. https://doi.org/10.6084/m9.figshare.21746813\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAgus Hidayat R, Depamede SN: Identifikasi Mutasi FecX Pada Gen BMP15 dan Pengaruhnya Terhadap Sifat Prolifik pada Kambing Lokal di Kabupaten Lombok Barat (Identification of Mutation on Gene FecX BMP15 and its Effects on Prolific Nature of Local Goats in West Lombok Regency). J. Ilmu Teknol. Peternak. Indones. 2015; 1(1): 1–10.\n\nFebriana A, Sutopo S, Kurnianto E, et al.: A Novel SNPs of KISS1 Gene Strongly Associated with Litter Size in Indonesian Goat Breeds. Trop. Anim. Sci. J. 2022; 45(3): 255–269. Publisher Full Text\n\nAhlawat S, Sharma R, Roy M, et al.: Association analysis of novel SNPs in BMPR1B, BMP15 and GDF9 genes with reproductive traits in Black Bengal goats. Small Rumin. Res. 2015; 132: 92–98. Publisher Full Text\n\nSasi R, Kanakkaparambil R, Thazhathuveettil A: Polymorphism of fecundity genes, BMPR1B, BMP15 and GDF9, in tropical goat breeds of Kerala. Gene Reports. 2020; 21: 100944. Publisher Full Text\n\nAhlawat S, Sharma R, Roy M, et al.: Genotyping of Novel SNPs in BMPR1B, BMP15, and GDF9 Genes for Association with Prolificacy in Seven Indian Goat Breeds. Anim. Biotechnol. 2016; 27(3): 199–207. PubMed Abstract \| Publisher Full Text\n\nDemars J, Fabre S, Sarry J, et al.: Genome-Wide Association Studies Identify Two Novel BMP15 Mutations Responsible for an Atypical Hyperprolificacy Phenotype in Sheep. PLoS Genet. 2013; 9(4): e1003482. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJalbani MA, Kaleri HA, Hameed Baloch A, et al.: Study of BMP15 gene Polymorphisim in Lehri Goat Breed of Balochistan. J. Appl. Environ. Biol. 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Proceedings of the International Conference on Improving Tropical Animal Production for Food Security (ITAPS 2021). Elsevier Inc.;2021; 3722–3734.\n\nMaharani D, Elieser S, Budisatria IGS, et al.:Polymorphism study of BMP15 gene in Indonesian Goats. IOP Conference Series: Earth and Environmental Science. Institute of Physics Publishing;2019. Publisher Full Text\n\nHerlina Mulyono R, Sumantri C, Rachman Noor R, et al.: Association of BMP15, BMPR1B, and KISS1 Genes with Fecundity Traits on Etawah-Grade does. J. Ilmu Pertan. Indones. 2019; 24(2): 83–92. Publisher Full Text\n\nFebriana A, Sutopo S, Kurnianto E, et al.: Phylogenetic study and association between prominent genotype and haplotype of KISS1 gene with FSH level in Idonesian native goat breeds. J. Indones Trop. Anim. Agric. 2021; 46(4): 282–294. Publisher Full Text\n\nBatubara A, Elieser S, Sumantri C: Study of BMP15 gene polymorphism in Boer, Kacang, and Boerka goats. Jurnal Ilmu Ternak dan Veteriner. 2018; 21(4): 224. Publisher Full Text\n\nChairunissa FAZ, Bintara S, Hartatik T: Single Nucleotide Polymorphism of Partial GDF9 Gene in Three Local Goat of Indonesia Compare with Several Goat in Asia. Bul. Peternak. 2022; 46(1): 41. Publisher Full Text\n\nRahayu S, Biologi J, Mipa F: Identifikasi Polimorfisme Gen GDF-9 dan BMP-15 pada Kambing Kacang.2011.\n\nHardyta G, Widayati DT, Maharani D: Association of SNP T125A on KiSS1 gene with reproduction hormone levels in Kaligesing goat. J. Indones. Trop. Anim. Agric. 2020; 45(4): 253–260. Publisher Full Text\n\nWang X, Yang Q, Wang K, et al.: Two strongly linked single nucleotide polymorphisms (Q320P and V397I) in GDF9 gene are associated with litter size in cashmere goats. Theriogenology. 2019; 125: 115–121. PubMed Abstract \| Publisher Full Text\n\nShaha M, Miah G, Lima A, et al.: Identiication of Polymorphisms in GDF9 and BMP15 Genes in Jamunapari and Crossbred Goats in Bangladesh.2021. Publisher Full Text\n\nDas A, Shaha M, das Gupta M , et al.: Polymorphism of fecundity genes (BMP15 and GDF9) and their association with litter size in Bangladeshi prolific Black Bengal goat.Publisher Full Text\n\nAhlawat S, Sharma R, Maitra A, et al.: Prolificacy in Indian goat breeds is independent of FecB mutation. Indian J. Anim. Sci. 2015; 85(6): 617–620.\n\nSankhyan V, Thakur YP, Dogra PK: Association of kisspeptin gene (KISS1) with litter size in migratory Gaddi goats in western Himalayan state of Himachal Pradesh.2019.\n\nWang Y, Li Y, Zhang N, et al.: Polymorphism of exon 2 of BMP15 gene and its relationship with litter size of two Chinese goats. Asian Australas. J. Anim. Sci. 2011; 24(7): 905–911. Publisher Full Text\n\nMaitra A, Sharma R, Ahlawat S, et al.: Association analysis of polymorphisms in caprine KiSS1 gene with reproductive traits. Anim. Reprod. Sci. 2014; 151(1–2): 71–77. PubMed Abstract \| Publisher Full Text\n\nAn XP, Hou JX, Lei YN, et al.: Polymorphism and DNA methylation in the promoter modulate KISS1 gene expression and are associated with litter size in goats. Anim. Reprod. Sci. 2015; 155: 36–41. PubMed Abstract \| Publisher Full Text\n\nAn XP, Han P, Hou JX, et al.: Molecular cloning and characterization of KISS1 promoter and effect of KISS1 gene mutations on litter size in the goat. Genet. Mol. Res. 2013; 12(4): 4308–4316. PubMed Abstract \| Publisher Full Text\n\nOthman EO, Hassan RD, Ahmed AE, et al.: DNA characterization and polymorphism of KISS1 gene in Egyptian small ruminant breeds. Afr. J. Biotechnol. 2015; 14(30): 2335–2340. Publisher Full Text\n\nShokrollahi B, Morammazi S: Polymorphism of GDF9 and BMPR1B genes and their association with litter size in Markhoz goats. Reprod. Domest. Anim. 2018; 53(4): 971–978. PubMed Abstract \| Publisher Full Text\n\nAhlawat S, Sharma R, Maitra A, et al.: New genetic polymorphisms in Indian goat BMPR1B gene. Indian J. Anim. Sci. 2014; 84(1): 37–42.\n\nZhao J, Liu S, Zhou X, et al.: A non-synonymous mutation in GDF9 is highly associated with litter size in cashmere goats. Anim. Genet. 2016; 47(5): 630–631. PubMed Abstract \| Publisher Full Text\n\nAn XP, Hou JX, Zhao HB, et al.: Polymorphism identification in goat GNRH1 and GDF9 genes and their association analysis with litter size. Anim. Genet. 2013; 44(2): 234–238. PubMed Abstract \| Publisher Full Text\n\nDas A, Shaha M, das Gupta M , et al.: Polymorphism of fecundity genes (BMP15 and GDF9) and their association with litter size in Bangladeshi prolific Black Bengal goat. Trop. Anim. Health Prod. 2021; 53(2): 230. PubMed Abstract \| Publisher Full Text" }	[ { "id": "162690", "date": "10 Feb 2023", "name": "Mohammadreza Mohammadabadi", "expertise": [ "Reviewer Expertise Animal genetics and biotechnology", "gene expression", "genomics", "transcriptomics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 \"Polymorphism studies and candidate genes associated with litter size traits in Indonesian goats\" needs major revision. Authors reviewed performed investigations on polymorphism and candidate genes associated with litter size traits in Indonesian goats, but there are some deficiency, especially in title, aims, material and methods, and conclusion sections. Please refer to comments given in the reviewed attached file of the manuscript.\n1- Title:\nThe title of the manuscript is misunderstanding. It is better rewrite it as below:\nReview of performed investigations on polymorphism and candidate genes associated with litter size traits in Indonesian goats.\n\n2-Abstract-Background:\nPlease add the aim of your study at the end of background.\n\n3-Abstract-Results:\nWhich markers? This sentence is not clear. Please rewrite and complete this sentence. Which type? What do you mean, this sentence is not clear. Please rewrite and complete this sentence. You mean marker assisted selection?\n\n4-Abstract-Conclusion:\nThis sentence is not conclusion, it is your aim of this study. Please add specific conclusion from your specific results.\n\n5- Introduction-at the end of Paragraph 2: It is better to explain about importance and applications of genetic diversity, conservation and its association with economic traits in animal breeding. For this you can use below sentences and references:\nMoreover, the study of breeds, using molecular techniques is very important and useful for their characterizing (Mohammadi et al., 2009; Mohammadabadi, 2021). Conservation of genetic diversity in animal species requires the proper performance of conservation superiorities and sustainable handling plans that should be based on universal information on population structures, including genetic diversity resources among and between breeds (Javanmard et al., 2008; Roudbar et al., 2018). Genetic diversity is an essential element for genetic improvement, preserving populations, evolution and adapting to variable environmental situations (Mousavizadeh et al., 2009; Masoudzadeh et al., 2020). On the other hands, determination of gene polymorphism is important in farm animals breeding (Mohammadabadi et al., 2011; Ahsani et al., 2010) in order to define genotypes of animals and their associations with productive, reproductive and economic traits (Nassiry et al., 2005; Norouzy et al., 2005; Sulimova et al., 2007).1,2,3,4,5,6,7\nMousavizadeh A, Mohammadabadi MR, Torabi A, Nasiri MR, Ghiasi H, 2009. Genetic polymorphism at the growth hormone locus in Iranian Talli goats by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). Iranian Journal of Biotechnology 7 (1), 51-53.\n6-Methods-Study characteristic:\nHow did you analyze? Did you use softwares? Please identify in the text of the manuscript.\n\n7-Conclusions-1: The discovery of polymorphisms in fecundity genes has aided in the selection of goats with superior reproductive performance, as a result of which goat litter size has increased. In this review, 36 SNP loci from the goat BMP15, KISS1, BMPR1B, and GDF9 genes were gathered and sorted, the relationship between part-potential SNPs and the trait of goat litter size was analyzed and discussed.\nThese sentences are parts of background and aims the study, not conclusion. Please remove from this section.\nPlease add specific conclusion from your specific results.\n7-Conclusions-2: Among these mutations, four were monomorphic: GDF9/V397I in Saanen, KISS1/ g.2425C>G in Senduro, BMP15/g.135G>C in Etawah, and BMP15/g.735A>G in Kosta. Meanwhile, these six SNPs were studied for their association with litter size traits in the Indonesian goat breeds (Table 2). In Indonesian goats, only four of the six SNPs were shown to be substantially associated with litter size traits (Table 2).\nThese sentences are repeat of results, not conclusion. Moreover, reference to tables and figures is not allowed in the conclusion section. Please remove from this section.\nPlease add specific conclusion from your specific results.\n7-Conclusions-3: The goats used in this study were reared or raised on institutions' farms and were chosen for their high performance of desirable traits such as productivity.\nThis sentence belongs to material and methods section, not conclusion. Please remove from this section.\nPlease add specific conclusion from your specific results.\n7-Conclusions-4: Your conclusion is very general and without your study it was clear and could be concluded. Please add specific conclusion from your specific results.\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", "responses": [ { "c_id": "9978", "date": "29 Nov 2023", "name": "mutasem abuzahra", "role": "Author Response", "response": "RESPOND TO REVIEWER 1 1- Title: The title of the manuscript is misunderstanding. It is better rewrite it as below: Review of performed investigations on polymorphism and candidate genes associated with litter size traits in Indonesian goats. AUTHOR respond: Thank you for your valuable comments, changed accordingly 2-Abstract-Background: Please add the aim of your study at the end of background. Author responds: I have added the purpose of the study at the end based on your request. 3-Abstract-Results: Which markers? This sentence is not clear. Please rewrite and complete this sentence. Which type? What do you mean, this sentence is not clear. Please rewrite and complete this sentence. You mean marker assisted selection? Author responds: I have rewrite and edited accordingly 4-Abstract-Conclusion: This sentence is not conclusion, it is your aim of this study. Please add specific conclusion from your specific results. Author responds: Thank you for your kind comments, I have rewritten the conclusion paragraph based on your request. 5- Introduction-at the end of Paragraph 2: It is better to explain about importance and applications of genetic diversity, conservation and its association with economic traits in animal breeding. For this you can use below sentences and references: Moreover, the study of breeds, using molecular techniques is very important and useful for their characterizing (Mohammadi et al., 2009; Mohammadabadi, 2021). Conservation of genetic diversity in animal species requires the proper performance of conservation superiorities and sustainable handling plans that should be based on universal information on population structures, including genetic diversity resources among and between breeds (Javanmard et al., 2008; Roudbar et al., 2018). Genetic diversity is an essential element for genetic improvement, preserving populations, evolution and adapting to variable environmental situations (Mousavizadeh et al., 2009; Masoudzadeh et al., 2020). On the other hands, determination of gene polymorphism is important in farm animals breeding (Mohammadabadi et al., 2011; Ahsani et al., 2010) in order to define genotypes of animals and their associations with productive, reproductive and economic traits (Nassiry et al., 2005; Norouzy et al., 2005; Sulimova et al., 2007).1,2,3,4,5,6,7 Mousavizadeh A, Mohammadabadi MR, Torabi A, Nasiri MR, Ghiasi H, 2009. Genetic polymorphism at the growth hormone locus in Iranian Talli goats by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). Iranian Journal of Biotechnology 7 (1), 51-53. Author responds: i have added these valuable information and references in the Introduction section. 6-Methods-Study characteristic: How did you analyze? Did you use softwares? Please identify in the text of the manuscript. Author responds: i did mention it in the section before 7-Conclusions 1-4 The discovery of polymorphisms in fecundity genes has aided in the selection of goats with superior reproductive performance, as a result of which goat litter size has increased. In this review, 36 SNP loci from the goat BMP15, KISS1, BMPR1B, and GDF9 genes were gathered and sorted, the relationship between part-potential SNPs and the trait of goat litter size was analyzed and discussed. These sentences are parts of background and aims the study, not conclusion. Please remove from this section. Author responds I have rewritten the entire section based on your request." } ] }, { "id": "185209", "date": "27 Jul 2023", "name": "Zhanerke Akhatayeva", "expertise": [ "Reviewer Expertise Animal genetics", "breeding and reproduction" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have summarized all papers related to \"major\" fecundity genes and the topic that they have chosen is a relevant one. However, the article needs significant improvements. The specific comments are below:\nWhy did the authors include the KISS1 gene? This gene belongs to a different gene family or axis. I think no sense to include this gene. Otherwise, the authors should include all genes related to HP-axis or reproductive traits;\n\nTGF should be TGF-beta;\n\nbooroola should be \"Booroola\";\n\nThe MAS technique and type of polymorphisms should be described in Introduction part;\n\nThe results are just repetition of what is given in the tables; The authors should try to compare the results with the work of other authors and discuss them;\n\nIn Table 2, the ''source or author\" should be given in the last column, please rearrange it; Besides, \"P\" should be \"P\";\n\nI think that there is a need to introduce every goat breed;\n\nThe most important, The Table 2 is unclear. Please, provide the gene name, name of loci;\n\nI suggest to remove the \"The candidate genes associated with prolificacies of some Indonesian goats\" section, and incorporate these association results into previous sections;\n\nThe conclusion section should be concise.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? No", "responses": [ { "c_id": "9979", "date": "29 Nov 2023", "name": "mutasem abuzahra", "role": "Author Response", "response": "Respond to reviewer 2 Why did the authors include the KISS1 gene? This gene belongs to a different gene family or axis. I think no sense to include this gene. Otherwise, the authors should include all genes related to HP-axis or reproductive traits I have mention KISS1 gene as on the gene that have investigated and study their association with litter size in goat in indonesia that is why i hvae mentioned here, particularly this study is review article aimed to invstigate the genes that have been studied in indonesian goats 2.TGF should be TGF-beta; Author respond: I have changed it in the manuscript 3.booroola should be \"Booroola\"; Author respond: I have changed it in the manuscript 4.The MAS technique and type of polymorphisms should be described in Introduction part; Author respond: I have added some information on the introduction part, also about the molecular diversity 5.The results are just repetition of what is given in the tables; The authors should try to compare the results with the work of other authors and discuss them; Author respond: I have discussed the results of previous and other papers from overseas with results of the Indonesian literature as it shown here and in the text\" The polymorphism in the goat KISS1 gene was found to have a substantial influence on the reproductive features in a prior study.9 Additionally, in Guangzhong, Saneen, and Xinong goats, a discernible link was found to exist between the KISS1 gene polymorphism and the litter size,11 a further SNP in the KISS1 gene was discovered in the Guanzhong breed of goat that was associated with litter size.30–32 Research conducted on Egyptian goat breeds (Zaraibi, Baladi, and Barki) indicated that two SNPs in the KISS1 promoter region were substantially linked with litter size. These SNPs were T2124A and C2270T. According to the findings of 29, there are three polymorphisms in Black Bengal goats that are related to larger litter sizes. These are G296C, G2510A, and C2540T. In the promoter region of the KISS1 gene, a new polymorphism called G231C was discovered. This polymorphism was found to have a statistically significant connection with the litter size in goats (P<0.05).10 6.In Table 2, the ''source or author\" should be given in the last column, please rearrange it; Besides, \"P\" should be \"P\"; Author Respond: Thank You very much, I have changed upon your request. 7.The most important, The Table 2 is unclear. Please, provide the gene name, name of loci; Author Respond: I have replaced and changed by mentioned the gene name for each box 8. I suggest to remove the \"The candidate genes associated with prolificacies of some Indonesian goats\" section, and incorporate these association results into previous sections; Author Respond: Thank You for your valuable suggestions. But i think it would be better to separate with the previous section specially they are two different discussions topics, the previous section discussed the genotype frequencies meanwhile this section is focused in the associated studies between these SNPs and the traits 9.The conclusion section should be concise. Author Respond: I have rewrite the section, Thank you for valuable time and generous comments." } ] } ]	1	https://f1000research.com/articles/12-61
https://f1000research.com/articles/12-912/v1	31 Jul 23	{ "type": "Research Article", "title": "How many university students perceive themselves to be overweight/obese and how many have eating disorders during remote education due to COVID-19? A cross-sectional study", "authors": [ "Jeel Moya-Salazar", "Eliane A. Goicochea-Palomino", "María Jesús S. Moya-Salazar", "Víctor Rojas-Zumaran", "Hans Contreras-Pulache", "Eliane A. Goicochea-Palomino", "María Jesús S. Moya-Salazar", "Víctor Rojas-Zumaran", "Hans Contreras-Pulache" ], "abstract": "Background: The COVID-19 pandemic caused a health crisis worldwide that ended up affecting the daily lives of university students. Considering prevention strategies for contagion and decreased physical activity, altered perceptions of body image were seen that may negatively disrupt their eating habits.\n\nMethods: Our cross-sectional survey-based study (N=180) had the objective to determine the association between body image perception and the risk of eating disorders in university students during the pandemic. We surveyed male and female university students aged 18-35 years using the Montero Anatomical Models questionnaire and the Eating Attitude Test-26 (EAT-26) as instruments.\n\nResults: Most of the university students were female (67.8%) with an average age of 22.8±3.9 years. 51.1% perceived themselves as overweight and 53.9% were at low risk of an eating disorder. This mainly affected women (47.5%), the 21-30 age group (43.2%), and those who perceived themselves as underweight (58.9%) or obese (50%). Likewise, we found differences in body image perception between genders (p=0.009), and no association was found between body image and eating disorders (p=0.661). Conclusion: Even though most university students perceived themselves as overweight, they had a low risk of an eating disorder. Considering the influence that body image perception has on their lifestyle, it is necessary to promote healthy eating habits and self-esteem strategies to prevent the appearance of eating disorders due to body dissatisfaction in the context of the “new normal”.", "keywords": [ "COVID-19", "body image", "mental disorders", "eating disorders", "students", "obesity", "overweight", "weight perception" ], "content": "Introduction\n\nThe COVID-19 pandemic has had major health, economic, financial, and social consequences worldwide.1 Not only because of the direct effects of this disease on the general health of people, but also because of the impact of infection prevention strategies that have led to unprecedented social restructuring.2 In spite of the implementation of mass lockdowns, cessation of mobility, social distancing and vaccination, the violent spread of the virus has not been fully controlled.3 Therefore, the fear of contagion and the possible decease of infected family members were particularly challenging circumstances that produced uncertainty and severely affected the mental health of people without discrimination.4 Especially because evidence indicates that social isolation brought with it manifestations of insomnia and other disorders such as anxiety disorders and depression.5 It should be noted that an alteration of body image in people was also observed as a result of the limitation of physical activity in freely available spaces.3,4 A study in a Chilean population indicated that people with less weekly physical activity time were more concerned about their body image, causing an increase in concern about weight and body shape, and in turn, negatively disturbing eating habits.3 Besides, overweight, and obese Argentinian women, compared to women of healthy weight, have been reported to have a greater concern and negative perception of their body image, with an increased frequency of snacking between meals, binge eating, dieting behavior and the use of laxatives, diuretics, and diet pills.6 Likewise, 5.2 million electronic health records of people under 30 years of age, mostly Americans, showed that the overall incidence of eating disorders increased by 15.3% with increased risk of suicidal behavior during 2020.7\n\nA recent systematic review found that university students may be more likely to be physically inactive during the COVID-19 pandemic since education and work became virtual, which forced them to spend more rest time.8 According to an Ecuadorian study, 73.3% of their university students answered that they had a sedentary lifestyle and, as a consequence, 54.2% considered that they had gained weight.9 For this reason, these sedentary behaviors are associated with a generally negative body image perception (fear of being overweight) exposing university students to the pressure to have a specific, athletic, and slim body appearance.10 This results not only in negative thoughts, but also in distorted appraisals of their bodies, leading to high levels of body dissatisfaction.11 As seen in university students in Panama, 66% had distorted body image and 79% felt dissatisfied with their body image. In addition, 47% engaged in risky eating behaviors and there was a significant relationship between these behaviors and self-perceived body image.12\n\nAs mentioned, the risk of having an eating disorder increased due to the psychological stress that occurred during the lockdown. This causes major public health challenges, as they often appear early in life and continue into adulthood.13 For this reason, university students are even more vulnerable to eating disorders during their adult transition, as they have an academic burden and frequent financial difficulties when integrating independently into society.14 A study in French university students showed that the prevalence of eating disorders is generally higher in females (51.6%) compared to males.14 Similar results were found on the perception of body image dissatisfaction in two universities in Latin America, namely in Peru and Chile (69.7% and 47.7% respectively) affecting more females.15,16 Considering the influence of body image, the risk of eating behaviors presents in the university population, and the long-term public health consequences of this type of disorder, it is key to understand the current scenario to carry out programs and interventions that promote self-esteem and the prevention of eating disorders.\n\nThe objective of this study is to determine the association between body image perception and the risk of eating disorders in university students during the COVID-19 pandemic. The study hypotheses were that i) there is a positive association between body image perception and risk of eating disorders, ii) there is a high frequency of body image perception in overweight and obese individuals, and iii) there is a high risk of eating disorders in Peruvian university students. Clearly this comprehensive approach to body image and eating practices is important to understand how the pandemic has affected these variables.\n\n\nMethods\n\nThis is a cross-sectional survey-based study. Peru, a South American country with approximately 33 million inhabitants, shares a common trend with many nations in the region—population centralism in its capital, Lima. Since March 15, 2020, Peru has confronted the challenges posed by the COVID-19 pandemic, enduring three distinct waves corresponding to each year of its duration. Notably, in 2022, the emergence of the SARS-CoV-2 omicron (B.1.1.529.1) variant resulted in a significant surge in infections between February and June of that particular year, adding to the complexity of the situation. In response to the pandemic, the country implemented measures including remote learning for all educational activities. However, starting from 2022, a hybrid model for university education was introduced, combining in-person and remote components as part of the country’s efforts to adapt to the changing circumstances. The study was carried out during the period of July to August 2022 within a hybrid/asynchronous educational setting. The participant pool comprised 180 university students, both male and female, hailing from Lima, Peru. All participants resided in urban areas and were from Health Sciences (i.e., nursing, medicine) (Table 1).\n\nParticipants met the inclusion criteria. They were students between 18 and 35 years of age, without physical disability or pathology that altered their perception of body image, and who belonged to the Universidad Norbert Wiener (UNW), the Universidad Tecnológica del Perú (UTP), and the Universidad Nacional Mayor de San Marcos (UNMSM) (Figure 1). Every university adhered to the Superintendencia Nacional de Educación Superior Universitaria (SUNEDU) regulations and allowed students to attend virtual or hybrid classes during the lockdown. UNW and UTP are private universities, while UNMSM is a major public university of Peru. These universities use digital platforms such as Zoom and Blackboard, and the effectiveness of these models has shown teaching effectiveness during the pandemic.17,18 We used simple randomized sampling and no pregnant women participated.\n\nTwo instruments were used in this research. These were shared as surveys conducted in Google FormsTM (Google, CA) through WhatsApp (Meta, CA) with the study groups of each semester, being completed virtually. We used the Montero’s Anatomical Models questionnaire.19 This instrument allows us to identify the body image perception of the participants based on average adult body sizes between 18 and 30 years of age, and with 7 anatomical models per gender.20 The Montero questionnaire has been validated in the general population and university students with high internal consistency (α=0.816). Each analysis was initially conducted by asking students to choose to classify their perceived nutritional status as: underweight, normal weight, overweight and obese, based on self-determined BMI.19\n\nThe second questionnaire used was the Eating Attitude Test-26 (EAT-26) to assess the risk of eating disorders in students. It was created in 1979 and originally had 40 items.21 It was later shortened to 26 items in 1982,22 and in 2005, it was translated and validated in Spanish.23 This instrument has a high internal reliability described in several previous studies in Spanish and English versions (α=0.850 to0.890).24,25 The responses are presented on a Likert scale with decreasing ordinality: always (3 points), very often (2 points), often (1 point), sometimes (0 points), rarely (0 points) and never (0 points). Only item 25 is scored in the opposite way. According to the scores obtained, the risk of eating disorder is categorized as low (≤20 points) and high (>20 points).23\n\nThe study variables were body image perception (underweight, normal weight, overweight and obese) and risk of eating disorder (low and high). Surveys were completed virtually on Google FormsTM (Google, CA) and then shared via WhatsApp (Meta, CA) through each semester’s study groups. Virtual informed consent was used prior to each survey and data were gathered directly to the Google storage array, where a total of 198 participants were obtained, but only 180 were considered after quality control of participant answers (Figure 1).\n\nInitially, the data were coded and entered into IBM SPSS v24.0 (Armonk, USA) for analysis. Then, we used the Kolmogorov-Smirnov test to find a normal distribution and used the non-paired T-test and one-way ANOVA with Bonferroni post hoc test to determine differences between perceived body images according to eating disorder. Finally, we used Spearman’s correlation coefficient to determine the association between variables and binary logistic regression to predict eating disorder and disturbed body image perception variables. For all tests we considered a threshold p=0.05 and a confidence interval of 95% as statistically significant.\n\n\nResults\n\nA total of 198 participants who met the inclusion criteria were initially obtained for the study. However, after conducting a quality check of the participants’ responses, 180 participants were considered for further analysis. The average age of the university students was 22.8±3.9 years (95% CI: 22.3 to 23.4), ranging from 18 to 35 years. The most common age group among the participants was 21 to 30 years, accounting for 65.6% (118/180), and the majority of the participants were women, constituting 67.8% (112/180). Among the participants, 46.1% (83/180) were employed, with the majority working on-site, accounting for 85.5% (71/180) of the employed participants. The full dataset can be found under Underlying data.44\n\nRegarding Body Image perception, 51.1% (92/180) perceived themselves as overweight and 22.2% (40/180) as obese. Overweight and obesity were more frequent in women (47.5%, 58/122 and 18.9%, 23/122, respectively), and in the 21-30 age group (53.4%, 63/118 and 25.4%, 30/118, respectively). We found differences in body image perception between genders (p=0.009). According to employment status, the majority perceived themselves as overweight, regardless of whether they were working (57.8%, 48/83) or unemployed (42.7%, 44/97) (Table 2).\n\n46.1% (83/180) of the university students were at high risk for an eating disorder. The majority were female (47.5%, 58/122) and in the 21-30 age group (43.2%, 51/118). 49.5% (48/97) were unemployed and of the working group and had high risk of developing an eating disorder, and 43.7% (31/71) were in a classroom-based modality (Table 3). Only gender was a predictor of body image (β=-0.342±0.129, 95%CI: -0.597 to -0.087) in university students during hybrid education (p=0.010).\n\nAlthough most of the participants answered that they never vomit after eating (80%,144/180) or feel like vomiting afterwards (72.2%, 130/180). Always, and very often 2.2% (4/180) and 6.7% (12/180) of students answered that they like to feel an empty stomach, 5% (9/180) and 8.3% (15/180) feel very guilty after eating, and 2.8% (5/180) and 3.3% (6/180) feel that food controls their life, respectively. Only 1.7% (3/180) and 5.6% (10/180) of students always and frequently exercise a lot to burn calories, while only 3.3% (6/180) always take into account the calories in the food they eat. On the other hand, 31.7% (57/180) and 25% (45/180) of students never or rarely eat food with a lot of carbohydrates (i.e., bread, rice). 35% (63/180) never noticed that others would prefer them to eat more and for 30.6%, (55/180) others never perceived them as too thin. We found no association between body image and eating disorders (p=0.662).\n\nFinally, we found that most of the participants who perceived themselves as underweight were at high risk of an eating disorder 58.9% (7/12). The same was true for 50% (20/40) of those who perceived themselves as obese (Figure 2). We found no association between body image and eating disorders (p=0.661).\n\nMost students at high risk of an eating disorder were overweight (n=41) and obese (n=20). Data in N, *p=0.598.\n\n\nDiscussion\n\nThis study showed that just over half and almost a quarter of the university students perceived themselves to be overweight and obese, respectively. Also, about half were at high risk for an eating disorder, mainly affecting females aged 21-30 years. Likewise, most students who perceived themselves as underweight were at high risk of developing an eating disorder, as were half of those who perceived themselves as obese.\n\nA strength of the study is it is the first association study of body image and eating disorders in university students who have undertaken remote education. Research in this area has been conducted in Peru16,26 but none has included an analysis of the university population during the third year of the COVID-19 pandemic, a year when they were transitioning from fully digital education to a hybrid model. On the other hand, this study has used an instrument that has anatomical silhouettes specifically made and applied to an adult population within the average age range of university students.19,20 The COVID-19 pandemic has posed challenges for on-site nutritional monitoring, leading to limited access to accurate BMI measurements among participants.8 In virtual and remote education settings, the use of silhouettes has emerged as a valuable tool for estimating body image and gauging the health status of university students. Furthermore, this study benefits from the utilization of the EAT-26 questionnaire, which possesses robust psychometric properties for evaluating eating disorders within this specific population.24,25 As the “new normal” has ushered in hybrid and remote education, disruptions in dietary habits during educational activities have become apparent.14,27 Our findings present a fresh perspective on assessing both nutritional aspects and offer insights to guide interventions aimed at addressing the adverse effects on students’ well-being. This framework contributes to a better understanding of the situation and promotes proactive measures to mitigate the negative impacts experienced by students.\n\nOur findings showed that females, participants aged 21-30 years and those perceived to be overweight or obese were at high risk of disordered eating. These results are consistent with the finding in French university students,14 where women (51.6%) and first- and second-year students had the highest prevalence of disordered eating, although only 13.5% were overweight and 5.4% obese. Also, even though American university students did not show statistically significant changes in BMI, 60% had increased concerns about body weight and shape and their eating habits since the start of COVID-19.28 This pressure on body appearance was also experienced by 57-85% of students at nine large universities in Norway, finding that it is negatively related to body esteem, self-esteem, and life satisfaction.10 Furthermore, they identified that this generates an unfavorable pattern in the mental health of university students related to their body image.\n\nA study in Colombian university students29 that also used anatomical silhouettes for body image perception supports our results which estimated that ~51% self-perceive themselves as overweight. Similarly, another Peruvian study30 conducted among university students in the Municipality of Arequipa in 2020 showed that 27.8%, 16.7% and 8.7% had mild, moderate, and extreme body image concerns, respectively. Another study conducted in the same municipality in 2021 showed that 69.7% of students were dissatisfied with their body image, 82.4% were female and 67.9% engaged in moderate- to high-intensity physical activity.16 Peruvian students have changed their body perception and satisfaction during the COVID-19 pandemic, and in the context of virtual education, this perception has been favored by study habits and remote activities. On the other hand, in both French and American university students, along with the prevalence or risk of eating disorders and body image concerns, a decrease in physical activity was observed in university students.14,28 In contrast, no change in BMI or body image was reported in Lithuanian university students despite a significant decrease in physical activity levels.30\n\nThis change was most marked in women, who reported an increase in body image satisfaction, even though their BMI increased. Our results have identified that more than half of the women had eating disorders and an over-perception of their body image (i.e., overweight), and although we did not assess physical activity, it is possible that a large proportion of these students may have reduced their physical activity during the virtual classes because of COVID-19, as a recent study has shown.8 It is important to develop a tripartite analysis of these variables since coping with bodily and nutritional changes may be optimal but also leads to a risk for the development of pathologies. As stated by the previously mentioned studies and reaffirmed by a systematic review, during the “new normal” the physical activity levels of university students tend to decrease or have negative changes as education and work become virtual, and they are forced to spend more time resting.8,14,30,31\n\nThus, there was an increase in sedentary behaviors, confirmed by two studies in American28 and Ecuadorian university students (73.3% led a sedentary lifestyle).9 In view of this, physical activity levels during the pandemic are important. A study of Brazilian university students showed that physically active university students during lockdown had positive changes in appearance, and 50.7% reported negative changes when faced with the demands of meeting social standards of beauty.30 These negative thoughts and distorted appraisals of their bodies can lead to high levels of body dissatisfaction.9,11 Similarly, there is a report of Chilean university students, who had dissatisfaction in their perception of their body image (47.7%), affecting women more frequently.15 Likewise, 79% of university students in Panama also felt dissatisfied with their body image, 66% had body image distortion, 47% had risky eating behaviors, and a significant relationship was found between these behaviors and self-perceived body image.12 These results are consistent with our findings and together expose possible nutritional disturbances in university students during the “new normal” of the COVID-19 pandemic.\n\nAccording to our results, no association was found between body image perception and risk of eating disorder. This is supported by another Peruvian study in the Municipality of Arequipa.16 Moreover, our results showed that only women showed a predicted increased risk of body image disturbance, but not the risk of an eating disorder, in agreement with studies in Norway, Ecuador, Chile, Peru and Brazil.9,10,11,15,16,32 Altogether, these studies show independent changes in the two variables, however, both may converge when there are risk factors (decreased physical activity, increased sedentary behaviors, psychological stress, insomnia) as previously reported.3,5,8,9,13,27\n\nA recent review33 has shown a considerable increase in eating disorders during the pandemic and a worsening of its symptoms due to the lack of care and treatment, disruption of daily routine, negative influence of the media and the internet,34 and isolation due to security measures against COVID-19. The short-term effects of the pandemic on eating disorders have been reported.14,35,36 These investigations and systematic reviews37 have not considered the university population of Latin American countries where the pandemic has hit differently. Even local or regional1–13,15,16,32 studies have evaluated EDs but have not proven their link to body image. College students’ physical expectations during the pandemic may lead to dissatisfaction with how they are portrayed in the pandemic’s virtual environment. It has been seen38 that the impact of social networks on the perception of body image could lead to eating disorders. Although in this study, we did not find a relationship between both variables, it is possible that in rural or peri-urban populations, as well as in specific groups of university students (i.e., high-performance athletes or models),39 the links between eating disorder could be different. It is important to comprehensively study these phenomena, including the family core,40 the political position on the body (body positive or neutrally),41 lifestyles,8 and access to technology and income.42\n\nThis study had limitations. First, the physical activity (including physical activity in the gym) performed by university students was not taken into account. Physical activity is a key factor because lockdown led to changes in daily life and thus decreased physical activity.8 Low levels of physical activity have been reported to be associated with increased body image concerns.3 In addition, since we were in an optional and asynchronous hybrid environment, we could not measure the height, weight, and BMI of the participants in this research with surveys. Second, demographic and work factors were considered in the analysis, but other factors such as social media use (which increased during lockdown) may lead to a negative perception of body image and increased risk of eating disorders.13 Third, the effects of remote education have not been evaluated as influential factors in changes in body image perception, the development of conduct and eating disorders, and reduced physical activity. Finally, we had a small sample of students from each university that could affect the results. However, this topic is important since several Peruvian universities continue to provide virtual, hybrid and asynchronous classes that place students in a “new” context and may support nutritional changes.\n\n\nConclusions\n\nUniversity students enrolled in virtual classes, aged 18 to 35, are commonly perceived as overweight and at a low risk of developing an eating disorder. This perception particularly affects women, with young students between 21 and 30 years old being more prone to being perceived as overweight or obese. Given the ongoing third year of the COVID-19 pandemic and the restrictions imposed by the Peruvian government, it is crucial to address the students’ situation and implement measures to enhance their nutritional well-being and promote healthy habits. Recognizing the significant impact that body image perception has on the lifestyle of university students, it becomes imperative to encourage the adoption of healthy eating practices and self-esteem enhancement strategies. By doing so, we can mitigate the risk of eating disorders stemming from dissatisfaction with one’s body, which is often influenced by societal beauty standards within the context of the “new normal.”\n\n\nEthics and consent\n\nThis study has complied with bioethical principles and the guidelines of the Helsinki declaration (WMA, 2013)43 and had the approval of the Ethics Committee of the Norbert Wiener University (Registration No. 01963-2022). Informed consent was obtained from all subjects involved in the study.\n\n\nAuthor contributions\n\nConceptualization, J.M.-S. and E.A.G.-P.; methodology, J.M.-S., H.C.-P., and E.A.G.-P.; software, V.R.-Z.; validation, J.M.S., M.J.S.M.-S. and E.A.G.-P.; formal analysis, J.M.-S. and E.A.G.-P.; investigation, H.C.-P.; resources, V.R.-Z.; data curation, M.J.S.M.-S. and E.A.G.-P.; writing—original draft preparation, J.M.-S. and E.A.G.-P.; writing—review and editing, J.M.-S., V.R.-Z., H.C.-P, and M.J.S.M.-S.; visualization, J.M.-S.; supervision, H.C.-P.; project administration, E.A.G.-P. All authors have read and agreed to the published version of the manuscript.", "appendix": "Data availability\n\nFigshare: 180 university students_perception of body image_eating disorders.xlsx, Doi: http://dx.doi.org/10.6084/m9.figshare.23247983. 44\n\nThis project contains the following underlying data:\n\n- 180 university students_perception of body image_eating disorders.xlsx\n\nThis project contains the following extended data:\n\n- Montero.docx\n\n- Questionnaire_EAT-26.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors thank the university students for their selfless and voluntary collaboration during the study. In addition, we thank the Nesh Hubbs team for their support in the statistical analysis and review of the manuscript.\n\n\nReferences\n\nDevoe D, Han A, Anderson A, et al.: The impact of the COVID-19 pandemic on eating disorders: A systematic review. Int. J. Eat. Disord. 2022; 56: 5–25. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIoannidis K, Hook RW, Wiedemann A, et al.: Associations between COVID-19 pandemic impact, dimensions of behavior and eating disorders: A longitudinal UK-based study. Compr. Psychiatry. 2022; 115: 152304. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLavalle-Mellado P, Guedda-Muñoz R, Lagos-Hernández R: Perception of the body image of the chilean population in a pandemic situation. Revista Iberoamericana de Ciencias de la Actividad Física y el Deporte. 2022; 11(1): 104–117. Publisher Full Text\n\nHuete Cordova MA: Eating disorder during the SARS-CoV-2 pandemic. Rev. Neuropsiquiatr. 2022; 85(1): 66–71. Publisher Full Text\n\nEscobar-Córdoba F, Ramírez-Ortiz J, Fontecha-Hernández J: Effects of social isolation on sleep during the COVID-19 pandemic. Sleep Sci. 2021; 14(nspe1): 86–93. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSanday J, Scappatura ML, Rutsztein G: IMPACT OF LOCK DOWN ON EATING HABITS AND BODY IMAGE IN OVERWEIGHT AND OBESE WOMEN. Anuario de Investigaciones. 2020; XXVII: 33–38.\n\nTaquet M, Geddes JR, Luciano S, et al.: Incidence and outcomes of eating disorders during the COVID-19 pandemic. Br. J. Psychiatry. 2022; 220(5): 262–264. Cambridge University Press. Publisher Full Text\n\nGoicochea EA, Coloma-Naldos B, Moya-Salazar J, et al.: Physical Activity and Body Image Perceived by University Students during the COVID-19 Pandemic: A Systematic Review. Int. J. Environ. Res. Public Health. 2022; 19(24): 16498. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGaibor Sánchez CG: Estudio descriptivo de las alteraciones en la imagen corporal de los estudiantes de la Universidad Politécnica Salesiana, a partir de la pandemia por COVID-19. Tesis. Universidad Politécnica Salesiana, Quito, Ecuador.2022. Reference Source\n\nSundgot-Borgen C, Sundgot-Borgen J, Bratland-Sanda S, et al.: Body appreciation and body appearance pressure in Norwegian university students comparing exercise science students and other students. BMC Public Health. 2021; 21(1): 532. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGaibor Sánchez CG: Estudio descriptivo de las alteraciones en la imagen corporal de los estudiantes de la Universidad Politécnica Salesiana, a partir de la pandemia por COVID-19. Tesis de Licenciatura, Universidad Politécnica Salesiana Sede Quito, Ecuador.2022. Reference Source\n\nHernández González CI: Conductas alimentarias de riesgo, autopercepción e insatisfacción de la imagen corporal en estudiantes de la Universidad Autónoma de Chiriquí. Tesis. Universidad Autónoma de Chiriquí. Facultad de Ciencias Naturales y Exactas. Panamá.2021. Reference Source\n\nYatche CM, Sanday J, Rutsztein G: Riesgo de trastornos alimentarios y consumo de redes sociales: el caso de Instagram en la pandemia por COVID-19. XIII Congreso Internacional de Investigación y Práctica Profesional en Psicología. XXVIII Jornadas de Investigación. XVII Encuentro de Investigadores en Psicología del MERCOSUR. III Encuentro de Investigación de Terapia Ocupacional. III Encuentro de Musicoterapia. Facultad de Psicología - Universidad de Buenos Aires, Buenos Aires.Reference Source\n\nTavolacci M-P, Ladner J, Dechelotte P: COVID-19 Pandemic and Eating Disorders among University Students. Nutrients. 2021; 13(12): 4294. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAndrades Vega LC, Candia Soto CF, Rincón Asenjo DI: Nivel de satisfacción corporal en estudiantes universitarios durante el periodo de pandemia por Covid-19 en el año 2021. Tesis de Pregrado Ciencias de la Salud. Universidad del Desarrollo. Facultad de Ciencias de la Salud, Chile.2021. Reference Source\n\nLipa Quisbert MA: Percepción de la imagen corporal relacionada a los hábitos alimentarios y actividad física durante la pandemia COVID-19 en estudiantes universitarios, Arequipa 2021. Tesis. Universidad Nacional de San Agustín de Arequipa, Facultad de Ciencias Biológicas, Escuela Profesional de Ciencias de la Nutrición. Perú.2021. Reference Source\n\nMoya-Salazar J, Jaime-Quispe A, Milachay YS, et al.: What is the perception of medical students about eLearning during the COVID-19 pandemic? A multicenter study in Peru. Electron. J. Gen. Med. 2022; 19(6): em402. Publisher Full Text\n\nMoya-Salazar J, Cañari B, Lozano-Zanelly G, et al.: eLearning impact on the graduate health programs during the COVID-19 pandemic in Peru. Open Learn. 2023; 19. in press. Publisher Full Text\n\nMontero P, Morales EM, Carbajal Á: Evaluation of the perception of body image by the use of anatomical models. Antropo. 2004; 8(8): 107–116. Reference Source\n\nPino VJL, López EMA, Moreno VAA, et al.: Body image, nutritional status and body composition perception of nutrition and dietetics students in University del Mar, Talca, Chile. Rev. Chil. Nutr. 2010; 37(3). Publisher Full Text\n\nGarner DM, Garfinkel PE: The Eating Attitudes Test: an index of the symptoms of anorexia nervosa. Psychol. Med. 1979; 9(2): 273–279. Cambridge University Press. Publisher Full Text\n\nGarner DM, Olmsted MP, Bohr Y, et al.: The Eating Attitudes Test: psychometric features and clinical correlates. Psychol. Med. 1982; 12(4): 871–878. Cambridge University Press. PubMed Abstract \| Publisher Full Text\n\nBaile J, Garrido E: Psychometric features of the “Eating Attitudes Test-26” in a sample of university females. Interpsiquis. 6° Congreso Virtual de Psiquiatría.2005. Reference Source\n\nSiervo M, Boschi V, Papa A, et al.: Application of the SCOFF, Eating Attitude Test 26 (EAT 26) and Eating Inventory (TFEQ) Questionnaires in young women seeking diet-therapy. Eat. Weight Disord. 2005; 10(2): 76–82. PubMed Abstract \| Publisher Full Text\n\nConstaín GA, Rodríguez-Gázquez ML, Ramírez Jiménez GA, et al.: Validez y utilidad diagnóstica de la escala Eating Attitudes Test-26 para la evaluación del riesgo de trastornos de la conducta alimentaria en población masculina de Medellín, Colombia. Aten. Primaria. 2017; 49(4): 206–213. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFlores LMF, Roman GA: Ejercicio físico, ansiedad e imagen corporal en mujeres universitarias de la ciudad de Arequipa. Master’s Thesis, Universidad Católica San Pablo, Arequipa, Peru.2020. Reference Source\n\nBranley-Bell D, Talbot CV: Exploring the impact of the COVID-19 pandemic and UK lockdown on individuals with experience of eating disorders. J. Eat. Disord. 2020; 8: 44. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKeel PK, Gomez MM, Harris L, et al.: Gaining “The Quarantine 15”: Perceived versus observed weight changes in college students in the wake of COVID-19. Int. J. Eat. Disord. 2020; 53: 1801–1808. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMárquez RV: Eating Habits, Perception of Body Weight and Lifestyles of First Semester Students Cohort 2130 of the Career of Nutrition and Dietetics Pontificia Universidad Javeriana-Bogotá. Ph.D. Thesis, Pontificia Universidad Javeriana-Bogotá, Bogotá, Colombia.2021. Reference Source\n\nBaceviciene M, Jankauskiene R: Changes in sociocultural attitudes towards appearance, body image, eating attitudes and behaviours, physical activity, and quality of life in students before and during COVID-19 lockdown. Appetite. 2021; 166: 105452. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRuiz Lázaro PJ: Medicina de la adolescencia. Medicine. 2010; 10(61): 4234–4237. Publisher Full Text\n\nBueno de Souza SD: Changes in the Appearance and Practice of Physical Activity in University Universities during Social Distancement among Pandemic COVID-19. Bachelor’s Thesis, Universidade Tecnológica Federal do Paraná, Curitiba, Brazil.2021. Reference Source\n\nDevoe DJ, Han A, Anderson A, et al.: The impact of the COVID-19 pandemic on eating disorders: A systematic review. Int. J. Eat. Disord. 2023; 56(1): 5–25. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVall-Roqué H, Andrés A, González-Pacheco H, et al.: Women’s body dissatisfaction, physical appearance comparisons, and Instagram use throughout the COVID-19 pandemic: A longitudinal study. Int. J. Eat. Disord. 2023; 56(1): 118–131. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEl-Akabawy G, Abukhaled JK, Alabdullah DW, et al.: Prevalence of eating disorders among Saudi female university students during the COVID-19 outbreak. J. Taibah Univ. Med. Sci. 2022; 17(3): 392–400. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRomano KA, Lipson SK, Beccia AL, et al.: Disparities in eating disorder symptoms and mental healthcare engagement prior to and following the onset of the COVID-19 pandemic: Findings from a national study of US college students. Int. J. Eat. Disord. 2023; 56(1): 203–215. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchneider J, Pegram G, Gibson B, et al.: A mixed-studies systematic review of the experiences of body image, disordered eating, and eating disorders during the COVID-19 pandemic. Int. J. Eat. Disord. 2023; 56(1): 26–67. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVall-Roqué H, Andrés A, Saldaña C: The impact of COVID-19 lockdown on social network sites use, body image disturbances and self-esteem among adolescent and young women. Prog. Neuro-Psychopharmacol. Biol. Psychiatry. 2021; 110: 110293. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFiroozjah MH, Shahrbanian S, Homayouni A, et al.: Comparison of eating disorders symptoms and body image between individual and team sport adolescent athletes during the COVID-19 pandemic. J. Eat. Disord. 2022; 10(1): 119. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmirapu A, Brady-Van den Bos M: Disordered eating in female Indian students during the Covid-19 pandemic: The potential role of family. Int. J. Eat. Disord. 2023; 56(1): 143–150. Publisher Full Text\n\nPerry M, Watson L, Hayden L, et al.: Using body neutrality to inform eating disorder management in a gender diverse world. Lancet Child Adolesc. Health. 2019; 3(9): 597–598. PubMed Abstract \| Publisher Full Text\n\nThornborrow T, Evans EH, Tovee MJ, et al.: Sociocultural drivers of body image and eating disorder risk in rural Nicaraguan women. J. Eat. Disord. 2022; 10: 133. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Medical Association: World Medical Association Declaration of Helsinki. JAMA. 2013; 310(20): 2191. Publisher Full Text\n\nGoicochea-Palomino EA: 180 university students_perception of body image_eating disorders.xlsx. Dataset. figshare. 2023. Publisher Full Text" }	[ { "id": "205819", "date": "06 Oct 2023", "name": "Hatice Colak", "expertise": [ "Reviewer Expertise Eating disorders", "gastroıntestinal system 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\nTable 1 and Table 2 almost hav esame information. That is why Table 1 can be removed.\n\nPlease check if “SPSS v24” is correct or not. Or should be SPSS 24?\n\nNormally, you need to calculate the sample size before starting the study. For university students, 180 people is usually not enough data for cross-sectional studies. Also, since it was conducted in a single faculty, it cannot be generalized to all university students. At this point, indicate if a sample size calculation has been made or report the method by which you included the number of participants.\n\nFigure 1 should be excluded because the explanation for this figure is written in the text.\n\nI am uncertain about the comprehensibility of figure 2. Which groups were the significance observed between?\n\nSome statistical data are not shown in the table but in the text. I think this causes confusion and is more difficult to understand and analyze, so it would be good to show the analysis of statistics that are not given in a table. For example these parts;\n“Only gender was a predictor of body image (β=-0.342_0.129, 95%CI: -0.597 to -0.087) in university students during hybrid education (p=0.010). “\n\n“Although most of the participants answered that they never vomit after eating (80%,144/180) or feel like vomiting afterwards (72.2%, 130/180) …………. perceived them as too thin. We found no association between body image and eating disorders (p=0.662).”\n\nWe found no association between body image and eating disorders (p=0.661).\n\nIn addition to this, there is no need to show number of participants, enough percent. Clarify like this (80%,144/180) à (%80)\n\nYou mentioned that it was the first study, but there are a lot of studies that were done in the covid period or in the post covid period. If you think that only peruda was the first, you should research it thoroughly and make it clear. Otherwise, you need to remove this statement.\n\nAt the same time, it would be better for flow to give the strengths of the study with limitations at the end of the text.\n\nI think it will not contribute to the literature in this form. I don't think the way the discussion is written is clear and adequate. These significant relationships could be explained in more detail and causally.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-912
https://f1000research.com/articles/12-210/v1	24 Feb 23	{ "type": "Research Article", "title": "Fractional spinal anesthesia and systemic hemodynamics in frail elderly hip fracture patients", "authors": [ "Fredrik Olsen", "Mathias Hård af Segerstad", "Keti Dalla", "Sven-Erik Ricksten", "Bengt Nellgård", "Mathias Hård af Segerstad", "Keti Dalla", "Sven-Erik Ricksten", "Bengt Nellgård" ], "abstract": "Background: Systemic haemodynamic effects of intrathecal anaesthesia in an aging and frail population has not been well investigated. We examined the systemic haemodynamics of fractional spinal anaesthesia following intermittent microdosing of a local anaesthetic and an opioid. Methods: We included 15 patients aged over 65 with significant comorbidities, planned for hip fracture repair. Patients received a spinal catheter and cardiac output monitoring using the LiDCOplus system. All measurements were performed prior to start of surgery. Invasive mean arterial pressure (MAP), cardiac index (CI), systemic vascular resistance index (SVRI), heart rate and stroke volume index (SVI) were registered. Two doses of bupivacaine 2.25 mg and fentanyl 15 µg were administered with 25-minute intervals. Hypotension was defined as a fall in MAP by >30% or a MAP <65 mmHg. Results: The incidence of hypotension was 30%. Hypotensive patients (n=5) were treated with low doses of norepinephrine (0.01-0.12 µg/kg/min). MAP showed a maximum reduction of 17% at 10 minutes following the first dose. CI, systemic vascular resistance index and stroke volume index decreased by 10%, 6%, and 7%, respectively, while heart rate was unchanged over time. After the second dose, none of the systemic haemodynamic variables were affected. Conclusions: Fractional spinal anaesthesia administered prior to surgery induced a minor to moderate fall in MAP, mainly caused by a reduction in cardiac output, induced by systemic venodilation, causing a fall in venous return. Our results are contrary to the widely held belief that hypotension is mainly the result of a reduction of systemic vascular resistance.", "keywords": [ "Spinal Anesthesia", "hip fracture surgery", "cardiac output", "hypotension", "elderly patients" ], "content": "Introduction\n\nA hip fracture in a frail elderly patient poses a major anesthesiologic challenge as these patients are mostly presented off-hours and many have comorbidities.1 The 30-day mortality among hip fracture patients is as high as 6-10%.2 Many factors have been associated with mortality, including time to start-of-surgery,3 cementation of hemi- or total arthroplasty,4 male sex,5 and preoperative morbidity assessed by the American Society of Anaesthesiologist (ASA) risk score and Nottingham Hip Fracture Score (NHFS).6,7 Preoperative cardiology consulting, however, rarely affects surgical management, but could alter anesthesiologic management.8\n\nThe peri-operative anaesthesia strategy for the management of the frail hip fracture patient differs worldwide: where many centers give general anaesthesia, while particularly in northern Europe, neuraxial anaesthesia is the preferred technique. However, both techniques frequently induce hypotension, requiring fluid resuscitation and/or the need for vasopressors.9 Perioperative hypotension is a problem predisposing patients to organ hypoperfusion with consequences such as myocardial injury, delirium and renal failure.9,10 The physiological origin of the hypotension is unclear, but many anesthesiologists believe that the decrease of systemic vascular resistance (SVR) is the main cause of hypotension,11 while others believe that hypotension is caused by a fall in cardiac output12 or a combination of both.\n\nIn our hospital, we routinely administer neuraxial anaesthesia for hip fracture surgery. We have a vast experience with this technique and in the present study we utilized the continuous spinal anaesthesia (CSA) technique to elucidate the hemodynamic response to fractional dosing without the influence of surgical manipulation. The use of CSA is well recognized to have a limited effect on hypotension.13 It also allows us to study the hemodynamics in a prolonged period prior to surgery, minimizing the potential for other factors such as positioning, sedation and surgical stress to influence the measurements in a way a single shot spinal does not. The hemodynamics were monitored with LiDCOplus. LiDCOplus is a validated system in which a lithium dilution technique is used to calibrate the arterial pulse contour analysis.14 The LiDCO system has previously been used in hip fracture patients in the perioperative setting.15–17 The advantage of LiDCO compared to other invasive hemodynamic devices is that lithium can be injected in a peripheral venous cannula and then lithium concentration is captured through a standard 20G arterial cannula. Thus, we could avoid more invasive monitoring using central venous catheters, femoral arterial cannula, or the Swan-Ganz catheter.\n\nThe aim of the present study was to investigate the systemic haemodynamic response to fractional spinal anaesthesia, in a group of elderly and comorbid patients with hip fracture, using the LiDCOplus system to monitor pre-surgical haemodynamic changes over time.\n\n\nMethods\n\nEthical approval was granted by the Gothenburg Regional Ethical Review Board (Dnr 2020-05684). During the study period we screened daily for patients planned for hip fracture surgery and these were identified through the theatre planning software (Orbit, TietoEVRY, Espoo, Finland). Inclusion criteria were: 1) patient with hip fracture, 2) >65 years of age, 3) ASA ≥2, 4) scheduled for neuraxial anaesthesia and 5) mentally fit to give written informed consent or permission by next-of-kin in cognitive impaired patients. Exclusion criteria were: a) lithium or anticoagulation medication, b) planned for general anaesthesia, c) ongoing atrial fibrillation, d) if surgery was delayed >72 hours, e) lack of informed consent and f) patient agitation requiring intermittent sedation. The study was carried out in accordance with the Declaration of Helsinki (2000). Finally, inclusion rate was dependent and affected by the primary investigator’s availability and the operative capacity, by recruiting consecutive cases within these limitations we aspired to recruit a representative selection of patients with regards to self-reported gender and level of comorbidity. NHFS was calculated, the scale going from 1-10 with higher numbers correlated to a higher 30-day mortality.6,18 ASA grade along with defined laboratory values, demographic data and chronic disease were also recorded after study inclusion.\n\nAfter arriving to the preoperative area, patients were given 5 liters of oxygen on a face mask and ECG and pulse-oximetry monitoring was started. Oral premedication with standardized doses of paracetamol (1 g) and oxycodone (5 mg) was given orally, followed by the placement of a venous 18G cannula in an antecubital vein and a radial arterial catheter (20G). The patient was also given a fascia iliaca compartment (FIC) block, or an ultrasound guided femoral nerve block with ropivacaine 3.5 mg/mL 20-40mL, to minimize discomfort and to avoid sedation or systematic analgesia when positioning for the neuraxial block. In addition, the LiDCOplus (LiDCO Group Plc, London, England) system was set up and calibrated according to manufacturer’s instructions. Calibration was performed with 0.3-0.45 mmol lithium chloride injection based on body weight. After calibration and baseline parameter registration, the LiDCOplus system provided cardiac output variables and based on these and the invasive blood pressure, haemodynamic variables could be derived.\n\nFollowing aseptic skin preparation of the lumbar area, a subarachnoid puncture by a 18G Tuohy needle was performed either between the L2 - L3 or the L3 - L4 interspaces, preferably using a mid-line approach. An intrathecal catheter 20G was then inserted 4-5 cm into the intrathecal space. This technique of a continuous spinal anaesthesia (CSA) was performed on all patients by a dedicated physician (FO).\n\nAn intrathecal mixture (10 mL) containing 1.5 mg/mL bupivacaine and 10 μg/mL fentanyl was prepared. Intrathecal anaesthesia was induced by giving 1.5 mL (2.25 mg of bupivacaine and 15 μg of fentanyl) of the mixture, followed by a second 1.5 mL injection after 25 min (i.e., a total intrathecal dos of 4.5 mg of bupivacaine and 30 μg of fentanyl). Sensory level was monitored by “cold spray”. Hemodynamic recordings were documented every five minutes up until 45 minutes after initial intrathecal dose when research monitoring was also terminated. The patient was then operated upon in the pre-planned time slot and was further managed at the discretion of the attending anesthetist.\n\nMean arterial blood pressure (MAP) was maintained, when needed, with a norepinephrine infusion to target a MAP >65 mmHg or to avoid more than 30% decline in MAP from baseline. In addition to SaO2 and ECG, the following parameters were recorded: cardiac index (CI), stroke volume index (SVI), systemic vascular resistance index (SVRI), systolic arterial pressure, (SAP), diastolic arterial pressure (DAP) and nor-epinephrine doses over time. Finally, effective arterial elastance (EA) was calculated by the formula; 0.9×SAP/SV.19 For indexing parameters, the Du Bois and Du Bois formula for body surface area (BSA) was used.20\n\nStatistical analysis was performed with RStudio for Mac (version 1.2.5033) and GPower version 3.1.9.6 (Franz Faul, Universität Kiel, Germany) to determine sample size. Normality was assessed with Shapiro-Wilk test prior to deciding appropriate variation testing, one-way repeated measures ANOVA for normally distributed and Friedmann test for non-normal distributions. For repeated measures, ANOVA was utilized to study changes in haemodynamic variables over time. A p-value <0.05 was considered statistically significant. A sample size of n=13 patients for the repeated measured ANOVA was needed to have an 80% power (β=0.20) for detection the effect size F=0.25 (α=0.05).\n\n\nResults\n\nThe clinical trial profile is shown in Figure 1. A total of 24 patients were eligible for the study inclusion, of whom 15 were finally included. Two patients withdrew consent, two patients were excluded due to logistical issues, two patients were excluded for agitated dementia and finally, three patients were excluded due to having new onset of neurological symptoms. Hypertension was the dominant comorbidity present in 73% of patients, while dementia was found in 47%. Prior or present malignancy was found in 33% of patients. Further demographic data of the studied patients are summarized in Table 1. The study population had a median age of 89 years and consisted primarily of women (12/15). The median ASA grade was 3 (range 2-4) and the median NHFS score was 5 (range 4-7). None of the patients had significant arrythmias during the experimental procedure and none required vasopressor support prior to the first intrathecal dose of the bupivacaine/fentanyl mixture was given.\n\nSensory and motor functions were assessed, revealing that all patients had satisfactory levels of sensory block at minimum (>Th 12) documented with sensation to cold or painful reaction to flexion of the hip, which is the same assessment used for the single shot spinal prior to surgery. In mentally intact patients, all had a temperature discrimination demonstrated by a sensory block <Th 8 level. Further, we noticed a high incidence of retained motor function after the initial neuraxial 1.5 mL dose (2.25 mg bupivacaine and 15 μg fentanyl), possibly due to a less dense blockade.\n\nData on systemic haemodynamics are shown in Figures 2–7. MAP, CI, SVRI, SVI and arterial elastance were all found to have normal distribution at each point of measurement according to Shapiro-Wilk’s test. After applying the one-way repeated measures ANOVA test, MAP, SVRI, SVI and CI all showed significant variance over time. Thus, MAP decreased by 17% from baseline with the lowest mean noted at 10 min after the first intrathecal dose was given. CI was reduced by 10% also after 10 minutes. SVRI showed a 6% reduction from baseline found directly after the intrathecal dose was given. SVI dropped by 7% with a lowest mean value at 10 minutes after anaesthesia induction and, finally, heart rate decreased non-significantly by 3% from baseline. Elastance did not show significant variation over time as measured by ANOVA. The largest reduction from the baseline value was -10% at 5 min after the initial spinal dose. One third (5/15) of the patients required norepinephrine infusion either to maintain a MAP>65 mmHg or to avoid a decrease by >30% from the baseline. The largest dose used was 0.12 μg/kg/min (Table 2).\n\n\nDiscussion\n\nThe main findings of the present study were that the hemodynamic aberrations after induction of fractional spinal anesthesia were minor to moderate, with a maximal fall in CI and MAP of 10-17%, 10 minutes following the first dose. After the second dose, no further changes in hemodynamics were seen arguing for a hemodynamic stability using CSA.\n\nInterestingly, the maximal fall in SVRI was 6% and appeared early after the first dose with no further fall after the second dose. Thus, the MAP reduction was less than expected and the major contributor to the fall in MAP was a fall in CI, which explained almost 60% of the MAP reduction. This leads us to the conclusion that fractional spinal anaesthesia, as described in the present study, induces a vasodilation more prominent in systemic venous capacitance vessels, which decreases venous return and cardiac preload, as reflected by a decrease in SVI.\n\nIn this study, we defined hypotension as having a MAP <65 mmHg or a decrease of MAP >30% from the baseline level, a definition previously used in other studies.21–23 Using this definition, the incidence of hypotension following single-shot spinal anaesthesia, has previously been described as being 28-69%, which is considerably higher than noted in the present study.24,25 Hypotension from a spinal anaesthesia has been described by Butterworth26 as a decrease in systemic vascular resistance and central venous pressure as a result of the sympathetic block, with vasodilation of both systemic resistance vessels as well as venous capacitance vessels, the latter causing redistribution of central blood volume to the lower extremities and splanchnic beds and thus impaired venous return. In the present study, MAP decreased by 17%, CI by 10%, SVRI by 6% and SVI by 7% at 10 minutes after the initial intrathecal injection. Our data imply that the MAP reduction can not be explained by a reduction in SVRI alone. The proportionally larger fall in CI implicates vasodilation more on the venous capacitance vessels, leading to reduced venous return and subsequently a fall in CI and MAP. These findings are in line with the findings of Jakobsson et al., showing that a single shot of spinal anaesthesia (15 mg bupivacaine) induced hypotension in 50% of the patients, mainly caused by a fall in CI (20%) and SVI (15%).12 Nakasuji et al., on the other hand, found that the hypotension seen after a single-shot spinal anaesthesia (10 mg bupivacaine), in elderly patients, was mainly caused by systemic vasodilation and a fall in SVRI.11 Our data exhibited a significantly smaller fall in SVRI than described by Salinas et al.,27 possibly due to lower dosing achieved with intermittent dosing and subsequently lower levels of sympathetic block. Effective arterial elastance (Ea) incorporates all elements of total LV afterload, including vascular resistance, arterial compliance and characteristic impedance.28 The finding that Ea was not affected by fractional spinal anaesthesia also indicates that the driving force of hypotension in the present study was systemic venodilation.\n\nSingle-shot neuraxial anaesthesia is predominantly used around the world in in this population of patients. Dosages have decreased over time and in our clinical routine, we rarely administer more than 2.5 mL of mixtures of local anesthetics and opioids. The injection time the mixture is given may have an effect on the hypotension severity and we await studies addressing this topic. In an interesting study by Szucs et al.29 they used the “up-and-down” method described by Dixon and Massey in 1969 to find the lowest intrathecal dose of local anesthetic to provide adequate anaesthesia for a hip fracture operation.30 They concluded that 0.24 mL of 5 mg/mL isobaric bupivacaine was enough as a single dose but still recommended a dose of 0.4 mL or more i.e. 2 mg. A more recent meta-analysis concluded that 6.5 mg of bupivacaine seems sufficient for hemodynamic stability, patient comfort and adequate motor block.31 This is in concert with the present investigation where we gave dosages of 2.25 mg of isobaric bupivacaine although diluted to 1.5 mg/mL with sodium chloride and fentanyl. The volume in this study was larger, being 1.5 mL of the above-stated-mixture. However, most clinicians would not consider administering such low doses with the eminent risk of blockade failure and forcing the attending anaesthesiologist to give general anaesthesia, an alternative considered worse at the preoperative evaluation.\n\nAn attractive alternative to single-shot spinal is the continuous spinal anaesthesia (CSA) a technique described in the 1940’s32 and improved by catheter insertion.33 CSA has been associated with fewer incidents of hypotension per se and less severe episodes of hypotension.34 This led us to revisit the technique at our clinic, as we have many hip fracture patients and many of them with variable severity of aortic stenosis.35–37 We confirm the result of Minville et al. that by carefully giving a CSA we can avoid severe hypotensive incidents even in frail patients.34 A side effect of this lower dosing was a less prominent motor blockage, also noted in the present investigation.\n\nLiDCOplus is a semi-invasive, (needing an arterial catheter), validated method enabling us to register haemodynamic variables without the need for central venous- and/or Swan-Ganz catheters. The LiDCO system is therefore less invasive and does not require a higher degree of invasiveness than is routinely included in the normal clinical management of hip fracture patients at our hospital. To our knowledge, the golden standard technique for measuring cardiac output is the use of a Swan-Ganz catheter with thermodilution, but this technique is hardly doable in a cohort of frail elderly hip fracture patients. Calibrated cardiac output (CO) using LiDCO monitoring is relatively easy and quick to start in patients already in need of arterial cannulation and provides a deeper insight into perioperative haemodynamic changes.\n\nWith only 15 included patients the generalizability of our findings may be limited. We were restricted by the dynamic nature of running an effective emergency operating list, but also by the prevalence of patient anticoagulation therapy limiting the use of neuraxial anaesthesia in general and indwelling spinal catheter in particular. Haemodynamic monitoring with LiDCOplus gives us estimations of cardiac output after calibration where all other haemodynamic variables are derived from CO from the pulse power analysis and invasive blood pressure together with the heart rate. A strength of our study is that the cohort was very homogenous with similar age, fracture type, sex and surgical procedure in a single tertiary orthopedic center. Demographically our patients were older with an elevated risk of higher mortality and morbidity versus the average hip fracture population (Table 1). All patients were included from the acute list and were operated upon during office hours.\n\nRegistry data of the Swedish hip fracture population demonstrates an average age of 82 and around 2/3 being female.2 Thus, our patient cohort was seven years older and thereby probably frailer than the average hip fracture patient. A surrogate marker for frailty in this investigation was ASA grading (mean value 3) and the NHFS score (mean value 5), both slightly elevated versus the Swedish average.2 Both scales assess comorbidity in various ways and are further used as prognostic scores for mortality risk in the perioperative and postoperative phase, like 30-day mortality.4,7 Therefore, we claim to have succeeded in finding a patient population with high comorbidity, speculatively having a higher risk for intraoperative hypotension than the average hip fracture population.\n\n\nConclusions\n\nThe initial blood pressure decline after fractional spinal anaesthesia is caused mainly by systemic venodilation, reducing venous return to the heart and followed by a consequent fall in CO and MAP. The incidence of hypotension was low and only one third of the patients needed nor-epinephrine infusions all at modest doses, highest infusion rate was 0.12 μg/kg/min nor-epinephrine. Our results contradict the idea of spinal anaesthesia-induced hypotension as being solely a result of a fall in SVRI due to loss of sympathetic vascular tone.\n\n\nAuthors contributions\n\nFO: Planned and designed the study. Established intrathecal catheter and set up LidCO monitoring, collected and analyzed data. Wrote the first draft.\n\nMHaS: Planned and designed the study and revised the manuscript\n\nKD: Revised the manuscript\n\nSER: Planned and designed the study and revised the manuscript\n\nBN: Planned and designed the study and revised the manuscript", "appendix": "Data availability\n\nOpen Science Framework: Fractional anesthesia lidco, https://doi.org/10.17605/OSF.IO/XAGBY. 38\n\nThis project contains the following underlying data:\n\n- fractionspinallidcoFO.csv\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nOpen Science Framework: TREND checklist for “Fractional spinal anesthesia and systemic hemodynamics in frail elderly hip fracture patients”, https://doi.org/10.17605/OSF.IO/D98VG. 39\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nWe are grateful for the assistance and support of the nursing staff at the Department of Anaesthesia and Intensive Care at Sahlgrenska University Hospital/Mölndal. This study was supported by Swedish State Support for Clinical Research (LUA-ALF).\n\nA version of this manuscript is available as a preprint on ResearchSquare (https://doi.org/10.21203/rs.3.rs-1053831/v1).\n\n\nReferences\n\nLunde A, Tell GS, Pedersen AB, et al.: The Role of Comorbidity in Mortality After Hip Fracture: A Nationwide Norwegian Study of 38,126 Women With Hip Fracture Matched to a General-Population Comparison Cohort. Am. J. Epidemiol. 2019; 188: 398–407. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRikshöft: Rikshöft 2018. Rikshöft Årsrapport.2018. Accessed December 16, 2020. Reference Source\n\nKristiansson J, Hagberg E, Nellgård B: The influence of time-to-surgery on mortality after a hip fracture. Acta Anaesthesiol. Scand. 2020; 64: 347–353. PubMed Abstract \| Publisher Full Text\n\nOlsen F, Hård Af Segerstad M, Nellgård B, et al.: The role of bone cement for the development of intraoperative hypotension and hypoxia and its impact on mortality in hemiarthroplasty for femoral neck fractures. Acta Orthop. 2020; 91: 293–298. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAslan A, Atay T, Aydoğan NH: Risk factors for mortality and survival rates in elderly patients undergoing hemiarthroplasty for hip fracture. Acta Orthop. Traumatol. Turc. 2020; 54: 138–143. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMoppett IK, Parker M, Griffiths R, et al.: Nottingham Hip Fracture Score: longitudinal and multi-centre assessment. Br. J. Anaesth. 2012; 109: 546–550. PubMed Abstract \| Publisher Full Text\n\nJohansen A, Tsang C, Boulton C, et al.: Understanding mortality rates after hip fracture repair using ASA physical status in the National Hip Fracture Database. Anaesthesia. 2017; 72: 961–966. PubMed Abstract \| Publisher Full Text\n\nSmeets SJM, van Wunnik BPW , Poeze M, et al.: Cardiac overscreening hip fracture patients. Arch. Orthop. Trauma Surg. 2020; 140: 33–41. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBeecham G, Cusack R, Vencken S, et al.: Hypotension during hip fracture surgery and postoperative morbidity. Ir. J. Med. Sci. (1971-). 2020; 1–10.\n\nJang WY, Jung J-K, Lee DK, et al.: Intraoperative hypotension is a risk factor for postoperative acute kidney injury after femoral neck fracture surgery: a retrospective study. BMC Musculoskelet. Disord. 2019; 20: 1–5.\n\nNakasuji M, Suh SH, Nomura M, et al.: Hypotension from spinal anesthesia in patients aged greater than 80 years is due to a decrease in systemic vascular resistance. J. Clin. Anesth. 2012; 24: 201–206. PubMed Abstract \| Publisher Full Text\n\nJakobsson J, Kalman SH, Lindeberg-Lindvet M, et al.: Is postspinal hypotension a sign of impaired cardiac performance in the elderly? An observational mechanistic study. Br. J. Anaesth. 2017; 119: 1178–1185. PubMed Abstract \| Publisher Full Text\n\nAlmeida CR, Cunha P, Vieira L, et al.: Low-dose spinal block for hip surgery: A systematic review. Trends Anaesth. Crit. Care. 2022; 45: 5–20. Publisher Full Text\n\nPearse RM, Ikram K, Barry J: Equipment review: An appraisal of the LiDCOTM plus method of measuring cardiac output. Crit. Care. 2004; 8: 1–6.\n\nWiles MD, Whiteley WJ, Moran CG, et al.: The use of LiDCO based fluid management in patients undergoing hip fracture surgery under spinal anaesthesia: neck of femur optimisation therapy-targeted stroke volume (NOTTS): study protocol for a randomized controlled trial. Trials. 2011; 12: 1–8. Publisher Full Text\n\nMoppett IK, Rowlands M, Mannings A, et al.: LiDCO-based fluid management in patients undergoing hip fracture surgery under spinal anaesthesia: a randomized trial and systematic review. Br. J. Anaesth. 2015; 114: 444–459. PubMed Abstract \| Publisher Full Text\n\nBartha E, Arfwedson C, Imnell A, et al.: Towards individualized perioperative, goal-directed haemodynamic algorithms for patients of advanced age: observations during a randomized controlled trial (NCT01141894). Br. J. Anaesth. 2016; 116: 486–492. PubMed Abstract \| Publisher Full Text\n\nMaxwell MJ, Moran CG, Moppett IK: Development and validation of a preoperative scoring system to predict 30 day mortality in patients undergoing hip fracture surgery. Br. J. Anaesth. 2008; 101: 511–517. PubMed Abstract \| Publisher Full Text\n\nJozwiak M, Millasseau S, Richard C, et al.: Validation and critical evaluation of the effective arterial elastance in critically ill patients. Crit. Care Med. 2019; 47: e317–e324. PubMed Abstract \| Publisher Full Text\n\nBurton RF: Estimating body surface area from mass and height: theory and the formula of Du Bois and Du Bois. Ann. Hum. Biol. 2008; 35: 170–184. PubMed Abstract \| Publisher Full Text\n\nKouz K, Hoppe P, Briesenick L, et al.: Intraoperative hypotension: Pathophysiology, clinical relevance, and therapeutic approaches. Indian J. Anaesth. 2020; 64: 90.\n\nSessler DI, Khanna AK: Perioperative myocardial injury and the contribution of hypotension. Intensive Care Med. 2018; 44: 811–822. PubMed Abstract \| Publisher Full Text\n\nSessler DI, Bloomstone JA, Aronson S, et al.: Perioperative quality initiative consensus statement on intraoperative blood pressure, risk and outcomes for elective surgery. Br. J. Anaesth. 2019; 122: 563–574. PubMed Abstract \| Publisher Full Text\n\nWood R, White S: Anaesthesia for 1131 patients undergoing proximal femoral fracture repair: a retrospective, observational study of effects on blood pressure, fluid administration and perioperative anaemia. Anaesthesia. 2011; 66: 1017–1022. PubMed Abstract \| Publisher Full Text\n\nCritchley LAH: Hypotension, subarachnoid block and the elderly patient. Anaesthesia. 1996; 51: 1139–1143. Publisher Full Text\n\nButterworth J: Physiology of spinal anesthesia: what are the implications for management? Reg. Anesth. Pain Med. 1998; 23: 370–373. PubMed Abstract \| Publisher Full Text\n\nSalinas FV, Sueda LA, Liu SS: Physiology of spinal anaesthesia and practical suggestions for successful spinal anaesthesia. Best Pract. Res. Clin. Anaesthesiol. 2003; 17: 289–303. PubMed Abstract \| Publisher Full Text\n\nSegers P, Stergiopulos N, Westerhof N: Relation of effective arterial elastance to arterial system properties. Am. J. Phys. Heart Circ. Phys. 2002; 282: H1041–H1046. Publisher Full Text\n\nSzucs S, Rauf J, Iohom G, et al.: Determination of the minimum initial intrathecal dose of isobaric 0.5% bupivacaine for the surgical repair of a proximal femoral fracture: a prospective, observational trial. Eur. J. Anaesthesiol. 2015; 32: 759–763. PubMed Abstract \| Publisher Full Text\n\nDixon WJ, Massey FJ Jr: Introduction to statistical analysis.1951.\n\nMessina A, Frassanito L, Colombo D, et al.: Hemodynamic changes associated with spinal and general anesthesia for hip fracture surgery in severe ASA III elderly population: a pilot trial. Minerva Anestesiol. 2013; 79: 1021–1029. PubMed Abstract\n\nLemmon WT: A method for continuous spinal anesthesia: A preliminary report. Ann. Surg. 1940; 111: 141–144. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTuohy EB: The use of continuous spinal anesthesia: utilizing the ureteral catheter technic. J. Am. Med. Assoc. 1945; 128: 262–264. Publisher Full Text\n\nMinville V, Fourcade O, Grousset D, et al.: Spinal anesthesia using single injection small-dose bupivacaine versus continuous catheter injection techniques for surgical repair of hip fracture in elderly patients. Anesth. Analg. 2006; 102: 1559–1563. PubMed Abstract \| Publisher Full Text\n\nCollard CD, Eappen S, Lynch EP, et al.: Continuous spinal anesthesia with invasive hemodynamic monitoring for surgical repair of the hip in two patients with severe aortic stenosis. Anesth. Analg. 1995; 81: 195–198. PubMed Abstract\n\nFuzier R, Murat O, Gilbert M, et al.: Continuous spinal anesthesia for femoral fracture in two patients with severe aortic stenosis. Vol 25. 2006; pp. 528–531.\n\nLópez MM, Guasch E, Schiraldi R, et al.: Continuous spinal anaesthesia with minimally invasive haemodynamic monitoring for surgical hip repair in two patients with severe aortic stenosis. Rev. Bras. Anestesiol. 2016; 66: 82–85. Publisher Full Text\n\nOlsen F: Fractional anesthesia lidco.2023, January 11. Publisher Full Text\n\nOlsen F: Fractional anesthesia lidco.2023, January 27. Publisher Full Text" }	[ { "id": "164674", "date": "11 Apr 2023", "name": "Luigi La Via", "expertise": [ "Reviewer Expertise Anesthesia", "Critical Care" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI read with great interest the manuscript by Olsen et al. on the effect of fractional spinal anesthesia on systemic hemodynamics in frail elderly hip fracture patients. The authors investigated the changes in haemodynamic variables caused by two doses of intrathecal bupivacaine 2.25 mg and fentanyl 15 µg in 15 patients aged over 65. The paper is sound and well written. However, there are some minor issues to be addressed.\nIntroduction\nWhen you state \"where many centers give general anaesthesia, while particularly in northern Europe, neuraxial anaesthesia is the preferred technique\" you should add an appropriate reference (for example, Neuman et al. (2021)1).\n\nSpinal anesthesia is also the preferred technique for other kind of surgeries2,3. Please briefly discuss and add these 2 references.\n\nResults\nPlease explain why \"two patients were excluded due to logistical issues\".\nDiscussion\nPlease discuss the results of the recently published meta-analysis on the investigated topic4.\nConclusion\nConsidering the limitations of this study, I would state \"The initial blood pressure decline after fractional spinal anaesthesia MIGHT BE caused mainly by systemic venodilation\".\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "9626", "date": "04 May 2023", "name": "Fredrik Olsen", "role": "Author Response", "response": "Thank you for taking the time and effort to review the paper, your comments are addressed individually in the following text and are reflected in the revisions of the updated draft. Introduction When you state \"where many centers give general anaesthesia, while particularly in northern Europe, neuraxial anaesthesia is the preferred technique\" you should add an appropriate reference (for example, Neuman et al. (2021)1). Reference added. Spinal anesthesia is also the preferred technique for other kind of surgeries2,3. Please briefly discuss and add these 2 references. These two references seem only peripherally relevant to this study, and for the sake of brevity will not be included Results Please explain why \"two patients were excluded due to logistical issues\". All participants had a preliminary time scheduled for their surgery and we performed the test protocol prior to this. If a slot in the program opened up the protocol stated that surgery would not be delayed to finish the study protocol. This was to keep the departments program flowing as smoothly as possible and to minimise potential harm to our patients. Discussion Please discuss the results of the recently published meta-analysis on the investigated topic4. The reference #31 has been changed to Messina 2022, which I suspect was the reference it was supposed to be all along. Nice observation from the reviewer! Conclusion Considering the limitations of this study, I would state \"The initial blood pressure decline after fractional spinal anaesthesia MIGHT BE caused mainly by systemic venodilation\". Edited in the revised draft to reflect reviewers comments" } ] } ]	1	https://f1000research.com/articles/12-210
https://f1000research.com/articles/12-196/v1	20 Feb 23	{ "type": "Systematic Review", "title": "Prevalence of carpal tunnel syndrome among dentists: a systematic review and meta-analysis", "authors": [ "Evangelos Kostares", "Georgia Kostare", "Michael Kostares", "Maria Kantzanou", "Georgia Kostare", "Michael Kostares", "Maria Kantzanou" ], "abstract": "Purpose: To estimate the prevalence of carpal tunnel syndrome (CTS) among dentists and the effect of possible moderators on it. Methods: A systematic literature search (Medline and Embase databases) was conducted independently by two reviewers. Quality assessment was performed. The pooled prevalence with 95% confidence intervals (CI) was estimated. Outlier and influential analysis were conducted. Moderator analysis was performed in order the effect of categorical and continuous variables on the estimated prevalence to be investigated. Results: In total, ten eligible studies (3,547 participants) were finally included in this meta-analysis. The overall prevalence of CTS among dental surgeons was estimated as 9.87% (95%CI 6.84%-14.03%) with significant heterogeneity between studies. No study was identified as influential. Potential sources of heterogeneity were not identified through the moderator analysis. In the subgroup analysis the prevalence was 12.47% (95%CI 6.38%-22.95%) for the group identified as having CTS through medical history and at least clinical examination or electrodiagnostic testing and 8.56% (95%CI 5.53%-13.01%) among those who identified solely through questionnaire (previously diagnosed). Conclusions: Our findings are important to provide the pooled prevalence of CTS among dentists. Our results were based on highly heterogeneous studies. Two of them were estimated as high quality (low risk of bias) and the remaining ones as moderate quality (moderate risk of bias). Our study reports a considerable prevalence, consequently, significance of awareness among dental surgeons regarding the etiology of this issue is more than necessary. More studies need to be conducted that could guide researchers in order this issue to be fully investigated.", "keywords": [ "carpal tunnel syndrome", "CTS", "entrapment neuropathy", "dentists", "dental surgeons", "prevalence", "meta-analysis" ], "content": "Introduction\n\nCarpal tunnel syndrome (CTS) is one of the most frequent and well-studied entrapment neuropathies. It occurs as the median nerve is being compressed and damaged through its passage within the narrow osteofibrous canal (carpal tunnel).27,34 Among the great variety of symptoms it may occur, pain, paraesthesias (especially, during the night) and dysaesthesias in the distribution of the median nerve (in the first three and a half digits of the affected hand), are the predominant ones. During the evolution of this neuropathy, all the relevant muscles (flexor pollicis brevis, abductor pollicis brevis, opponens pollicis) which are innervated by branches of the median nerve are being atrophied and weakened, resulting the patient’s declined functionality.9,14,23,24 Regarding the type of diagnostic method, a combination of a comprehensive patient’s history as well as a thorough clinical examination (including Tinel, Phalen and Durkan’s tests) seems to be the most value option available. Other advanced procedures (electrodiagnostic tests) such as the nerve conduction studies, which can validate nerve dysfunction with extreme sensitivity, are usually performed in treatment decision making.27 Many risk factors have been identified throughout the years such as obesity, diabetes, hypothyroidism, pregnancy, lupus erythematosus, Reynaud’s phenomenon however, specific interest exists regarding the occurrence of CTS in certain occupations, such as in the field of dentistry.2,13,20,21 Dental procedures require the use of vibratory tools, strong griping, uncomfortable hand position and the performance of long-lasting repetitive tasks.29 Due to the nature of this occupation, it is expected to have higher rates of CTS occurrence.31 Mainly, the prevalence of CTS is estimated between 4% and 5% of the general middle-aged population.12 Therefore, we conducted a systematic review and meta-analysis in order to gain a reliable estimation regarding the prevalence of CTS among dentists.\n\n\nMethods\n\nThis review is reported in line with the PRISMA guidelines.38\n\nA literature search of Medline (PubMed search engine) and Embase (Scopus search engine) database was conducted through inception up to December 16th, 2022, following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines.28 The literature search was independently performed by two reviewers, using the following algorithm: (carpal tunnel syndrome OR CTS OR entrapment neuropathy OR median nerve compression) AND (“dentists” OR “dental surgeon”).\n\nThe reference lists of all identified eligible studies were evaluated by both reviewers for potentially missed articles from the initial literature search. Following the aforementioned procedure, all studies were stored in the Zotero reference management software (version 6.0.18) and the duplicate citations were removed.36 The remaining articles were independently screened by two investigators to identify studies that met the pre-determined inclusion criteria. The study selection was conducted in two stages. First, article titles and abstracts were reviewed and those that did not meet our inclusion/exclusion criteria were removed. Secondly, the full texts of the remaining articles were retrieved and evaluated. If an absence in studies selection procedure was notified, the final decision was reached by team consensus.\n\nArticles that examined specifically the prevalence rates of CTS among dentists were included. Only observational studies written in English language were inserted with no restriction on publication date. Case reports, case series with less than ten participants, review articles, clinical trials, animals studies, letters to the editor, books, expert opinion, conference abstracts, studies with no full-text available, studies not written in English language, articles reported solely the prevalence of CTS’ symptoms, studies regarding dental laboratory technicians and dental hygienists were excluded. In articles with overlapping populations, the most recent or most complete publication was considered eligible. The following variables were obtained from each study: the first author’s name, year of publication, study design, continent of origin, study period, total number of patients, proportion of males, mean age, participants with CTS and diagnostic procedures.\n\nQuality appraisal was independently performed by two investigators using the National Heart, Lung, and Blood Institute (NHLBI) Quality Assessment Tools. The NHLBI quality assessment tool for Observational Cohort and Cross-Sectional Studies was employed. Individual studies were assessed for potential flaws in accordance the study methodology or the conduct of each survey that could jeopardize internal validity. For each of the fourteen questions, investigators could select one of the following answers: “yes”, “no”, “cannot determine” (e.g. data were unclear or contradictory) or “not reported” (e.g. missed data) or “not applicable” (e.g. not relevant question regarding this type of study). Study quality was defined as “low”, “moderate” or “high” risk of bias.25\n\nStatistical analysis was carried out using RStudio (version: 022.12.0+353) software (RStudio Team (2022)).32 The meta-analysis was conducted through metafor package.33 The DerSimonian and Laird random-effects model was used to estimate the pooled prevalence and its respective 95% confidence intervals (CI). Logit transformation was performed. Heterogeneity presence between studies was evaluated through visual inspection of the forest plot and by using the Cochran’s Q statistic and its respective p value. The Higgins I2 statistic and its respective 95% CI were used for quantifying the magnitude of true heterogeneity in effect sizes. An I2 value of 25%, 50%, and 75% indicated low, moderate, and high heterogeneity, respectively. To determine if the potential outlying effect sizes (as evaluated in the forest plot) were also influential, screening for externally studentized residuals with z-values larger than two in absolute value and leave-one-out diagnostics were performed.34 Due to high heterogeneity remaining, a moderator analysis was performed. In the conducted subgroup analysis, the continent of origin and the diagnostic procedure (verified during the implementation of each study or previously diagnosed) were chosen as the categorical moderators on effect sizes. In the performed meta-regression analysis with continuous variables, the year of publication and the proportion of males were assessed as moderators on effect sizes. Owing to the limited availability of data (less than ten studies for each covariate) regarding other variables (e.g mean age, obesity, diabetes, hypothyroidism, pregnancy, autoimmune diseases), these data were not included in this analysis.17 Unless otherwise stipulated, the statistical significance was established at p=0.05 (two-tailed). Tests to evaluate publication bias, such as Egger’s test,10 Begg’s test5 and funnel plots, were developed in the context of comparative data. They assume studies with positive results are more frequently published than studies with negative results, however in a meta-analysis of proportions there is no clear definition or consensus about what a positive result is.4 Therefore, publication bias in this current meta-analysis was assessed qualitatively.\n\n\nResults\n\nAs reported in the relevant section (Criteria for study selection and data extraction), manuscript that were only related to the prevalence of CTS’ symptoms (such as the study conducted from Prasad, D.A. et al.30) and studies regarding dental hygienists (such as the study conducted from Anton D., et al3 and Cherniack M., et al.8) were excluded. In total, ten (n=10) eligible studies (3,547 participants) were finally included in this analysis (see Figure 1 for the PRISMA flow chart).37 The descriptive characteristics of the incorporated research are presented in Table 1. All articles were published from 2001 to 2021 (conducted from 1997 to 2019). All of them were found to be of cross-sectional design. Most studies were contemplated in Asia (Iran, Lebanon, Saudi Arabia, n=6), followed by America (USA, Brazil, n=2) and Europe (Czech, Germany, n=2). The average percent of males was 54.22% while the mean age of participants ranged from 35 years to 46.4 years (median=38.2 years). Lastly, two studies were estimated as high quality (low risk of bias) and the remaining ones as moderate quality (moderate risk of bias).\n\nA random-effects model analysis yielded an initial overall CTS prevalence of 9.87% (95%CI 6.84%-14.03%) with significant heterogeneity between studies I2=90.55% (95%CI 79.29%-97.31%, p<0.01) (Figure 2). The influence diagnostics are presented in Figure 3. The forest plot illustrating the results of the leave-one-out analysis is presented in Figure 4. As per them, no study was identified as being influential. In other words, there was no study identified that was capable of turning the effect of the analysis into some direction.\n\nAbbreviations used—rstudent: studentized deleted residuals; dffits: DFFITS values; cook.d: Cook’s distances; cov.r: covariance ratio; tau2.del: estimated τ2 values; QE.del: estimated Cochran’s Q values.\n\nTo investigate the effect of potential risk factors in the heterogeneity, a moderator analysis was performed. Forest plots of the subgroup analysis are illustrated in Figure 5 and Figure 6. The prevalence was 7.02% (95%CI 1.44%-27.99%) among studies conducted in Europe, 8.06% (95%CI 2.88%-20.60%) among studies conducted in America and higher among those conducted in Asia (11.71%) (95%CI 8.25%-16.35%). The prevalence was 12.47% (95%CI 6.38%-22.95%) for the group identified as having CTS through medical history and at least clinical examination or electrodiagnostic testing and 8.56% (95%CI 5.53%-13.01%) among those who identified solely through questionnaire (previously diagnosed, self-reported). Heterogeneity remained high in the subgroup analysis by both continent of origin and type of diagnostic procedure. In the meta-regression analysis with continuous variables, the year of publication and the proportion of males, no statistically significant (positive or inverse) modification was found as presented in Table 2.\n\n\nDiscussion\n\nCTS is one of the most frequently diagnosed entrapment neuropathy, accounting for high disability among different occupations.24 To date, only systematic reviews regarding musculoskeletal disorders (which is a general term referring to injuries in muscles, ligaments, tendons, nerves, blood vessels, bones and joints) among dental healthcare providers exist in the scientific literature. One indicative example of the above is the meta-analysis conducted by Chenna et al, in which the authors combined data from 88 studies and found out that seven out of ten dental healthcare workers (including dentist, dental students, dental hygienist and dental auxiliaries) experienced a musculoskeletal disorder. As per the location of the disorders, the most affected sites were the neck, the back, the lower back, the shoulder, the upper back and the wrist with a prevalence of 51%, 50%, 46%, 41%, 35% and 31%, respectively.7\n\nThis is the first attempt to calculate the prevalence of CTS among dentists, through a systematic review. We do not have previously published data to compare our pooled estimate with. The prevalence of the existing observational studies varies considerably in the scientific literature. Our study provides evidence for 9.87% (95%CI 6.84%-14.03%) prevalence of CTS among dentists. Overall, the results are based on highly heterogeneous articles. Through the moderator analysis, we do not manage to identify sources of heterogeneity between the eligible studies. In the subgroup analysis, the prevalence was 12.47% (95%CI 6.38-22.95) for the group identified as having CTS through medical history and at least clinical examination or electrodiagnostic testing while, the prevalence was 8.56% (95%CI 5.53%-13.01%) among those who identified solely through questionnaire (previously diagnosed, self-reported). It should be noted that the latter pooled estimate may underestimate the dental surgeons with CTS due to the diagnostic method used. In matter of other oral health care professionals, Anton D., et al, found an 8.4% prevalence of CTS among 95 dental hygienists3 while, Cherniack M., et al, calculated a 14.9% prevalence among 94 dental hygienists.8 In a recent meta-analysis, Epstein S., et al, combining data from seven eligible studies, found a 9% (95%CI 5%-16%) prevalence of CTS among 2449 physicians (from different specialties including general surgeons, plastic surgeons, orthopedic surgeons and urologists) with significant heterogeneity between studies I2=94.5%.11 All the aforementioned results align with our estimation, providing more evidence that CTS can be considered as an occupational hazard among health care professionals.\n\nIt should be noted that there are many treatments available for this entrapment neuropathy. Patients developing mild or moderate symptoms should be treated conservatively through splinting, local corticosteroid injection or oral prednisone. Other treatments available, such as physical therapy, have not proven their effectiveness yet. Surgical decompression is the treatment of choice for patients developing severe symptoms.16,35 Our study reports a considerable prevalence, consequently, the importance of awareness among dentists, regarding the etiology of this issue is more than necessary. More research should be conducted in order to explore the association between CTS among dentists and potential risk factors, such as gender, obesity, endocrine conditions (hypothyroidism, acromegaly and diabetes) and trauma.\n\nThe main strength was the comprehensive methodology applied for literature search, study selection, specific inclusion/exclusion criteria, screening for eligibility, quality assessment and pooling analysis of prevalence data from ten studies. Nonetheless, the present study had several limitations. It should be noted that the unidentified heterogeneity remained on high levels, therefore, the results should be interpreted with caution. The highly heterogenous outcomes across the included studies were expected due to the nature of this type of studies. Owing to the limited availability of data (less than ten studies for each covariate) regarding variables such as mean age, obesity, diabetes, hypothyroidism, pregnancy, autoimmune diseases, these data were not included in this analysis. Lastly, only observational studies written in English language were included resulting in the occurrence of reporting bias.\n\n\nConclusion\n\nIn conclusion, the prevalence of CTS among dentists is estimated at 9.87% (95%CI 6.84%-14.03%). Our results were based on highly heterogeneous studies. Sources of heterogeneity were not identified. Our findings point to several directions for future research. Therefore, further studies, both prospective and retrospective need to be conducted in order this issue to be fully investigated.", "appendix": "Data availability\n\nFigshare: Main characteristics and data outcome of the included studies. https://doi.org/10.6084/m9.figshare.22087427.v1. 37\n\nFigshare: PRISMA_2020_checklist.pdf. figshare. https://doi.org/10.6084/m9.figshare.22069034.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\nAlhusain FA, Almohrij M, Althukeir F, et al.: Prevalence of carpal tunnel syndrome symptoms among dentists working in Riyadh. Ann. Saudi Med. 2019; 39(2): 104–111. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlKhodier H, Alqahtani M, Alshenaifi A, et al.: Prevalence of First Carpometacarpal Joint Osteoarthritis and Carpal Tunnel Syndrome Among Dentists in Saudi Arabia. Cureus. 2022; 14: e23876. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAnton D, Rosecrance J, Merlino L, et al.: Prevalence of musculoskeletal symptoms and carpal tunnel syndrome among dental hygienists. Am. J. Ind. Med. 2002; 42(3): 248–257. PubMed Abstract \| Publisher Full Text\n\nBarker TH, Migliavaca CB, Stein C, et al.: Conducting proportional meta-analysis in different types of systematic reviews: a guide for synthesisers of evidence. BMC Med. Res. Methodol. 2021; 21(1): 189. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBegg CB, Mazumdar M: Operating characteristics of a rank correlation test for publication bias. Biometrics. 1994; 50(4): 1088–1101. PubMed Abstract \| Publisher Full Text\n\nHaghighi B, Khosropanah H, Vahidnia F, et al.: Association of Dental Practice as a Risk Factor in the Development of Carpal Tunnel Syndrome. J. Dent. 2013; 14(1): 37. [Accessed 28 Jan. 2023]. Reference Source\n\nChenna D, Pentapati KC, Kumar M, et al.: Prevalence of musculoskeletal disorders among dental healthcare providers: A systematic review and meta-analysis. F1000Res. 2022; 11: 1062. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCherniack M, Brammer AJ, Nilsson T, et al.: Nerve conduction and sensorineural function in dental hygienists using high frequency ultrasound handpieces. Am. J. Ind. Med. 2006; 49(5): 313–326. Publisher Full Text\n\nde Jesus Júnior LC , Tedesco TK, Macedo MC, et al.: A self-report joint damage and musculoskeletal disorders data among dentists: a cross-sectional study. Minerva Dent. Oral Sci. 2018; 67(2): 62–67. PubMed Abstract \| Publisher Full Text\n\nEgger M, Smith GD, Schneider M, et al.: Bias in meta-analysis detected by a simple, graphical test. BMJ. 1997; 315(7109): 629–634. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEpstein S, Sparer EH, Tran BN, et al.: Prevalence of Work-Related Musculoskeletal Disorders Among Surgeons and Interventionalists. JAMA Surg. 2018; 153(2): e174947. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGarcia JO, Scott D, Parikh P, et al.: Understanding carpal tunnel syndrome. JAAPA. 2022; 35(12): 19–26. PubMed Abstract \| Publisher Full Text\n\nGenova A, Dix O, Saefan A, et al.: Carpal Tunnel Syndrome: A Review of Literature. Cureus. 2020; 12: e7333. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHamann C, Werner RA, Franzblau A, et al.: Prevalence of carpal tunnel syndrome and median mononeuropathy among dentists. J. Am. Dent. Assoc. 2001; 132(2): 163–170. PubMed Abstract \| Publisher Full Text\n\nHaghighat A, Khosrawi S, Kelishadi A, et al.: Prevalence of clinical findings of carpal tunnel syndrome in Isfahanian dentists. Advanced. Biomed. Res. 2012; 1: 13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHernández-Secorún M, Montaña-Cortés R, Hidalgo-García C, et al.: Effectiveness of Conservative Treatment According to Severity and Systemic Disease in Carpal Tunnel Syndrome: A Systematic Review. Int. J. Environ. Res. Public Health. 2021; 18(5): 2365. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHandbook-5-1.cochrane.org: 9.6.5.1 Ensure that there are adequate studies.n.d. [Accessed 27 Dec. 2022]. Reference Source\n\nHodacova L, Sustova Z, Cermakova E, et al.: Self-reported risk factors related to the most frequent musculoskeletal complaints among Czech dentists. Ind. Health. 2015; 53(1): 48–55. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJaoude SB, Naaman N, Nehme E, et al.: ‘Work-Related Musculoskeletal Pain among Lebanese Dentists: An epidemiological study. Niger. J. Clin. Pract. 2017; 20: 1002–1009. PubMed Abstract \| Publisher Full Text Reference Source\n\nKhosrawi S, Kelishadi A, Sajadieh S, et al.: Prevalence of clinical findings of carpal tunnel syndrome in Isfahanian dentists. Adv. Biomed. Res. 2012; 1(1): 13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMaghsoudipour M, Hosseini F, Coh P, et al.: Evaluation of occupational and non-occupational risk factors associated with carpal tunnel syndrome in dentists. Work. 2021; 69(1): 181–186. PubMed Abstract \| Publisher Full Text\n\nMeisha DE, Alsharqawi NS, Samarah AA, et al.: Prevalence of work-related musculoskeletal disorders and ergonomic practice among dentists in Jeddah, Saudi Arabia. Clin. Cosmet. Investig. Dent. 2019; 11: 171–179. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMurphy KA, Morrisonponce D: Anatomy, Shoulder and Upper Limb, Median Nerve.2020. Reference SourceReference Source\n\nNewington L, Harris EC, Walker-Bone K: ‘Carpal tunnel syndrome and work’, Best Practice & Research. Clin. Rheumatol. 2015; 29(3): 440–453. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNIH: Study Quality Assessment Tools\|National Heart, Lung, and Blood Institute (NHLBI).2009. [Accessed 15 Dec. 2022]. Reference SourceReference Source\n\nOhlendorf D, Naser A, Haas Y, et al.: Prevalence of Musculoskeletal Disorders among Dentists and Dental Students in Germany. Int. J. Environ. Res. Public Health. 2020; 17(23): 8740. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPadua L, Coraci D, Erra C, et al.: Carpal tunnel syndrome: clinical features, diagnosis, and management. Lancet Neurol. 2016; 15(12): 1273–1284. Publisher Full Text\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. BMJ. 2021; 372: n71. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPejčić N, Petrović V, Marković D, et al.: Assessment of risk factors and preventive measures and their relations to work-related musculoskeletal pain among dentists. Work. 2017; 57(4): 573–593. Publisher Full Text\n\nPrasad D, Appachu D, Kamath V, et al.: Prevalence of low back pain and carpal tunnel syndrome among dental practitioners in Dakshina Kannada and Coorg District. Indian J. Dent. Res. 2017; 28(2): 126–132. PubMed Abstract \| Publisher Full Text\n\nRice VJ, Nindl B, Pentikis JS: Dental Workers, Musculoskeletal CumulativeTrauma, and Carpal Tunnel Syndrome: Who is at Risk? A Pilot Study. Int. J. Occup. Saf. Ergon. 1996; 2(3): 218–233. PubMed Abstract \| Publisher Full Text\n\nRStudio Desktop: 2022. Reference Source\n\nViechtbauer W: Conducting Meta-Analyses in R with the metafor Package. J. Stat. Softw. 2010; 36(3). Publisher Full Text\n\nViechtbauer W, Cheung MW-L: Outlier and influence diagnostics for meta-analysis. Res. Synth. Methods. 2010; 1(2): 112–125. Publisher Full Text\n\nWipperman J, Goerl K: Carpal Tunnel Syndrome: Diagnosis and Management. Carpal Tunnel Syndrome. 2016; 94(12). Reference Source\n\nwww.zotero.org: Zotero\|Your personal research assistant.n.d. [Accessed 15 Dec. 2022]. Reference Source\n\nKostares E, Kostares M, Kostare G, et al.: Main characteristics and data outcome of the included studies.xlsx. [Dataset]. figshare. 2023. Publisher Full Text\n\nKostares E, Kostare G, Kostares M, et al.: PRISMA_2020_checklist.pdf. Dataset. figshare. 2023. Publisher Full Text" }	[ { "id": "163987", "date": "06 Mar 2023", "name": "Essam Ahmed Al‐Moraissi", "expertise": [ "Reviewer Expertise Oral and Maxillofacial Surgery" ], "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 systematic review (SR) assessed the prevalence of CTS among dentists. The study is of interest. However, there are some major revisions that need to be made as follows:\nAbstract: The authors should clearly state the inclusion criteria, as well as the predictor and outcome variables in the abstract. The results of the risk of bias assessment should be included in the results section and not in the conclusion.\nIntroduction: The authors should state the rationale for the study and summarize the results of previous studies on CTS.\nMethod: This SR should be prepared in accordance with PRISMA guidelines and should follow the PRISMA checklist (which is mandatory). The inclusion criteria should be based on PICOS criteria. The authors should clearly define how CTS was diagnosed in the included studies. If the authors estimated proportions or used subgroup analyses, the synthesis of results (statistics) should be clearly explained.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? No\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? No", "responses": [ { "c_id": "9452", "date": "20 Mar 2023", "name": "Ευάγγελος Κωσταρές", "role": "Author Response", "response": "Dear Reviewer, On behalf of all authors, we would like to thank you for your kind words and valuable input regarding our manuscript. Please find a point-to-point response to each of your comments. Comment #1 This systematic review (SR) assessed the prevalence of CTS among dentists. The study is of interest. Response #1 Thank you for your remark. Yet, please note that our attempt exceeds the spectrum of a systematic review by utilizing statistical methods (meta-analysis) to summarize the results of the studies identified through the systematic review of the available literature. Comment #2 Abstract: The authors should clearly state the inclusion criteria, as well as the predictor and outcome variables in the abstract. The results of the risk of bias assessment should be included in the results section and not in the conclusion. Response #2 Thank you for your comment. Taking into consideration your input, the abstract has been reformed accordingly. Yet, if additional modifications should be performed, please provide us with some guidance to amend the relevant section as soon as possible. Comment #3 Introduction: The authors should state the rationale for the study and summarize the results of previous studies on CTS. Response #3 Thank you for your comment. Taking into consideration your input, the rationale, the results of other studies as well as the aim of the current study have been altered and stated in the two last paragraphs of the introduction. Yet, please note that within this section, the results of other studies on CTS are only being reported as findings, since they are being analyzed in the results and discussion section later within the same document as well as given that they are not “systematic” or “meta-analytic” data. Comment #4 Method: This SR should be prepared in accordance with PRISMA guidelines and should follow the PRISMA checklist (which is mandatory). Response #4 Thank you for your comment. Please be aware that without any change of the original manuscript, the requested information can be found in two sections of the manuscript: (a) the first line of the Methods and (b) The Data availability – Underlying data. Additionally, the PRISMA flow chart is illustrated as Figure 1. Yet, in case there are additional requirements set by the PRISMA guidelines that oblige the authors on reporting additional information that are not being included, please, provide us with a response to conform our manuscript as soon as possible. Comment #5 The inclusion criteria should be based on PICOS criteria. Response #5 Thank you for your comment. To the best of our knowledge, the PICO(S) criteria, are being used in a way of formulating one or several research questions (Aslam, S., & Emmanuel, P. (2010). Formulating a researchable question: A critical step for facilitating good clinical research. Indian journal of sexually transmitted diseases and AIDS, 31(1), 47–50. https://doi.org/10.4103/0253-7184.69003). Therefore, their main use is related to the basis on which the whole research will be made while the inclusion criteria, are more associated with the methodology that will be followed for data identification, selection and extraction given that different criteria may apply in various occasions (such as in times where language restrictions exist). In such scenario, manuscripts that would be included in the original pool can be excluded if these restrictions are valid and are being reported in the methodology to produce a repetitive result. Therefore, even if not mentioned, our inclusion criteria were based on PICO(S) criteria and their selection was not only justified through them but through the methodology that was used as reported in “Criteria for study selection and data extraction” subsection. Yet, if additional information should be included, please provide us with some guidance to amend the relevant subsection as soon as possible. Comment #6 The authors should clearly define how CTS was diagnosed in the included studies. Response #6 Thank you for your comment. Please be aware that without any change of the original manuscript, the requested information can be found in Table 1 (Column 10 – Diagnosis). Nevertheless, a brief explanation has been included in “Search results and characteristics of the included studies” subsection (line 6-8). Comment #7 If the authors estimated proportions or used subgroup analyses, the synthesis of results (statistics) should be clearly explained. Response #7 Thank you for your comment. Please be aware that without any change of the original manuscript, the requested information can be found in the Statistical Analysis and Results sections. To the best of our understanding, by re-evaluating the provided in-text explanations, the methodology that was used (that may be referred to as the standard one utilized for the conduction of proportional meta-analyses) as well as the content of other meta-analyses available in the literature (in form of a brief comparison), we strongly believe that the information reported in this manuscript are adequate to enable a reader with a medium or less experience in meta-analyses to understand the approach that was followed. Yet, in case you believe that additional information should be included, please, provide us with a response to conform our manuscript as soon as possible. Hopefully, our changes as well as the responses provided above will be sufficient to accept our effort. Best regards, The corresponding author" } ] } ]	1	https://f1000research.com/articles/12-196
https://f1000research.com/articles/12-524/v1	22 May 23	{ "type": "Study Protocol", "title": "Immunoexpression of E-cadherin in oral potentially malignant disorders, oral squamous cell carcinoma and its correlation with clinicopathological parameters", "authors": [ "Padmashri Kalmegh", "Alka Hande", "Madhuri Gawande", "Swati Patil", "Archana Sonone", "Aayushi Pakhale", "Alka Hande", "Madhuri Gawande", "Swati Patil", "Archana Sonone", "Aayushi Pakhale" ], "abstract": "The most common malignancy of the head and neck region is “oral squamous cell carcinoma” (OSCC) because of its low survival rate and the increasing incidence in some geographic areas. The process of invasion and metastasis, which is noted in most cancers, requires loss of cell-to-cell attachment. It is therefore important to identify a marker that would help in the identification of lesions that would acquire the ability to transform into OSCC. Cell-to-cell adhesion and cell motility are monitored by E-cadherin; its loss is associated with OSCC progression. Early detection, proper analysis, and correct handling of oral potentially malignant disorder (OPMD) are beneficial to preventing its malignant progression. Thus, the purpose of the present study is to identify the expression and determine the role of E-cadherin in OPMD and OSCC.", "keywords": [ "Cell adhesion", "E-cadherin", "Oral potential malignant disorder", "Oral squamous cell carcinoma", "Malignant transformation", "Immunoexpression", "Immunohistochemistry" ], "content": "Introduction\n\nCarcinoma is the second highest cause of morbidity after cardiovascular disorders in developed countries.1 Globally, oral squamous cell carcinoma (OSCC) positions sixth amongst all categories of carcinoma. India has the highest number of OSCC cases which contributes to one-third of the total OSCC cases all over the world. This causes a huge challenge for developing countries.2 Per annum, around 75,000-80,000, new cases and 50,000-55,000 deaths from OSCC are reported in India. OSCC is the commonest type of carcinoma in India and it contributes the highest incidence among Asian countries This rise in the prevalence of OSCC is an alarming sign for community health.3,4 According to the American Joint Committee on Cancer, in India, 65-75% of patients are detected in the Stage III-IV of OSCC, which is significantly higher than in western countries. As these cases are detected in the advanced phase, the treatment becomes unmanageable. The five to ten-year survival rate of OSCC patients has increased to nearly 50% over the previous few decades.5,6 OSCC has become the major cause of morbidity and mortality in the Indian population due to the habit of chewing smokeless tobacco and areca nuts.7\n\nIt has been observed that oral potentially malignant disorders (OPMDs) can progress into OSCC.1,8,9 Early detection, proper analysis, and correct handling of OPMDs are beneficial to prevent their malignant progression.1 There are numerous cutting-edge diagnostic methods that can predict the progression and assess the malignant transformation of OPMDs. In order to reduce the death rate and enhance the patient’s general health, the management of OPMD is crucial. The World Health Organization (WHO) defined OPMDs as the presence of a lesion or disease that poses a risk of malignancy at the time of initial diagnosis or at a later period. The prevalence of OPMDs, in the general population, is 1-5%.8 In the current era, five percent of cases of OPMD are detected under the age of 30 years.9\n\nAccording to WHO, OSCC is classified into well-differentiated, moderately differentiated and poorly differentiated; upon which the management and the life span of the patient depends.10,11 It has been observed that aggressive OSCC is preceded by the pre-invasive stage which continues for a long duration. In the preinvasive stage, along with the progression of the condition, disturbances at the molecular level occur which leads to loss of cellular cohesion.\n\nCellular adhesion can be defined as a process by which cells intermingle and attach to neighboring cells via specific molecules on the cellular surface. For the proper functioning of multicellular organisms, cellular adhesion is necessary. This is regulated by cell adhesion molecules (CAMs), including cellular interactions, cellular migrations, cell cycle and cellular signalling as well as in morphogenesis during the development and regeneration of tissue.12,13 CAMs play a crucial role in various pathological conditions including inflammatory disorders, infectious and autoimmune diseases oncogenesis.14 In carcinomas, transformed cells of the epithelial layer grows abnormally, breaking through the basement membrane which leads to invasion of the underlying mesenchyme. In determining cancer prognosis, the rate of differentiation and the grade of invasiveness of carcinomas has significant value.14,15 Atypical genetic expression is intricately involved in cell proliferation and genetic elements that regulate cellular adhesion and cellular motility are features of tumour start and progression.16\n\nCAMs are transmembrane Ca2+-dependent homophilic adhesion receptors. On the basis of structure, four main families of CAMs are identified: integrin, selectin, immunoglobulin gene (IgG-like superfamily), and cadherin. In addition to serving as a molecular bond, it also has a role in maintaining cell-to-cell connections, controlling cell polarity, morphogenesis, cell recognition, and cell sorting during development.17 E-cadherin (E-Cadh) is located on the epithelial cell surface in the areas of intercellular contacts known as “adherens junction”, a major molecule in cell-to-cell adhesion.18,19 In addition, this highly conserved molecule has a significant role in tumor development, progression and its malignant cell transformation. The association between decreased expression of E-cadh and invasive properties may not be a general phenomenon, since the invasiveness of cells and dedifferentiation of carcinomas can occur even in the presence of E-Cadh.19\n\nE-Cadh glycoprotein encoded by CDH 1 gene represents a calcium-dependent intercellular adhesion molecule; its loss is related to invasion and metastasis in various cancer models. Thus, CDH 1 gene is considered a tumor suppressor gene. The cytoplasmic moiety of E-cadh binds to β- and γ-catenin, linked to the cytoskeleton through α-catenin, and the moiety present extracellularly is a calcium-dependent receptor that maintains the homophilic interactions. The first discovered classical cadherins were the E-cadh family, which prompts intercellular adhesion.20 Reduced E-cadh expression is indicative of its function in preventing tumor invasion/metastasis. It has been observed that the probability of metastasis is increased when the activity of tumor differentiation decreased.21–23\n\nWith this premise, we designed the following protocol for the evaluation of E-cadh immunoexpression in OPMDs, OSCC, and its correlation with clinicopathological parameters.\n\n\nProtocol\n\nTo evaluate E-cadh immunoexpression in OPMDs and OSCC.\n\n\n\n1. To assess the E-Cadh immuno-expression in OPMDs.\n\n2. To evaluate the E-Cadh immuno-expression in OSCC.\n\n3. To compare and co-relate the E-Cadh expression between the OPMDs, OSCC and normal mucosa.\n\n4. To assess the immuno-expression of E-cadh in OSCC and its correlation with clinicopathological parameters.\n\n\nMethods\n\nIn this cross-sectional study, a total of 90 samples will be divided into three groups: The groups are as follows:\n\nGroup I: 30 samples with OPMD.\n\nGroup II: Thirty samples with OSCC.\n\nGroup III: Thirty samples with normal oral mucosa (NOM).\n\nInclusion and exclusion criteria\n\nFor the OPMD group, we will select 30 samples of erythroplakia, leukoplakia, oral submucous fibrosis (OSMF), and oral lichen planus. A total of 30 samples of the NOM, which will be used as controls, will be collected from the gingival and vestibular mucosa after the extraction of the impacted teeth. The 30 samples of OSCC that have undergone surgical treatment the most frequently and have been histopathologically and clinically diagnosed will be considered in the eligibility criteria for the study.\n\nPatients having a past history of oral malignancy, recurrent or distant disease and pre-operative chemotherapy, radiation therapy, and the study will not include patients who have undergone surgery, with the exception of biopsy.\n\nIn demographic data clinical presentation, habits and their duration, histopathological findings, and operative details will be noted in detail. Following disease-free survival for four to five years, follow-up information will be gathered. Each hematoxylin and eosin-stained tissue section will be closely examined at low power magnification (100×).\n\nAfter receiving approval from the institutional ethical committee [DMIMS (DU)/IEC/2022/759] at the Datta Meghe Institute of Medical Sciences, Deemed to be University, Sawangi (M), Wardha, Maharashtra, India, this study will be conducted at the Department of Oral Pathology and Microbiology, Sharad Pawar Dental College and Hospital.\n\nA total sample size of 90 samples will be chosen after clinical and histopathological confirmation. For surgically collected OSCC samples from 2005 to 2018 in this institute, the department’s archives will be searched. A total of 90 cases will be selected randomly; study Group I – OPMD (30 samples), Group II – OSCC (30 samples), and Group III – Normal mucosa (30 samples). OSCC patients will be histopathologically graded using Broder’s grading system.\n\nUsing the Single Proportion Formula and the 2% prevalence of OPMD and OSCC cases in the Oral Pathology and Microbiology outpatient department, the sample size is determined as follows:\n\nWhere,\n\nZα/22 - The level of significance at 5%\n\ni.e. 95% confidence interval = 1.96\n\np - Sample showing positive E-cadherin expression focally in small group\n\ncells in the basal layer of epithelium = 35% = 0.35\n\nE - Error of margin = 10% = 0.10\n\nn = 1.962 × 0.35 × (1-0.35)/0.102\n\nn = 87.39\n\nn = 90\n\nFormula reference - Cochran W. G. et al. (1977)24\n\nImmunostaining\n\nA paraffin block having a suitable mass of tumor and an acceptable amount of normal tissue will be selected. On Poly-L-Lysine coated slides, sections with thicknesses of 3 μm will be cut and placed. For de-paraffinization, sections are placed in the xylene solution. Sections will be rehydrated by subjecting them to descending concentrations of alcohol. In order to wash sections, tap water will be used. The washing time for sections in distilled water is 60 seconds. After washing all the sections will be transferred to a Coplin jar containing the retrieval buffer solution. The solution which is used for antigen retrieval will be composed of 30 mL of retrieval solution in 1500 mL of distilled water for 15 to 20 minutes in the pressure cooker. Cooling will be done at room temperature.\n\nSections will be dipped once in distilled water. Sections will be washed with Tris buffer solution for at least five minutes at room temperature. This step is repeated thrice. For peroxidase blocking a mixture of 3,5 hydrogen peroxide and methanol will be used for 30 minutes. Tris buffer solution will be used for washing the sections three times for five minutes each. E-cadh will be applied at room temperature for one hour. Once again washing of sections will be done in Tris buffer solution thrice five minutes each. Visualization will be performed by utilizing a labelled polymer for 30 minutes at room temperature. For washing the sections Tris buffer solution will be used thrice for five minutes.\n\nThe application of the DAB (3,3′-diaminobenzidine) substrate will be done for 15 to 20 minutes. The working DAB solution is comprised of the following – one mL of DAB buffer and 25 μL of DAB concentrate. This time, washing of sections will be done by Tris buffer, for 15-20 minutes. Sections will be cleaned in distilled water. For counterstaining, Mayer’s hematoxylin will be used, which will be done for five minutes. Again, the washing of sections will done under tap water. These will be dried; once the sections are dried, they will be mounted in DPX. After that, examination will be carried out under a microscope.\n\nExpected results\n\nThe current study will determine the expression of E-cadh by immunohistochemistry in OPMD and OSCC. There will be variation in the immunoexpression of E-cadh amongst the OPMD and OSCC. Further, there will be a positive correlation of E-cadh immunoexpression with the clinicopathological parameters of OSCC.\n\nResults will be published in an indexed journal.\n\nThe proposed study is under process.\n\n\nDiscussion\n\nCurrent research has directed to awareness of the mechanism of cellular adhesion. It observed that a strong intercellular adhesion is necessary for the formation of tight tissue sheets. This is one of the classical properties of the generation of epithelia. In order to fulfill the accomplishment of cell-to-cell adhesion, the composition and function of cells of the epithelium must be strongly maintained. E-cadh is a type I superfamily member and a calcium-dependent transmembrane glycoprotein. It is also known as the invasion or tumor suppressor gene which is important for regulating the structural integrity and organization of the epithelium. It is determined by the CDH-1 gene that is located on chromosome 16q-22.1.25–27\n\nGurkiran Kaur et al. (2009) assessed the E-Cadh expression in OSCC by immunohistochemistry (IHC) in 37 samples. They concluded that “E-Cadh expression is reduced in advanced cases of OSCC and inverse relation between loss of cell differentiation, cellular adhesion and E-Cadh”.28\n\nYuwanati et al. (2011) investigated E-cadh expression in OPMD and OSCC by in vivo study. There was evidence that during the progression of OPMD to OSCC, a significant role was played by E-cadh. In order to compare E-cadh expression in normal healthy mucosa, OPMD and OSCC, 20 cases of each OPMD and OSCC were included in the study. After they studied 40 cases in context to patient’s age, sex, tumor location, TNM classification, and clinical stage, it was concluded that decreased expression of E-cadh may serve as a helpful indicator for the transformation of OPMD into OSCC.29\n\nvon Zeidler et al. (2014) observed the function of E-cadh as a significant biomarker in the malignant tranformation of OPMDs. For E-cadh immunostaining, they excised specimens surgically diagnosed with OPMDs and OSCC. They concluded that dysplastic changes in the epithelium increase the risk of malignant transformation, which decreases E-cadh expression and therefore E-cadh can be utilized as a potential biomarker to find lesions with a high risk of developing into cancer.30\n\nAkhtar et al. (2016) investigated the diagnostic and prognostic significance of E-Cadh in OSCC metastasis. This was an –in vivo study, where biopsies and specimens were evaluated for all premalignant lesions as well as OSCC. Since it was an in vivo trial, alterations brought on by therapy and patient follow-up were also examined. Their research determined that E-cadh immunohistochemistry stains can be used to measure the invasiveness and recurrence of OSCC. Also, they noted that the biomarker E-cadh may be used in upcoming studies on early detection, diagnosis, and patient survival.31\n\nKushwaha et al. (2019) evaluated the immunohistochemical and histopathological expression of E-cadh in OSCC. In addition, the evaluation of qualitative and quantitative expressions of E-cadh and its correlation with the number of tumor cells was done. There were 20 samples of well-differentiated OSCC, 20 samples of moderately differentiated OSCC, and 10 samples of normal mucosa. The result was that there was a notable reduction in E-cadh expression as OSCC advanced from well-differentiated to higher histological grades. The authors further concluded that E-cadh was a reliable indicator for evaluating the invasiveness of OSCC.32\n\nIlangani Sathish et al. (2020) evaluated E-Cadh expression in OPMD, in a prospective study. Their study was intended to evaluate the relationship amid the E-Cadh expression & OPMD. For this, 50 patients were chosen, of whom 25 samples were sent for histological analysis and the other 15 patients underwent real-time PCR to assess E-Cadh expression. According to their analysis, “high E-Cadh expression in OPMD & also concluded reduction in E-Cadh expression can be employed as tumor marker which might determine the progression of normal and OPMD to OSCC”.33\n\nThe study to be conducted is an in-vitro, cross-sectional study, and its application in clinical practice is recommended.\n\nThe immunoexpression of E-cadh may grow from NOM to leukoplakia to OSCC.\n\nA review of the literature reveals a correlation between the expression of E-cadh and the development of OPMDs and OSCC cases. In the case of OPMDs, the disease’s development and prognosis might be tracked. The management of immunotherapy for different patients might be considered based on the E-cadh immunoexpression status.\n\n\nEthical considerations\n\nEthical approval was received from the institutional ethical committee at the “Datta Meghe Institute of Medical Sciences, Deemed to be University, Sawangi (M), Wardha, Maharashtra, India”.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: STROBE checklist for “Immunoexpression of E-Cadherin in oral potentially malignant disorders, oral squamous cell carcinoma and its correlation with clinicopathological parameters”, https://doi.org/10.5281/zenodo.7715199.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe acknowledge the support of laboratory technicians from Department of Oral and Maxillofacial Pathology and Microbiology, Sharad Pawar Dental College and Hospital, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha.\n\n\nReferences\n\nGeorge A, Sreenivasan BS, Sunil S, et al.: Potentially malignant disorders of oral cavity. Oral Maxillofac Pathol J. 2011 Jan 1; 2(1): 95–100.\n\nGupta B, Bray F, Kumar N, et al.: Associations between oral hygiene habits, diet, tobacco and alcohol and risk of oral cancer: A case–control study from India. Cancer Epidemiol. 2017 Dec 1; 51: 7–14. PubMed Abstract \| Publisher Full Text\n\nSharma S, Satyanarayana L, Asthana S, et al.: Oral cancer statistics in India on the basis of first report of 29 population-based cancer registries. J. Oral Maxillofac. Pathol. 2018 Jan; 22(1): 18–26. PubMed Abstract \| Publisher Full Text\n\nKhandekar SP, Bagdey PS, Tiwari RR: Oral cancer and some epidemiological factors: A hospital based study. Indian J. Community Med. 2006 Jul 1; 31(3): 157.\n\nVeluthattil AC, Sudha SP, Kandasamy S, et al.: Effect of hypofractionated, palliative radiotherapy on quality of life in late-stage oral cavity cancer: a prospective clinical trial. Indian J. Palliat. Care. 2019 Jul; 25(3): 383–390. PubMed Abstract \| Publisher Full Text\n\nZhou J, Huang S, Wang L, et al.: Clinical and prognostic significance of HIF-1α overexpression in oral squamous cell carcinoma: a meta-analysis. World J. Surg. Oncol. 2017 Dec; 15: 1–8. Publisher Full Text\n\nAcharya S, Rahman S, Hallikeri K: A retrospective study of clinicopathological features of oral squamous cell carcinoma with and without oral submucous fibrosis. J. Oral Maxillofac. Pathol. 2019; 23(1): 162. PubMed Abstract \| Publisher Full Text\n\nAmagasa T, Yamashiro M, Uzawa N: Oral premalignant lesions: from a clinical perspective. Int. J. Clin. Oncol. 2011 Feb; 16(1): 5–14. PubMed Abstract \| Publisher Full Text\n\nWarnakulasuriya S, Johnson NW, Van der Waal I: Nomenclature and classification of potentially malignant disorders of the oral mucosa. J. Oral Pathol. Med. 2007 Nov; 36(10): 575–580. PubMed Abstract \| Publisher Full Text\n\nSchipper JH, Frixen UH, Behrens J, et al.: E-cadherin expression in squamous cell carcinomas of head and neck: inverse correlation with tumor dedifferentiation and lymph node metastasis. Cancer Res. 1991 Dec 1; 51(23_Part_1): 6328–6337.\n\nThompson LD: Squamous cell carcinoma variants of the head and neck. Curr. Diagn. Pathol. 2003 Dec 1; 9(6): 384–396. Publisher Full Text\n\nTrzpis M, McLaughlin PM, de Leij LM , et al.: Epithelial cell adhesion molecule: more than a carcinoma marker and adhesion molecule. Am. J. Pathol. 2007 Aug 1; 171(2): 386–395. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWinter MJ, Cirulli V, Briaire-de Bruijn IH, et al.: Cadherins are regulated by Ep-CAM via phosphaditylinositol-3 kinase. Mol. Cell. Biochem. 2007 Aug; 302: 19–26. PubMed Abstract \| Publisher Full Text\n\nWinter MJ, Nagelkerken B, Mertens AE, et al.: Expression of Ep-CAM shifts the state of cadherin-mediated adhesions from strong to weak. Exp. Cell Res. 2003 Apr 15; 285(1): 50–58. PubMed Abstract \| Publisher Full Text\n\nOzawa M, Baribault H, Kemler R: The cytoplasmic domain of the cell adhesion molecule uvomorulin associates with three independent proteins structurally related in different species. EMBO J. 1989 Jun; 8(6): 1711–1717. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang J, Weinberg RA: Epithelial-mesenchymal transition: at the crossroads of development and tumor metastasis. Dev. Cell. 2008 Jun 10; 14(6): 818–829. PubMed Abstract \| Publisher Full Text\n\nBehrens J, Mareel MM, Van Roy FM, et al.: Dissecting tumor cell invasion: epithelial cells acquire invasive properties after the loss of uvomorulin-mediated cell-cell adhesion. J. Cell Biol. 1989 Jun; 108(6): 2435–2447. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHedrick L, Cho KR, Vogelstein B: Cell adhesion molecules as tumour suppressors. Trends Cell Biol. 1993 Feb 1; 3(2): 36–39. Publisher Full Text\n\nGall TM, Frampton AE: Gene of the month: E-cadherin (CDH1). J. Clin. Pathol. 2013 Nov 1; 66(11): 928–932. PubMed Abstract \| Publisher Full Text\n\nThompson LD: Squamous cell carcinoma variants of the head and neck. Curr. Diagn. Pathol. 2003 Dec 1; 9(6): 384–396. Publisher Full Text\n\nZaid KW: Immunohistochemical assessment of E-cadherin and β-catenin in the histological differentiations of oral squamous cell carcinoma. Asian Pac. J. Cancer Prev. 2014; 15(20): 8847–8853. PubMed Abstract \| Publisher Full Text\n\nBringuier PP, Umbas R, Schaafsma HE, et al.: Decreased E-cadherin immunoreactivity correlates with poor survival in patients with bladder tumors. Cancer Res. 1993 Jul 15; 53(14): 3241–3245. PubMed Abstract\n\nDeng QW, He BS, Pan YQ, et al.: Roles of E-cadherin (CDH1) genetic variations in cancer risk: a meta-analysis. Asian Pac. J. Cancer Prev. 2014; 15(8): 3705–3713. PubMed Abstract \| Publisher Full Text\n\nCochran WG: Sampling techniques. John Wiley & Sons; 1977.\n\nLindblom A, Rotstein S, Skoog L, et al.: Deletions on chromosome 16 in primary familial breast carcinomas are associated with development of distant metastases. Cancer Res. 1993 Aug 15; 53(16): 3707–3711. PubMed Abstract\n\nDoğan A, Wang ZD, Spencer J: E-cadherin expression in intestinal epithelium. J. Clin. Pathol. 1995 Feb 1; 48(2): 143–146. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuta H, Noguchi M, Kanai Y, et al.: E-cadherin gene mutations in signet ring cell carcinoma of the stomach. Jpn. J. Cancer Res. 1996 Aug; 87(8): 843–848. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKaur G, Carnelio S, Rao N, et al.: Expression of E-cadherin in primary oral squamous cell carcinoma and metastatic lymph nodes: an immunohistochemical study. Indian J. Dent. Res. 2009 Jan 1; 20(1): 71–76. PubMed Abstract \| Publisher Full Text\n\nMehendiratta M, Solomon MC, Boaz K, et al.: Clinico-pathological correlation of E-cadherin expression at the invasive tumor front of Indian oral squamous cell carcinomas: An immunohistochemical study. J. Oral Maxillofac. Pathol. 2014 May; 18(2): 217–222. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nvon Zeidler SV , de Souza BT , Mendonça EF, et al.: E-cadherin as a potential biomarker of malignant transformation in oral leukoplakia: a retrospective cohort study. BMC Cancer. 2014 Dec; 14(1): 1–7. Publisher Full Text\n\nAkhtar K, Ara A, Siddiqui S, et al.: Diagnostic and Prognostic Significance of E-Cadherin and Vimentin in Oral Cancer Metastasis. Annals of Pathology and Laboratory Medicine. 2016 Feb 7; 3(1): A8–A13.\n\nKushwaha SS, Joshi S, Arora KS, et al.: Correlation of E-cadherin immunohistochemical expression with histopathological grading of oral squamous cell carcinoma. Contemp. Clin. Dent. 2019 Apr; 10(2): 232–238. PubMed Abstract \| Publisher Full Text\n\nSathish II, Asokan K, Krithika CL, et al.: Expression of E-Cadherin and Levels of Dysplasia in Oral Leukoplakia-A Prospective Cohort Study. Asian Pac. J. Cancer Prev. 2020; 21(2): 405–410. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "186793", "date": "20 Jul 2023", "name": "Reetoja Nag", "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\nGiven the high incidence of OSCC in India, this study is significant in the sense that assessment of E-cadherin expression in OPMDs may help in early detection and prevention of OSCC. However, the authors can take a few points in consideration.\nThe authors plan on checking the E-cadherin expression in different types of OPMDs (erythroplakia, leukoplakia, oral lichen planus, oral submucous fibrosis).They should take into consideration that there have been studies in which the E-cadherin expression is different for different types of OPMDs and ensure that there is uniform distribution of the different types of OPMDs (within the OPMD section)so that there is minimal chance of bias (Reference: Sridevi, Ugrappa, et al. \"Expression of E-cadherin in normal oral mucosa, in oral precancerous lesions and in oral carcinomas.\" European journal of dentistry 9.03 (2015): 364-372).\n\nThe authors should give a short detail about how they are assessing the E-cadherin expression between the groups (Normal, OPMD, OSCC). Are they checking the intensity of the expression or any other feature(s)? Are they doing visual assessment or using any image analysis software for this purpose? If they are using image analysis software, are they taking reference from recently conducted studies or using a different methodology of their own?\n\nIf possible, it would be very useful if the authors can show some initial results of their methodology, from publicly available datasets/cases. For example: Some university archives may provide data upon request, or some websites like human protein atlas (https://www.proteinatlas.org/), TCGA (https://www.cancer.gov/ccg/) may contain cases/datasets.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [ { "c_id": "9948", "date": "28 Jul 2023", "name": "Padmashri Kalmegh", "role": "Author Response", "response": "Respond to comment 1. I have added suggested information and reference under the discussion subheading, cited as 34. Respond to comment 2. I have mentioned the method to assess the intensity of E-cadherin under the heading Assessment of E-cadherin immunoreactivity. Respond to comment 3. The results for the methodology from previous studies/researches has been mentioned under discussion subheading. Following studies has been referred. Gurkiran Kaur et al. (2009) Yuwanati et al. (2011) von Zeidler et al. (2014) Sridevi et al. (2015). Akhtar et al. (2016) Kushwaha et al. (2019) Ilangani Sathish et al. (2020) Thank you." } ] } ]	1	https://f1000research.com/articles/12-524
https://f1000research.com/articles/10-1091/v1	27 Oct 21	{ "type": "Research Article", "title": "Clinical use of antiviral, antibiotic and immunomodulatory drugs in hospitalized COVID-19 patients: a retrospective study in Bandung, Indonesia", "authors": [ "Heni Muflihah", "Santun Bhekti Rahimah", "Tulus Widiyanto", "Yeni Mahwati", "Thaigarajan Parumasivam", "Herri S. Sastramihardja", "Santun Bhekti Rahimah", "Tulus Widiyanto", "Yeni Mahwati", "Thaigarajan Parumasivam", "Herri S. Sastramihardja" ], "abstract": "Background: Evidence of highly effective repurposed drugs for coronavirus disease 2019 (COVID-19) is insufficient. However, empirical therapy using antiviral, antibiotic and immunomodulatory drugs is massive. Studies evaluating the clinical use of these drugs in Indonesia are sparse. Methods: We performed a retrospective study using medical records of hospitalized COVID-19 patients from July 2020 to March 2021 in Bandung, Indonesia. Data were collected at relevant timelines: age, sex, comorbid condition, peripheral oxygen saturation (SpO2), and hematology at admission; antiviral, antibiotic, and immunomodulator treatment during hospitalization; length of stay hospitalization (LOS) and death at discharge. Clinical use of the drug regimens included dose, frequency, and duration of therapy. The main outcome of hospitalization care was LOS and death. Results: Out of 249 patients, 43.3% had a comorbid condition, 74.7% had non-severe COVID-19 (SpO2 ≥ 90%), and almost all received antiviral or antibiotic agents. Remdesivir was the most frequent drug composing various antiviral regimens. Patients receiving a combination of remdesivir and favipiravir had lower SpO2 compared to those receiving oseltamivir (p=0.01). The short LOS was associated with remdesivir alone (p=0.03), the combination of favipiravir and oseltamivir (p=0.01), and the combination of intravenous levofloxacin and ceftriaxone (p<0.0001). Immunomodulatory drugs (methylprednisolone, dexamethasone, tocilizumab) were used in 47.1% of patients with low SpO2 (p=0.001). Its use was associated with prolonged LOS (p=0.0043). The increased risk of death in patients treated with the combination of remdesivir and favipiravir (OR 4.1;95%CI 1.4-12.2), and immunomodulatory drugs (OR 6.2; 95%CI 1.7-23.3) was confounded by the baseline characteristics of older age, comorbid condition, SpO2 level, and low lymphocyte number. Conclusions: Some treatment regimens were associated with short LOS, but there were drug regimens which might increase the risk of death. Further study should control the clinical conditions of COVID-19 patients at admission to confirm the outcome of death following drug therapy.", "keywords": [ "antibiotic", "antiviral", "COVID-19", "immunomodulators", "levofloxacin", "remdesivir." ], "content": "Introduction\n\nSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had caused at least 240 million cases of coronavirus disease 2019 (COVID-19) and more than 4.8 million deaths worldwide until 18 October 2021.1 At that time, Indonesia has reported 4.2 million confirmed COVID-19 cases with over 140 thousand deaths.2 The management of COVID-19 using repurposed drugs has been authorized since the beginning of the pandemic3 to rapidly control the mortality and morbidity of this new disease in the absence of evidence of clinical trial results.\n\nExploration on the effectiveness of repurposed drugs for COVID-19 in the first year of pandemic remains inconclusive. For example, a clinical trial on the most promising antiviral remdesivir showed its benefit on the clinical improvement at day 15.4 However, the interim report of the World Health Organization’s (WHO) Solidarity trial showed the lack of benefit of remdesivir on the reduction of mortality and hospitalization duration.5 Similarly, the Indonesian national guideline for COVID-196,7 recommends the antiviral favipiravir. However, this drug is not part of the recommendation from the WHO guideline based on the evidence from clinical trials evaluating remdesivir and favipiravir for COVID-19 therapy.8 The latest version of the WHO guidelines for COVID-19 therapy provides strong recommendation for systemic corticosteroid in severe and critical COVID-19, and conditional recommendation against remdesivir in hospitalized COVID-19.9 Corticosteroid and tocilizumab are drugs modulating the immune response that plays a critical role in the pathogenesis of severe COVID-19. As pneumonia is the main clinical manifestation of COVID-19, the use of antibiotics for COVID-19 patients regardless of the evidence of bacterial infection is concerning.10\n\nThe report on the pharmacological therapy of COVID-19 in Indonesia is not as extensive as that in other Asian countries with high cases of COVID-19, such as China and India. This retrospective study aimed to investigate the clinical use of antiviral, antibiotic and immunomodulatory agents in hospitalized COVID-19 patients during the first year of the pandemic. The treatment using these drugs were considered common based on the pathogenesis of infection and inflammation on COVID-19 disease. These drugs are also listed in the Indonesian national guideline for COVID-19.6,7 We also evaluated the outcome of length of stay (LOS) and death following hospitalization to understand the benefit of pharmacological therapy of antiviral, antibiotic and immunomodulators.\n\n\nMethods\n\nThis study was conducted in two main hospitals affiliated with the Faculty of Medicine Universitas Islam Bandung, Indonesia. One of the hospitals was a private hospital located in the Eastern of Bandung City, whereas another hospital was a referral government hospital for the West Java Province area located in Bandung Suburb. We performed a retrospective study using medical records of patients who were hospitalized during the first year of the COVID-19 pandemic from July 2020 to March 2021. The inclusion criteria for the subjects of this study were ≥ 18 years old, had confirmed COVID-19 and had peripheral oxygen saturation (SpO2) at admission. The minimum sample size of 172 patients was calculated to compare two independent means11 using the standard deviation of LOS from a previous study.12 The sample was collected based on a non-probability sampling procedure resulting in 249 patients. A confirmed COVID-19 patient was proven by a laboratory result for positive detection of the nucleic acid of SARS-CoV-2 virus using a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) test from the nasopharyngeal and oropharyngeal sample. The severity of COVID-19 disease was categorized as severe (SpO2 < 90%) and non-severe (SpO2 ≥ 90%).\n\nThe main antiviral drugs evaluated in this study were remdesivir, favipiravir, and oseltamivir. Azithromycin, levofloxacin, and ceftriaxone were the main antibiotics assessed. Immuno-modulators included methylprednisolone, dexamethasone, and tocilizumab. We evaluated the LOS and death as two main outcomes of therapy. An additional outcome evaluated was the use of a mechanical ventilator indicated by intensive care unit (ICU) admission. As the mortality in hospitalized COVID-19 was also associated with sociodemographic characteristics and laboratory result at admission,13 we also addressed these potential confounder factors.\n\nThe data on medical records were collected based on three relevant timelines. Baseline data at admission time were demographic characteristics (age, sex), comorbid disease (diabetes mellitus, hypertension, asthma, other conditions), SpO2 measurement, and hematology results. Data during the hospitalization period were pharmacological therapy using antiviral, antibiotics, and immunomodulatory drugs. The outcome of therapy was evaluated at the end of hospitalization. To validate the evaluation of therapy, the subjects were excluded if the duration of hospitalization was shorter than three days regardless of the causes. This period is suggested for clinical evaluation of community-acquired pneumonia (CAP) in adults.14 This approach is to minimize the bias on data collection for evaluating the outcome of therapy.\n\nThe numeric data was first analyzed for normality using the Kolmogorov-Smirnov test for further relevant parametric or non-parametric analysis. Statistically significant difference of SpO2 or LOS between two groups of therapies was analyzed by Mann-Whitney test, unless otherwise stated, whereas for more than two groups Kruskal-Wallis with Dunn’s multiple comparison test was used. The association of pharmacological therapy with the death was analyzed using Fisher’s exact test. The screening for potential confounding factors that are comorbidity, age and laboratory results was analyzed by Fisher’s exact, student t-test and Mann-Whitney, respectively. The difference was considered statistically significant if the p-value was less than 0.05. A multivariable logistic regression model was constructed for all variables reached p-value <0.25 in the screening to determine the odd ratio and identify confounding factors for the outcome of death. A confounding factor was defined as a variable that changed the odds ratio of the pharmacological therapy >10% after the adjustment for the relevant variable. The statistical analysis and data display was performed using GraphPad Prism V.8 software (La Jolla, CA). The logistic regression was performed using SPSS version 23 (Armonk, NY: IBM Corp).\n\nThe protocol of this study was approved by the Institutional Review Board and Health Research Ethics Committee of Al Islam Hospital No.001/KEPPIN-RSAI/02/2021. The data collection, management and storing ensured patient privacy.\n\n\nResults\n\nThe demographic and clinical characteristics of 249 patients are shown in Table 1.36 Most of the patients were aged 40-60 years (54.2%) and categorized as having non-severe COVID-19 (74.7%). Slightly more patients were male (55.4%) than female (44.6%). Almost half of patients had comorbid conditions (43.3%) with hypertension (12.5%) and diabetes mellitus (9.2%) as the two most frequent single comorbidities.\n\nCOVID-19 = coronavirus disease 2019, SpO2 = peripheral oxygen saturation.\n\nPharmacotherapy of main drugs in the management of hospitalized confirmed COVID-19 patients is shown in Table 2. All patients received antiviral drugs and almost all patients were treated with antibiotic agents. Patients who were treated using antiviral drugs were more likely to receive a single (55.4%) or double combination (33.7%) of drugs. Remdesivir was the most frequent drug used in antiviral regimens for single drug (36.3%), and double combination with faviriavir (22.1%) or with oseltamivir (6%). A triple combination of these drugs was prescribed to a few patients (2.4%). Remdesivir was used via the intravenous (IV) route with a loading dose of 200 mg and maintenance dose of 100 mg once daily. Favipiravir was used orally or IV with a loading dose 1600 mg and maintenance dose of 600 mg twice daily. Oseltamivir was given orally with the dose 75 mg twice daily. The same dose for these drugs was used in different regimens of the drug combination. The duration of antiviral therapy varied from 1 day to 21 days at the most prolonged period. The mean duration of remdesivir and favipiravir was about 7 days in various regimens. The mean duration of oseltamivir as a single drug therapy was 7 days, however the duration was shorter in the combination regimens.\n\na loading dose: 200 mg.\n\nb loading dose: 1600 mg.\n\nc sd: single dose.\n\nAntibiotic therapy occurred in most patients (86.9%) using a regimen consisting of two drugs. A combination of levofloxacin and ceftriaxone was the main regimen given to 71.9% of patients (Table 1). Levofloxacin and ceftriaxone were delivered intravenously once daily, and ceftriaxone was often used as a single dose. Levofloxacin had a standard dose of 500 mg with some patients receiving 750 mg, whereas ceftriaxone had the common dose of 2000 mg. There were 16.5% of patients receiving a combination of levofloxacin and azithromycin in which the oral route favoured. Azithromycin 500 mg once daily was the main oral antibiotic for COVID-19 in various regimens and had the longest mean of duration therapy in the single (10.9 days), double (10.7 days) and triple (12 days) combinations. Thus, the main antibiotic therapy was the combination of IV levofloxacin and ceftriaxone, while azithromycin was the main antibiotic for oral delivery.\n\nFewer than half (47.1%) of patients were treated with immunomodulatory drugs which were mainly used in a single regimen (36.3%) (Table 1). Methylprednisolone was the most frequent (24.1%) immunomodulatory drug used, followed by dexamethasone (11.6%). The mean duration of immunomodulatory drugs (2-4 days) was generally shorter than that of the previous antiviral and antibiotic therapy.\n\nPeripheral oxygen saturation is one of the indications of drug therapy in the Indonesian guideline of COVID-19 management. We evaluated whether different combinations of antiviral and antibiotic drugs or immunomodulatory therapy were associated with the baseline of SpO2 recorded at admission (Figure 1). The level of SpO2 in the group of patients receiving the double combination of remedisivir and favipiravir or other antivirals (lopinavir/ritonavir and isoprinosine) was significantly lower than that when receiving oseltamivir alone (p = 0.01 or p = 0.034, respectively) (Figure 1A). Among the antibiotic drug regimens, Figure 1B shows that patients receiving the combination of levofloxacin and ceftriaxone had higher levels of SpO2 than those receiving combination of azithromycin and levofloxacin (p = 0.019). However, few patients with a very low level of SpO2 were found in both of groups as shown by plots below 80% of SpO2 in Figure 1B. In contrast, the treatment of immunomodulatory drugs was very likely indicated by the level of SpO2 as shown by Figure 1C that the patients receiving immune-modulators were strongly associated with the lower level of SpO2 (p = 0.001) compared to those not treated with immune-modulators (Figure 1C).\n\n(A) Baseline SpO2 and the antiviral therapy using remdesivir, favipiravir, and oseltamivir in the various drug combinations. (B) Initial SpO2 and antibiotic combination of relevant azithromycin, levofloxacin, and ceftriaxone. (C) Immunomodulatory therapy using methylprednisolone, dexamethasone, and tocilizumab. Data are presented as median and interquartile range (IQR). Statistical differences were analyzed by Kruskal-Wallis and Dunn’s multiple comparisons (A, B) or Mann-Whitney test (C).\n\nThe efficacy of pharmacological therapy in hospitalized COVID-19 patients was evaluated by the LOS and the death as the main outcome, and the use of mechanical ventilator as the additional outcome. Out of 249 patients in this study, there were 22 deaths (8.8%) and three patients required mechanical ventilators (Table 3). The median of LOS from all patients was 7 days with interquartile range (IQR) 5-10 days. Patients who were treated with remdesivir or the combination of favipiravir and oseltamivir had a shorter LOS compared to those who were treated with the other antiviral drugs (p = 0.03 and p = 0.01, respectively). However, treatment with the combination of remdesivir and favipiravir was associated with the deaths (p < 0.0001).\n\nSD = standard deviation; IQR = interquartile range.\n\nPatients who were treated with the combination of levofloxacin and ceftriaxone had significantly shorter LOS (p < 0.0001) compared to those receiving the combination of azithromycin and levofloxacin. However, the combination of levofloxacin and ceftriaxone was also associated with the outcome of death (p = 0.0018). The use of immunomodulatory drugs was associated with a longer LOS (p = 0.0043) and death (p < 0.0001) compared to the patients who were untreated with immunomodulatory drugs. Thus, regimen therapies associated with shorter LOS were remdesivir alone, the combination of favipiravir and oseltamivir, and the combination of levofloxacin and ceftriaxone. However, the outcome of death was associated with the combination of remdesivir and favipiravir, the combination of levofloxacin and ceftriaxone, and the immunomodulatory drugs.\n\nTable 4 showed the baseline characteristics of patients that were statistically associated with death. Compared to patients who were discharged alive, death patients had older age (p = 0.0115), comorbid conditions (0.0058), lower lymphocyte number (p = 0.0061) and higher neutrophil to lymphocyte ratio (NLR) (p = 0.004). To note, the group of discharged alive had no data of hematology (lymphocyte, thrombocyte, and NLR) for seven patients.15 This screening suggests baseline clinical characteristics were potential confounding factors for the outcome of death following hospitalization.\n\nSD=standard deviation; SpO2 = peripheral oxygen saturation; IQR = interquartile range.\n\na Student t-test.\n\nb Fisher’s Exact test.\n\nc Mann-Whitney test.\n\n* p<0.05.\n\n** p<0.01.\n\nTo confirm the confounding factors of pharmacological therapy, we performed multivariable analysis for the outcome of death but not for the LOS, because the data of LOS was not normally distributed. Patients treated with the combination of remdesivir and favipiravir or treated with immunomodulatory drugs had increased risk of death (odds ratio [OR] 4.1;95% confidence interval [CI] 1.4-12.1 or OR 6.3; 95%CI 1.7-23.5, respectively) before adjustment. This remained significant after adjustment for age, sex, gender, comorbid, and lymphocyte count (OR 4.1;95% CI 1.4-12.2 or OR 6.2; 95%CI 1.7-23.3, respectively) (Table 5). However, all the clinical characteristics at admission, except for the NLR, were confounding factors for the risk of death following therapy using combination of remdesivir and favipiravir or immunomodulatory drugs.\n\nSpO2 = peripheral oxygen saturation.\n\n\nDiscussion\n\nOur study evaluated the clinical use of antiviral, antibiotic and immunomodulatory drugs for hospitalized patients confirmed with COVID-19. We found that antivirals and antibiotics were the standard treatment delivered to almost all the patients, whereas the immunomodulator treatment was an additional therapy. We assessed the clinical use of these drugs with SpO2 for the indication of therapy, and with LOS and death for the outcome of therapy.\n\nThe results showed that remdesivir is the primary drug composing various antiviral regimens. Remdesivir was recommended conditionally for COVID-19 patients who required oxygen supplementation16 and severe COVID-19 patients defined by a low level of SpO2.8 However, treatment with remdesivir alone in our study did not correlate significantly with the level of SpO2 compared to favipiravir or oseltamivir. Patients with more severe COVID-19 were more likely to receive the combination of remdesivir and favipiravir or other antiviral drugs (lopinavir/ritonavir or isoprinosine). On the other hand, oseltamivir seems to be the first antiviral choice for the non-severe COVID-19. The initial SpO2 was not the main indication for the choice of the rest antiviral regimens.\n\nRemdesivir in this study was used intravenously with a loading dose of 200 mg followed by 100 mg/day for a mean duration of 7 days. This dose provides an effective conversion of its metabolite into intracellular adenosine triphosphate analogue that selectively inhibits viral RNA polymerase.17 The same dose of remdesivir was used in other studies,5,18,19 however, some studies used remdesivir for 5 days18,20 or 10 days.18,19 The 5-day remdesivir was associated with better outcome at day 11,18 but another study found no differences.20 A meta-analysis revealed that the 5-day remdesivir provided similar benefit but fewer adverse events than the 10 day.21 Favipiravir in our study was given with a loading dose of 1200 mg and a daily dose of 600 mg. This dose was half of that used in several studies on COVID-19,16 but the same dose as a recent study evaluating favipiravir in recurrent COVID-19.22 Favipiravir (Avigan®) selectively inhibits viral RNA polymerases of influenza viruses and has a broad-spectrum antiviral activity for neglected and emerging RNA viruses.23,24 Treatment with favipiravir alone was considered safe and effective to shorten viral shedding in recurrent positive COVID-19 patients.22 Few studies showed the benefit of combined therapy of favipiravir with methylprednisolone.16 Combination of remdesivir and favipiravir was the most common antiviral regimen in our study, however, this was not available on the list of drug therapy used in clinical trials of COVID-19.16,25 Therefore, the safety and the efficacy of the combination of remdesivir and favipiravir is unknown. Indeed, clinical judgement to guide management decisions is part of WHO’s conditional recommendation.9 Further studies should evaluate clinical symptoms for comprehensive evidence for clinical judgement.\n\nThe empiric antimicrobial therapy for COVID-19 patients in our study was very high (98.2%). This proportion is higher than that reported in the United Kingdom (UK) (85.2%),26 Netherland (60.1%),10 and Surabaya Indonesia (75.3%).27 In fact, microbiological testing showed that the bacterial infection and co-infection among hospitalized COVID-19 patients was infrequent.10 Several studies reported 1.25 % of 925 patients,10 19.7% of 218 patients,27 1107 of 48902 patients were confirmed bacterial co-infection. In COVID-19 patients in the UK, the most frequent etiology of respiratory co-infection was Staphylococcus aureus and Haemophilus influenza, of secondary respiratory infection was Enterobacteriaceae and S aureus, and in bloodstream infection was Escherichia coli and S aureus.26 In the Indonesian setting, Gram-negative was the common causative agents of bacterial infection in COVID-19 patients.27 These findings suggested that the choice for empirical antimicrobial should be treated for Gram-negative bacteria and S aureus until the results of culture available.\n\nOur study showed that IV levofloxacin (500/750 mg), IV ceftriaxone (200 mg), and oral azithromycin (500 mg) were the common antibiotic therapy used in COVID-19 patients. The combination of intravenous levofloxacin and ceftriaxone was the most frequent antibiotic regimen prescribed. The choice of levofloxacin for COVID-19 patients is probably because fluoroquinolone antibiotic has a broad-spectrum activity. Fluoroquinolone antibiotic is used in severe CAP, and has the potency of antiviral and immune-modulator.28 Ceftriaxone is a broad-spectrum beta-lactam antibiotic that has been one of the choices for treating community-onset pneumonia (COP). The dose of 1000 mg has a similar cure rate to 2000 mg.29 Azithromycin is a macrolide antibiotic that is effective against Gram-positive, Gram-negative, and atypical bacteria. It has primarily been used as a treatment for upper and lower respiratory infection with its potential application for COVID-19 due to its effect of antiviral and immune-modulator.30 A systematic review and meta-analysis study reported the prevalence of antibiotic use in COVID-19 patients was 24.5% azithromycin, 10% fluoroquinolone, and 9% ceftriaxone.31 However, the study found the lack of data on the specific indication and specific name antibacterial agents. The standard broad-spectrum antibiotics in our study were not supported by the type of bacteria found in most studies.26,27,31 However, our study has added value in providing the name of antibacterial agents used.\n\nThe latest version of living WHO guideline recommends both corticosteroid and IL-6 receptor blocker (tocilizumab) for severe and critical COVID-19 patients.9 Our study found that patients who were treated with immunomodulatory drugs (methylprednisolone, dexamethasone, and tocilizumab) had a significantly lower level of SpO2 compared to those who were untreated with these drugs (p = 0.001). Systemic corticosteroid such as 6 mg of oral or intravenous dexamethasone or 50 mg of intravenous hydrocortisone was strongly recommended for severe and critical COVID-19, but not for the non-severe COVID-19 because of the low certainty evidence on the increased risk of death.32 Similarly, the RECOVERY clinical trial showed the efficacy of dexamethasone on reducing the incidence of death was for the severe and critical, but not on the non-severe COVID-19.33 Interestingly, in our study, the use of immunomodulators was associated with prolonged LOS (p = 0.0043) and a higher number of deaths (p < 0.0001) compared to the non-immunomodulatory drug user. Thus, the treatment of more severe COVID-19 patients with immunomodulatory drugs did not improve the outcome.\n\nOur study evaluated the LOS and death as the outcome for clinical use of antiviral, antibiotic, and immunomodulatory therapy. Our study found that remdesivir alone was associated with shorter LOS than therapy using other antiviral drugs (lopinavir/ritonavir or isoprinosine). This is in line with a recent review updating the results of randomized clinical trials (RCT) on antiviral agents which showed that remdesivir could increase clinical improvement but lacked benefit on preventing death.25 A study in Surabaya reported that COVID-19 patients confirmed with bacterial infection had longer LOS and higher mortality than those without bacterial infection.27 However, the study did not evaluate the outcome of antibiotic therapy as we did. Multivariable analysis in our study found concerning safety issues for two regimen therapies. Patients who were treated with the combination of remdesivir and favipiravir had a four times higher risk of death compared to those receiving antiviral drugs other than this regimen. Similarly, patients treated with immunomodulatory drugs had a six times higher risk of death compared to those untreated with immune-modulators. However, several baseline clinical characteristics including age, gender, sex, comorbid condition, SpO2 level, and lymphocyte contributed to this risk and became confounding factors. It has been known from the beginning of COVID-19 pandemic that older age and comorbid disease, in particular hypertension and diabetes mellitus, were associated with higher death rate.34 Lower lymphocyte count was also associated with the severity of COVID-19.27,35 Further confirmation studies should control the baseline clinical characteristics of COVID-19 patients to validate the increased risk of death following the treatment with the combination of remdesivir and favipiravir or immunomodulatory drugs.\n\nThis study has several limitations. The non-probability sampling may affect the ability to generalize of the result to a broader population. Our study did not include data on the clinical symptoms of COVID-19 patients and the microbiological testing that would provide more comprehensive clinical judgment for antiviral and antibiotic therapy. However, to our understanding, this is among the first retrospective study reporting the details on the specific name of drugs and drug combination of antiviral and antibiotic for COVID-19 patients. Further prospective study to ensure the drug interaction and safety profile of combination drug regimens is warranted.\n\n\nConclusions\n\nClinical use of antiviral drugs and antibiotics in our study were very likely the standard therapy applied to almost all hospitalized COVID-19 patients. On the other hand, the treatment of COVID-19 patients using the immunomodulatory drugs was an additional therapy. The most common antiviral regimen was the combination of remdesivir and favipiravir, whereas the most frequent antibiotic regimen was the combination of levofloxacin and ceftriaxone. Treatment of hospitalized COVID-19 with remdesivir alone, the combination of favipiravir and oseltamivir, and the combination of levofloxacin and ceftriaxone was associated with short LOS. There was increased risk of death in patients treated with the combination of remdesivir and favipiravir and the immunomodulatory drugs. However, clinical characteristics at admission including age, sex, comorbid condition, SpO2 level, and lymphocyte count contributed to this risk.\n\n\nData availability\n\nFigshare: Clinical use of antiviral, antibiotic and immunomodulatory drugs in hospitalized COVID-19 patients: a retrospective study in Bandung Indonesia.\n\nhttps://doi.org/10.6084/m9.figshare.16530615.36\n\nThis project contains the following underlying data:\n\n‐ Clinical characteristics, therapy of antiviral, antibiotic and immunomodulatory drugs, hematology results for all patients\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).", "appendix": "Acknowledgements\n\nWe would like to thank Adzan Fitri and health workers at the hospitals Guntur Sepatapati, Diah Zakiah Ismawati and Andri Muhammad Ramdani for supporting this study on data collection. All these people had given a written permission to be named in this section of article.\n\n\nReferences\n\nWHO: WHO Coronavirus (COVID-19) Dashboard.2021. 18 October ed.\n\nKemenkes: COVID-19 Indonesia.2021.18 October ed.\n\nWHO: Off-label use of medicines for COVID-19.March 31 2020. (accessed December 1 2020).Reference Source\n\nBeigel JH, Tomashek KM, Dodd LE, et al.: Remdesivir for the Treatment of Covid-19 - Final Report. N. Engl. J. Med. 2020; 383(19): 1813–1826. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPan H, Peto R, Karim QA, et al.: Repurposed antiviral drugs for COVID-19 –interim WHO SOLIDARITY trial results. N. Engl. J. Med. 2021; 384(6): 497–511.\n\nKemenkes: Protocol of COVID-19 Management in Indonesia, pocket book 2nd edition (Protokol Tatalaksana COVID-19 di Indonesia, buku saku ed 2). Jakarta:The Indonesian Ministry of Health (Kemenkes);2021.\n\nKemenkes: Guideline on the Prevention and the Control of Coronavirus Disease 5th Revision (Pedoman Pencegahan dan Pengendalian Coronavirus Disease Revisi Ke-5). Jakarta:The Indonesian Ministry of Health (Kemenkes);2020.\n\nWHO: Therapeutics and COVID-19: living guideline, 20 November 2020. CC BY-NC-SA 3.0 IGO. Geneva:World Health Organization;2020.\n\nWHO: Therapeutics and COVID-19: living guideline.2021. 6 July 2021 ed.\n\nKarami Z, Knoop BT, Dofferhoff ASM, et al.: Few bacterial co-infections but frequent empiric antibiotic use in the early phase of hospitalized patients with COVID-19: results from a multicentre retrospective cohort study in The Netherlands. Infect. Dis. 2021; 53(2): 102–110. PubMed Abstract \| Publisher Full Text\n\nDhand NK, Khatkar MS: Statulator: An online statistical calculator. Sample Size Calculator for Comparing Two Independent Means.2014. (accessed 3 December 2020).Reference Source\n\nLagier J-C, Million M, Gautret P, et al.: Outcomes of 3,737 COVID-19 patients treated with hydroxychloroquine/azithromycin and other regimens in Marseille, France: A retrospective analysis. Travel Med. Infect. Dis. 2020; 36: 101791. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCastro VM, McCoy TH, Perlis RH: Laboratory Findings Associated With Severe Illness and Mortality Among Hospitalized Individuals With Coronavirus Disease 2019 in Eastern Massachusetts. JAMA Netw. Open. 2020; 3(10): e2023934-e. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFile TM: Treatment of community-acquired pneumonia in adults who require hospitalization.2021.2 May 2021 ed.\n\nMuflihah H, Rahimah SB, Widiyanto T, et al.: Clinical use of antiviral, antibiotic and immunomodulatory drugs in hospitalized COVID-19 patients: a retrospective study in Bandung Indonesia;Figshare.2021. Publisher Full Text\n\nSreekanth Reddy O, Lai W-F: Tackling COVID-19 Using Remdesivir and Favipiravir as Therapeutic Options. Chembiochem. 2021; 22(6): 939–948. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHumeniuk R, Mathias A, Kirby BJ, et al.: Pharmacokinetic, Pharmacodynamic, and Drug-Interaction Profile of Remdesivir, a SARS-CoV-2 Replication Inhibitor. Clin. Pharmacokinet. 2021; 60(5): 569–583. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSpinner CD, Gottlieb RL, Criner GJ, et al.: Effect of Remdesivir vs Standard Care on Clinical Status at 11 Days in Patients With Moderate COVID-19: A Randomized Clinical Trial. JAMA. 2020; 324(11): 1048–1057. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang Y, Zhang D, Du G, et al.: Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial. Lancet. 2020; 395(10236): 1569–1578. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGoldman JD, Lye DCB, Hui DS, et al.: Remdesivir for 5 or 10 Days in Patients with Severe Covid-19. N. Engl. J. Med. 2020; 383(19): 1827–1837. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRezagholizadeh A, Khiali S, Sarbakhsh P, et al.: Remdesivir for treatment of COVID-19; an updated systematic review and meta-analysis. Eur. J. Pharmacol. 2021; 897: 173926. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhao H, Zhang C, Zhu Q, et al.: Favipiravir in the treatment of patients with SARS-CoV-2 RNA recurrent positive after discharge: A multicenter, open-label, randomized trial. Int. Immunopharmacol. 2021; 97: 107702. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDelang L, Abdelnabi R, Neyts J: Favipiravir as a potential countermeasure against neglected and emerging RNA viruses. Antivir. Res. 2018; 153: 85–94. PubMed Abstract \| Publisher Full Text\n\nFuruta Y, Gowen BB, Takahashi K, et al.: Favipiravir (T-705), a novel viral RNA polymerase inhibitor. Antivir. Res. 2013; 100(2): 446–454. PubMed Abstract \| Publisher Full Text\n\nLai C-C, Chao C-M, Hsueh P-R: Clinical efficacy of antiviral agents against coronavirus disease 2019: A systematic review of randomized controlled trials. J. Microbiol. Immunol. Infect. 2021; S1684-182(21).00135–00133.\n\nRussell CD, Fairfield CJ, Drake TM, et al.: Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study. Lancet Microbe. 2021; 2: e354–e365. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAsmarawati T, Rosyid A, Suryantoro S, et al.: The clinical impact of bacterial co-infection among moderate, severe and critically ill COVID-19 patients in the second referral hospital in Surabaya [version 2; peer review: 2 approved]. F1000Res. 2021; 10(113): 113. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKarampela I, Dalamaga M: Could Respiratory Fluoroquinolones, Levofloxacin and Moxifloxacin, Prove to be Beneficial as an Adjunct Treatment in COVID-19?. Arch. Med. Res. 2020; 51(7): 741–742. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHasegawa S, Sada R, Yaegashi M, et al.: 1g versus 2 g daily intravenous ceftriaxone in the treatment of community onset pneumonia - a propensity score analysis of data from a Japanese multicenter registry. BMC Infect. Dis. 2019; 19(1): 1079. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVenditto VJ, Haydar D, Abdel-Latif A, et al.: Immunomodulatory Effects of Azithromycin Revisited: Potential Applications to COVID-19. Front. Immunol. 2021; 12: 574425. Publisher Full Text\n\nSharma S, Singh A, Banerjee T: Antibacterial agents used in COVID-19: A systematic review and meta-analysis. Environ Sustain. 2021; 4: 503–513. Publisher Full Text\n\nWHO: Corticosteroids for COVID-19: Living Guidance 2 September 2020.2020.\n\nRECOVERY: Dexamethasone in Hospitalized Patients with Covid-19. N. Engl. J. Med. 2020; 384(8): 693–704. Publisher Full Text\n\nZhou F, Yu T, Du R, et al.: Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. Lancet. 2020; 395(10229): 1054–1062. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFu J, Kong J, Wang W, et al.: The clinical implication of dynamic neutrophil to lymphocyte ratio and D-dimer in COVID-19: A retrospective study in Suzhou China. Thromb. Res. 2020; 192: 3–8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuflihah H, Bhekti Rahimah S, Widiyanto T, et al.: Clinical use of antiviral, antibiotic and immunomodulatory drugs in hospitalized COVID-19 patients: a retrospective study in Bandung Indonesia. figshare. Dataset. 2021. Publisher Full Text" }	[ { "id": "122796", "date": "02 Mar 2022", "name": "Harapan Harapan", "expertise": [ "Reviewer Expertise Virology and Public Health" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this article, authors reporting the use of antiviral, antibiotic and immunomodulatory drugs and the effects on the outcomes (LOS and mortality) among hospitalized COVID-19 patients in Bandung. Although the number of the patients is relatively small the information are important in particular with limited data from Indonesia.\n\nAbstract\n\nI have some suggestions to improve the article: I cannot see the objective in the Abstract section.\nAbstract: \" Patients receiving a combination of remdesivir and favipiravir had lower SpO2 compared to those receiving oseltamivir (p=0.01).\" Was it compared to oseltamivir alone?\n\n\"The short LOS was associated with remdesivir alone (p=0.03), the combination of favipiravir and oseltamivir (p=0.01), and the combination of intravenous levofloxacin and ceftriaxone (p<0.0001).\" This statement should have comparison in order to able to understand this text correctly: treatment with remdesivir had short LOS compared to what?\n\"Immunomodulatory drugs (methylprednisolone, dexamethasone, tocilizumab) were used in 47.1% of patients with low SpO2 (p=0.001)\" This is unclear. T]he use of immunomodulatory drugs associated with low SpO2? I think this is only the nature of the data where the severe COVID-19 were treated with dexamethasone for example. This is similar with \"Its use was associated with prolonged LOS (p=0.0043).\"\n\"The increased risk of death in patients treated with the combination of remdesivir and favipiravir (OR 4.1;95%CI 1.4-12.2), and immunomodulatory drugs (OR 6.2; 95%CI 1.7- 23.3) was confounded by the baseline characteristics of older age, comorbid condition, SpO2 level, and low lymphocyte number.\" This text indicates that the treatment with remdesivir and favipiravir or mmunomodulatory drugs increased the mortality of the patients. Such interpretation might not be true.\nIn short I believe authors should re-write the manuscript and interpret the findings very carefully.\n\nIntroduction\n\"We also evaluated the outcome of length of stay (LOS) and death following hospitalization\" I think the better way is \"We also evaluated the length of stay (LOS) and the outcome of COVID-19 following hospitalization...\" This because the authors assessed both outcomes of COVID-19 (death and survival).\n\nMethods\nStatistical methods\nThere is no consistency between the objective and the analysis that was conducted.\n\n\"Statistically significant difference of SpO2 or LOS between two groups of therapies was analyzed by Mann-Whitney test, unless otherwise stated, whereas for more than two groups Kruskal-Wallis with Dunn’s multiple comparison test was used.\" Sp.O2 (or severity of COVID-19) was not mentioned as the outcome in this study.\nAuthors did not adjust their analyses based on severity of the disease (or did sub-group analysis based on diseases severity) and this could misleading the interpretation of the study. Authors should do this otherwise the findings might not be genuine.\n\nResults\nTable 1, the abbreviation should be on the bottom of the table.\n\nTable 2. Such significant variations of therapy duration could cause significant bias of the finding. I am afraid the finding could be misleading and this potentially have consequence on COVID-19 treatment.\n\nDrug regimens indicated by baseline peripheral oxygen saturation\n\"We evaluated whether different combinations of antiviral and antibiotic drugs or immunomodulatory therapy were associated with the baseline of SpO2 recorded at admission\".\nThis analysis is misleading. The authors measured the SpO2 at admission (method) and here authors assessed the association with the treatment of antiviral and antibiotic drugs or immunomodulatory that given later during the hospitalisation and concluded \"The level of SpO2 in the group of patients receiving the double combination of remedisivir and favipiravir or other antivirals (lopinavir/ritonavir and isoprinosine) was significantly lower than that when receiving oseltamivir alone (p = 0.01 or p = 0.034, respectively)\" I am afraid this is interpretation is not appropriate: how have authors assessed that SpO2 was associated with the treatments that were given later during the treatment.\n\nTable 3. The positions of the p-values are confusing. The position of the p-value should be on the first row such <0.0001b should be on on row with \"Antiviral\" if this for who whole group. The p-values on LOS are consuming either. Why only some have p-values. If the p-value is not available due to unable to be calculated please indicate as NA or something that is easy to understand not blank. Also the p-value should be consistent (preference 0.000 if less write <0.001. Please do not mix the p-values 0.03, 0.01, 0.0043 (Table 3). This is true for all tables. The last column \"Mechanical ventilator\" is confusing, why is this column here. This is one of my major concern.\n\nTable 4. Why there is no p-value on Sex?\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "9441", "date": "28 Jul 2023", "name": "Heni Muflihah", "role": "Author Response", "response": "In this article, authors reporting the use of antiviral, antibiotic and immunomodulatory drugs and the effects on the outcomes (LOS and mortality) among hospitalized COVID-19 patients in Bandung. Although the number of the patients is relatively small the information are important in particular with limited data from Indonesia. Abstract I have some suggestions to improve the article: I cannot see the objective in the Abstract section. Respond: Revised abstract - the objective was added: “This study aimed to evaluate the clinical use of these drugs and the outcome of hospitalization in COVID-19 patients” Abstract: \" Patients receiving a combination of remdesivir and favipiravir had lower SpO2 compared to those receiving oseltamivir (p=0.01).\" Was it compared to oseltamivir alone? Respond: Yes. Revised abstract - “oseltamivir alone (p=0.01).\" \"The short LOS was associated with remdesivir alone (p=0.03), the combination of favipiravir and oseltamivir (p=0.01), and the combination of intravenous levofloxacin and ceftriaxone (p<0.0001).\" This statement should have comparison in order to able to understand this text correctly: treatment with remdesivir had short LOS compared to what? Respond: Revised abstract - Remdesivir alone and combination of favipiravir and oseltamivir had shorter LOS compared to the other antivirals (p=0.03 and p=0.01 respectively). \"Immunomodulatory drugs (methylprednisolone, dexamethasone, tocilizumab) were used in 47.1% of patients with low SpO2 (p=0.001)\" This is unclear. T]he use of immunomodulatory drugs associated with low SpO2? I think this is only the nature of the data where the severe COVID-19 were treated with dexamethasone for example. This is similar with \"Its use was associated with prolonged LOS (p=0.0043).\" Respond: The timeline of the study as mentioned in the method of abstract, that SpO2 was measured at admission (initial hospitalization) whereas the LOS was measured at the end of hospitalization. This nature of data timeline was interpreted that the level of SpO2 was an indication/reasoning for the treatment given, whereas the LOS is the outcome. To make this clear, we revised the statement: “Immunomodulatory drugs (methylprednisolone, dexamethasone, tocilizumab) were prescribed in patients with lower baseline SpO2 (p=0.001) and resulted in longer LOS (p=0.0043) compared to those with no immunomodulators.” To note, two sentences were deleted from the abstract version 1 because the number of words exceeded the limit (300) after revision adding the comparison group in some sentences. \"The increased risk of death in patients treated with the combination of remdesivir and favipiravir (OR 4.1;95%CI 1.4-12.2), and immunomodulatory drugs (OR 6.2; 95%CI 1.7- 23.3) was confounded by the baseline characteristics of older age, comorbid condition, SpO2 level, and low lymphocyte number.\" This text indicates that the treatment with remdesivir and favipiravir or mmunomodulatory drugs increased the mortality of the patients. Such interpretation might not be true. In short I believe authors should re-write the manuscript and interpret the findings very carefully. Respond: We understand that the result of our study is against the plausibility. However, we have confirmed the data and the analysis was true for the interpretation. A previous clinical trial also showed that, compared to the placebo group, the remdesivir group had higher total number of patients who died or had adverse events: Wang Y, Zhang D, Du G, et al.: Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial. Lancet. 2020; 395(10236): 1569–1578. PubMed Abstract \| Publisher Full Text \| Free Full Text. Our result showed combination of remdesivir and favifiravir, but not the remdesivir alone, had increased risk of death. Introduction \"We also evaluated the outcome of length of stay (LOS) and death following hospitalization\" I think the better way is \"We also evaluated the length of stay (LOS) and the outcome of COVID-19 following hospitalization...\" This because the authors assessed both outcomes of COVID-19 (death and survival). Respond: Revised - \"We also evaluated the length of stay (LOS) and the outcome following hospitalization\" Methods Statistical methods There is no consistency between the objective and the analysis that was conducted. \"Statistically significant difference of SpO2 or LOS between two groups of therapies was analyzed by Mann-Whitney test, unless otherwise stated, whereas for more than two groups Kruskal-Wallis with Dunn’s multiple comparison test was used.\" Sp.O2 (or severity of COVID-19) was not mentioned as the outcome in this study. Respond: The tests were mentioned based on the data analyzed. Indeed, we have never mentioned SpO2 as the outcome. We consistently stated the SpO2 was the baseline data as an indication for initiating therapy. We mentioned in the “Clinical data” section about timeline for data collection, the SpO2 was collected at admission or as baseline data which clearly was not part of the outcome. Instead, the SpO2 here was meant as an indication for initiating the treatment based on the guidelines for therapy that we stated in the result section: 'Drug regimens indicated by baseline peripheral oxygen saturation'. Authors did not adjust their analyses based on severity of the disease (or did sub-group analysis based on diseases severity) and this could misleading the interpretation of the study. Authors should do this otherwise the findings might not be genuine. Respond: We have presented, in Table 5, the multivariable analysis adjusted on the SpO2, in numeric data, as the indicator for severity of the disease. We have performed stratification analysis for each main variable (RDV+FAV, LVX+CRO, Immunomodulatory) based on severity level in categorical SpO2. We found that the severity was not interaction variable for RDV+ FAV (P=0.601) nor for Immunomodulator (P=0.163). We were unable to analyze this for LVX+CRO due to large difference in the number of subject between LVX+CRO (178) and non LVX+CRO (15). We added the statement: “We had performed the stratificational analysis based on the severity of the disease, and it was not interaction variable”. Based on these analysis, we have consistently stated in the result and abstract that SpO2 level was a “confounder factor for the risk of death following therapy using combination of remdesivir and favipiravir or immunomodulatory drugs”. Results Table 1, the abbreviation should be on the bottom of the table. Respond: Revised position of abbreviation for Table 1, Table 4, and Table 5. Table 2. Such significant variations of therapy duration could cause significant bias of the finding. I am afraid the finding could be misleading and this potentially have consequence on COVID-19 treatment. Respond: We understand the nature of observational study using medical record has such bias and resulted in lower level of evidence compared to the trials. In this study, we aimed to evaluate the empirical therapy of COVID-19 at the time that the evidence of trials was insufficient or inconclusive. Drug regimens indicated by baseline peripheral oxygen saturation \"We evaluated whether different combinations of antiviral and antibiotic drugs or immunomodulatory therapy were associated with the baseline of SpO2 recorded at admission\". This analysis is misleading. The authors measured the SpO2 at admission (method) and here authors assessed the association with the treatment of antiviral and antibiotic drugs or immunomodulatory that given later during the hospitalisation and concluded \"The level of SpO2 in the group of patients receiving the double combination of remedisivir and favipiravir or other antivirals (lopinavir/ritonavir and isoprinosine) was significantly lower than that when receiving oseltamivir alone (p = 0.01 or p = 0.034, respectively)\" I am afraid this is interpretation is not appropriate: how have authors assessed that SpO2 was associated with the treatments that were given later during the treatment. Respond: The SpO2 was not the outcome, the association was meant as indication or reasoning for initiating the therapy. The different level of SpO2 was to show whether the therapy was chosen based on the level of SpO2 as the guideline for COVID-19 treatment. Table 3. The positions of the p-values are confusing. The position of the p-value should be on the first row such <0.0001b should be on on row with \"Antiviral\" if this for who whole group. The p-values on LOS are consuming either. Why only some have p-values. If the p-value is not available due to unable to be calculated please indicate as NA or something that is easy to understand not blank. Also the p-value should be consistent (preference 0.000 if less write <0.001. Please do not mix the p-values 0.03, 0.01, 0.0043 (Table 3). This is true for all tables. The last column \"Mechanical ventilator\" is confusing, why is this column here. This is one of my major concern. Respond: We only showed the significant p-values, but we did revision to show all the p-values. Revised Table 3 - The p-value located on the whole group row (Antiviral or Antibiotic or Immunomodulator for all group analysis) and on the relevant sub-group row for multiple comparison. We located all the p-values on the column p-value and showed the relevant test and/or comparison group used as mentioned in statistical analysis. On the study design, the mechanical ventilator was stated as an additional outcome. Therefore, to avoid confusion, we showed the result with revision that the mechanical ventilator data was not shown in the table but only in the text. Table 4. Why there is no p-value on Sex? Respond: There was p-value: 0.155 on the row Sex" } ] } ]	1	https://f1000research.com/articles/10-1091
https://f1000research.com/articles/12-898/v1	28 Jul 23	{ "type": "Research Article", "title": "Changes in the readiness of healthcare systems to provide diabetes- and cardiovascular disease-related services: A comparison of indices using data from the 2014 and 2017 Bangladesh Health Facility Surveys", "authors": [ "Farhana Jahan", "Anisuddin Ahmed", "Faroque Md. Mohsin", "Sorforajur Rahman", "Abu Sayeed", "Lailatun Nahar", "Diapk Kumar Mitra", "Farhana Jahan", "Anisuddin Ahmed", "Sorforajur Rahman", "Abu Sayeed", "Lailatun Nahar", "Diapk Kumar Mitra" ], "abstract": "Background: The increasing prevalence of non-communicable diseases (NCDs) in Bangladesh is a significant obstacle for the government's already under-resourced healthcare centers and healthcare management. This study aimed to determine whether healthcare services are prepared to handle cardiovascular disease (CVD) and diabetes in the future. Methods: This cross-sectional study used the Bangladesh Health Facilities Survey (BHFS) 2014 and 2017 data. The BHFS 2014 completed assessment of 317 facilities providing diabetes care and 407 facilities providing CVD care, while the 2017 BHFS included 305 and 368 facilities providing diabetes and CVD care, respectively. Results: A slight increase in facility readiness status was observed in 2017 compared with 2014, though it was not statistically significant. District hospitals (DHs) and Upazila health complexes (UHCs) showed improvement in staff and guidelines, basic equipment, diagnostic capabilities, and essential drugs, as their Readiness Index (RI) value increased in 2017 from 2014. The RI values of non-governmental organizations (NGOs) clinics were 48.65% in 2014, whereas the value was slightly increased to 55.28% in 2017. For private clinics, the RI value diminished in 2017 (56.11%), which was lower than the 2014 survey (60.62%). There was a slightly mixed trend for public and private facilities regarding managing CVDs. In DHs and UHCs, the RI value decreased to 58.5% and 53.06% in 2017 from 64.04% and 53.02% in 2014. NGO clinics were valued at 48.65% in 2014, which dropped to 44.53%. For private clinics, the value showed a decreasing trend as the value in 2017 was 61.58%, lower than the value of 2014 (64.15%). Conclusions: In Bangladesh, public and private healthcare facilities lack readiness for healthcare towards DM and CVD maintenance. It is noteworthy that this improvement has been insignificant over the years in this regard. Healthcare policy reform is urgently required to strengthen NCD healthcare, particularly in public healthcare facilities.", "keywords": [ "Health system", "NCDs", "Diabetes", "CVD", "Facility readiness", "Bangladesh" ], "content": "Introduction\n\nThe incidence of non-communicable diseases (NCDs) has been resolutely increasing worldwide over the last few decades.1 Diabetes mellitus and cardiovascular diseases (CVDs), including coronary heart disease, peripheral arterial disease, and rheumatic heart disease, are among the NCDs that are prevalent and impact individuals of different ages, geographical areas, and nations.2 The World Health Organization (WHO) estimates that more than 15 million people between the ages of 30 and 69 years die every year from an NCD worldwide, with low-to-middle-income countries (LMICs) accounting for three-fourths (77%) of all early fatalities. According to the WHO, CVDs cause the death of 17.9 million people every year, whereas diabetes claims the lives of 1.5 million individuals each and every year.\n\nBangladesh is a prosperous nation that is undergoing both epidemiologic and demographic transitions at the same time. This is due to the fact that the disease burden is moving from communicable illnesses to NCDs.2 WHO reported in 2011 that NCDs represent 61% of the overall illness burden in Bangladesh and preliminary research estimates that these diseases are responsible for 51% of the country’s yearly deaths.3 The number of people living with diabetes in Bangladesh is always increasing. According to the International Center for Diarrheal Disease Research in Bangladesh (ICDDR, B), the number of individuals living with diabetes in 2015 was around 7.1 million, and the disease was responsible for approximately 129,000 fatalities. Studies also showed that diabetes raises the chance of debilitating CVDs,4 and patients with diabetes have a significantly increased risk of dying from CVDs.4\n\nAn analysis of a case study set within the parameters of Bangladesh found a variety of healthcare system preparedness challenges; the CVD rate is increasing, making it difficult for Bangladesh to treat these diseases.5 In particular, this previous study found that a lack of comprehensive cooperation among many partners hindered the preparedness of the healthcare systems.5 With the changing epidemiological and demographic conditions, the healthcare system faces new challenges such as increasing mortality due to CVDs, diabetes and other NCDs in Bangladesh.6,7 Preventing and managing NCDs differs from addressing acute conditions, in which healthcare system readiness can play an important role.6 Without long-term medical support, early identification of NCDs, mental health promotion, identification of risk factors, self-management, behavior modification, palliative care, and adherence to treatments and medications, NCDs are unlikely to be prevented or managed.8 The lack of healthcare facilities, inadequate infrastructure, access to healthcare professionals, lack of health literacy, and unavailability of medications negatively impact patients with NCDs.2\n\nHowever, the readiness of a country’s healthcare system is one of the significant aspects that show a country’s readiness to adopt essential and timely steps to minimize any disease, including NCDs. The idea of healthcare system readiness emphasizes the degree to which healthcare systems are ready to handle any particular sickness as well as any and all general disorders.9 Because the readiness identifies possible obstacles that might stand in the way of achievement, it is essential to assess readiness in healthcare systems (U. S. Department of Health and Human Services Health Resources and Services Administration). Diabetes and CVDs are responsible for exponential increases in medical expenses and a diminished capacity for activity.4 In addition to this, the enormous expenditures associated with medical treatment have an impact on the financial situation of a family.4 Research has shown that diabetes significantly increases the risk of developing severe CVDs.7 Heart conditions may create disruptions in the normal flow of fluid out from the lungs, which can result in a variety of abnormalities.10 All of these diseases are linked to one another and are all accountable for the devastation of human lives and the economy.\n\nThe healthcare system in Bangladesh is facing an increasingly difficult task as a result of the prevalence of NCDs, notably CVDs and diabetes.11 Previous research focused on determining whether or not the healthcare system in Bangladesh was prepared to provide treatment for NCDs.5,12 It would be more beneficial to identify the illnesses specific readiness (for example, readiness for individuals with diabetes and CVDs, etc.) of the healthcare system to offer services for a given condition if we focused on each specific NCD on its own.13\n\nBased on the information from the Bangladesh Health Facilities Survey (BHFS) in 2014, there has been only one study done so far that investigates whether or not healthcare institutions are prepared for increasing cases of diabetes and CVDS.13 According to what was discovered, just 0.4% to 0.9% of facilities satisfied all four preparedness characteristics (guidelines, trained staff, equipment, and medicine).13 Despite the fact that it is vital to understand the preparedness of the healthcare system in Bangladesh, particularly for services connected to diabetes and CVDs. According to our understanding, the preparedness of the healthcare system to deliver services related to diabetes and CVDs utilizing the most recent BHFS 2017 data has not yet been quantified or analyzed. We studied the readiness of the healthcare system in Bangladesh, especially for diabetes and CVD-related services, by comparing the BHFS from 2014 to 2017 and basing our findings on this constraint.\n\n\nMethods\n\nThis study arose from the first author’s master’s thesis and when the first author submitted a proposal for their thesis, the study protocol was approved by the Institutional Review Board (IRB) of North South University in Bangladesh (Ref-2020/OR-NSU/IRB/206). However, as this study used secondary data analyses, ethical approval was not required.\n\nThe 2014 and 2017 BHFS surveys were designed as cross-sectional studies and used a stratified random sampling technique of 1,596 and 1,600 healthcare facilities, respectively, to represent all formal healthcare facilities in Bangladesh. Both the 2014 and 2017 BHFS surveys contained questions on the healthcare facilities of Bangladesh’s administrative divisions. The BHFS 2014 survey was fielded between May 22nd and July 20th 2014, whereas the BHFS 2017 survey was fielded during the months of July and October 2017. The goal of the survey was to determine the availability and preparedness of healthcare institutions to provide services in the areas of maternity and child health, family planning, selected NCDs (diabetes and CVDs), and tuberculosis. The study also examined the availability of human resources, basic services, and logistics in healthcare institutions, including equipment, essential pharmaceuticals, laboratory services, and infection control measures that followed standard standards. We extracted the data from the dataset (BHFS 2014 and 2017) between January and March 2020.\n\nThis study mainly consists of two waves (2014 and 2017) of the BHFS dataset. This survey makes use of a standardized questionnaire of service provision assessment from the United States Agency for International Development’s (USAID) demography and health survey program. Together, the National Institute of Population Research and Training (NIPORT) and the Ministry of Health and Family Welfare (MOHFW) were responsible for conducting this survey with funding support from the Government of Bangladesh and USAID, the ICDDR, B aided NIPORT with field monitoring and quality assurance.\n\nThe number of active healthcare facilities that served as the sample frames for the BHFS in 2014 and 2017 was 19,184 and 19,811 correspondingly. Following a stratified random sample, a total of 1,596 and 1,600 healthcare institutions throughout the nation were chosen for the 2014 BHFS and 2017 BHFS, accordingly. The 2014 and 2017 BHFS samples were planned to contain facilities from the country’s seven administrative divisions (Barisal, Chittagong, Dhaka, Khulna, Rajshahi, Rangpur, and Sylhet). District hospitals (DHs), maternal and child welfare centers, Upazila health complexes (UHCs), upgraded union healthcare and family welfare centers, union subcenters/rural dispensaries, and community clinics (CCs), as well as private hospitals with at least 20 beds and non-governmental organization (NGO) static clinics/hospitals, were all included. In addition, the number of records that were available for the BHFS in 2014 was 1,548, whereas in 2017 it was 1,524. The research examined the infrastructures that provide services for CVDs in order to evaluate how well they are prepared for CVDs. Additionally, the research also examined the facilities that provide services for diabetes in order to evaluate how well they are prepared for diabetes. The Bangladesh healthcare system provides services for NCDs up to the UHC. The study, therefore, excluded facilities like MCWC, UHFWC and CC and also those with missing values. Based on the exclusion criteria, a total of 407 diabetes facilities and a total of 386 CVDs facilities were included in our study (Figures 1 and 2).\n\nCVD, cardiovascular disease.\n\nCVD, cardiovascular disease.\n\nThe data collection process consisted of using the facility inventory questionnaire. In order to gather data about general and specialized service preparedness, the facility inventory questionnaire was employed. Within the framework of Bangladesh, the questionnaires were modified, verified, and field-tested in advance. Earlier, the comprehensive 2014 and 2017 BHFS were made available to the public.\n\nThe use of a methodical electronic questionnaire allowed for the collection of data. Following a training period of 15 days, a total of 40 data collecting teams, each consisting of two interviewers, were organized. The Associates for Community and Population Research (ACPR) and the NIPORT were responsible for supervising data collection. Each one of the seven field monitoring groups was provided with a trained data processing specialist and a medical doctor, the former of whom also acted as a position of master trainer. The data collecting teams had frequent visits from the field supervision teams so their performance could be evaluated and data quality could be monitored. Participants consented to the questionnaire before they provided their answers.\n\nFollowing extraction of the relevant information from the BHFS 2014 and 2017 datasets, the dataset required for this research was compiled. Then, in accordance with The Service Availability and Readiness Assessment tool by WHO (WHO-SARA), the analyses for the objectives that were unique to each service (diabetes and cardiovascular diseases) were performed. The service area was taken into consideration as the binary variable, with the value “1” being assigned for availability and “0” being assigned for non-availability. The WHO-SARA score criteria for healthcare system preparation for NCDs was used in the evaluation, which resulted in the assessment. WHO-SARA guidelines for the analyses of the objectives that were unique to each service (diabetes and CVDs) are presented in Table 1. Comparison of healthcare facility characteristics and healthcare system readiness for diabetes and CVDs from 2014 and 2017 survey were performed by using descriptive statistics, statistical significance tests (paired t-test) by using Stata 14 (RRID:SCR_012763) and graphical presentation are provided.\n\n\nResults\n\nA comparative distribution among two surveys (2014 and 2017) in diabetes health care facilities is shown in Table 2. The 2017 survey showed an increase in facility coverage at the private clinics but a decrease at NGO clinics compared with the 2014 study.\n\nTable 3 shows the distribution of healthcare facilities for patients with CVDs between 2014 and 2017. We found that survey coverage of the facility at private clinics increased in 2017 compared with 2014 but declined at NGO clinics.\n\nTable 4 presents the readiness scores for facilities of each domain of diabetes in 2014 and 2017. As compared with 2014, the district hospital readiness score for diabetes increased from 60.62 to 59.04, the UHC readiness score increased from 45.01 to 52.29, and the NGO clinic readiness score increased from 48.65 to 55.28 in 2017. By contrast, at the private clinic, the score decreased from 63.12 to 56.11.\n\nCompared with 2014, in 2017, the readiness score of trained staff and guideline domain dropped in the district from 67.79 to 48.38, UHCs from 58.4 to 52.19, NGO clinics from 40.44 to 38.1, and private clinics from 40.84 to 21.85. On the contrary, the readiness score of the equipment domain increased at the district hospital in 2017 from 90.32 to 85.88, at the UPHC from 92.46 to 82.35, at the NGO clinic from 93.97 to 85.29 and at the private clinics from 83.17 to 80.28. Similarly, the district hospital had a domain readiness score of 73.12 compared with 65.53, UHC scored 47.45 with 43.69, and NGO clinics scored 76.51 with 67.15. At the same time, the private clinics’ scores declined from 79.81 to 76.7 in 2017. In 2017, the medicine domain’s score increased at the UHC from 17.1 to 11.34 and at NGO clinics from 12.57 to 11.39, while it decreased at the district hospital from 28.6 to 29.66 and at private clinics from 42.72 to 48.94.\n\nThe readiness scores for all CVD facilities are shown in Table 5. Table 5 lists the readiness scores for all CVD facilities. There was a decrease in the total mean readiness scores of CVDs at the district hospitals from 64.04 to 58.50, UHC from 53.06 to 53.0, NGO clinics from 44.53 to 48.65, and private clinics from 61.58 to 64.15 in 2017 compared with 2014. Similarly, compared with 2014, in 2017, readiness scores for trained staff and guidelines decreased at district hospitals from 52.42 to 58.48, UHC from 48.52 to 57.14, NGO clinics from 26.09 to 42.25, and private clinics from 18.63 to 40.58. The readiness score of the equipment domain increased at UHC (88.02 vs. 91.67) and private clinics from 92.75 to 95.34; however, at district hospitals, it dropped from 89.11 to 92.37 in 2017 compared with 2014. In 2017, the readiness score of the medicine domain went up at private clinics from 51.76 to 50.69; instead, the score rose at district hospitals from 36.45 to 44.07, UHC from 23.99 to 24.2, and NGO clinics from 18.84 to 20.34.\n\nFigure 3 depicts the region’s preparedness score. The bar chart shows the readiness score for both diabetes and CVD between 2014 and 2017 and informs us that the readiness score for diabetes and CVD management by region has not exceeded the 70% cutoff limit.14 In terms of diabetes treatment, the RI score dropped in urban regions, and increased in rural areas. The difference between urban and rural regions was significant (P=0.0001), however it did not hold over time (P=0.4443). However, the availability of CVD services in healthcare institutions is declining in both urban and rural areas. For CVD, the difference between urban and rural areas was substantial (P=0.0001), however it was not significant over time (P=0.3665).\n\nCVD, cardiovascular disease.\n\nFigure 4 depicts the readiness score for diabetes and CVD services by division. There is no division in which the readiness score has a high RI value. The difference in preparedness scores throughout the division was not statistically significant. Except for the Rajshahi division, the RI score for diabetes management indicated a downward trend. In 2017, all CVD divisions had lower RI scores than in 2014.\n\nCVD, cardiovascular disease.\n\n\nDiscussion\n\nThis research was effective in describing a thorough scenario of the availability of services and preparedness of healthcare systems in Bangladesh to deliver care associated with diabetes and CVDs. We have also identified the positive or negative changes that occurred from 2014 to 2017, identified the gaps in facilities regarding readiness towards diabetes and CVD services and compared the findings of previous research.13 The public health facilities in Bangladesh consist of CCs, Union health and family welfare centers (UHFWCs), UHCs, and DHs. The UHCs are the focal points for providing NCD services in Bangladesh. Moreover, recently MOHFW published an NCD management protocol and is trying to establish an NCD management model through establishment of a rereferral system between CCs and UHC.14\n\nHistorically, the healthcare system of Bangladesh has focused on infectious diseases, immunization, and maternal, child and reproductive health through public health facilities.11 Although, Bangladesh is among the top countries having large proportion of patients with diabetes, there is still a lack of information on it. The scenario is worse for CVD and it is associated with a large number of mortalities in Bangladesh.11 The overall improvement of healthcare facilities during 2014 to 2017 regarding readiness to provide NCD (DM, CVD) services is not quite satisfactory. In terms of services towards diabetes, the mean readiness score increased in 2017 for district hospitals, UHC, and the NGO clinic from 2014, although this improvement was not statistically significant. However, at the private clinics, the facility readiness score decreased. The MOHFW and owners of the private centers need to take effective actions for significant improvement.\n\nThere has always been a lack of trained human resources in healthcare facilities of Bangladesh.15 It a matter of concern that the readiness score of trained staff and guideline domain dropped in all four types of facilities we assessed. The government should revise their training modules and guidelines for the overall improvement of human resources. The MOHFW and DGHS of the Government of Bangladesh need to come forward to take effective action to reduce the human resource gap. Recent studies published in Bangladesh and other countries have observed low number of trained healthcare providers on diabetes management.15,16 While there is a lack of trained human resources in facilities, the readiness score of the equipment domain is quite satisfactory and increased at all types of facilities during the targeted three years. The effective use of equipment requires trained human resources, which is also very much essential for better service delivery. For diagnostic facility domain, the status increased in DHs, UHCs and NGO clinics, however it decreased for private facilities. A large proportion of our population are dependent on private healthcare facilities.17 Therefore, the diagnostic facility needs to be improved in private clinics.\n\nAccording to our data, the score in medicine domain was found to be quite low and the situation was worse in district hospitals and private clinics during 2014 to 2017. The medicine domain’s score increased at the UHC and NGO clinics. These results are consistent with the findings of a large number of studies conducted in LMICs, which suggest that healthcare providers are not yet totally equipped to deliver comprehensive diabetes care services.18,19 Our results are in line with those of prior research conducted in Bangladesh, which found that basic healthcare facilities had a major deficiency in the availability of relevant and important drugs for diabetes as well as an insufficient or restricted supply of such medicines.15\n\nThe prevalence of CVDs in Bangladesh is around 5%, and this percentage is consistent across all forms of CVD, sex and geographic locations, and for this reason, CVDs are the leading cause of death in Bangladesh.20 There was a decrease in the mean readiness scores of CVDs at the district hospitals, NGO clinics, and private clinics from 2014 to 2017. Similar to diabetes, readiness scores for trained staff and guidelines decreased in all types of facilities. The score of the equipment domain was decreased at district hospitals. The availability of skilled employees to deliver CVD–related healthcare services is of the utmost important. As a result, establishing specialist training for CVDs might provide optimal treatment.21 The readiness score of the medicine domain also reduced at district hospitals from UHC and NGO clinics. According to the findings of a number of studies conducted in Bangladesh, one of the primary difficulties faced by public healthcare facilities is a shortage of medications for CVDs.22 According to the findings of a study that was carried out recently, it was found that one of the primary reasons for patients’ disappointment with the government healthcare facilities is that there are not enough drugs or that they are of low quality.23 Disagreement has also been found in research conducted in India, on the availability of the sorts of pharmaceuticals suggested for the treatment of CVDs.24\n\nIn addition, despite the existence of a national standard for the treatment of diabetes, it is not followed appropriately in the vast majority of healthcare institutions at both the primary and secondary levels. Moreover, CVD management is not part of the national NCD management model in Bangladesh. Therefore, the respective authorities must incorporate CVD management guidelines into the national NCD management policy.\n\nThis study has identified the changes that took place in terms of facility readiness regarding NCD care from 2014 to 2017. The samples are typical of the nation as a whole and include data from all of Bangladeshi administrative units. On the other hand, this research does have a few restrictions when it comes to the method and the time frame. The BHFS 2017 was completed in 2017 and only covered information about DHs, UHCs, NGO clinics and private facilities. After 2017, no BHFS has been conducted until 2022, therefore most of the data are outdated. The tools used in these surveys are also outdated, which may also require modification for future surveys. These issues make it challenging for our study to reach a specific conclusion. The authors recommend collecting primary data with updated tools for a better understanding of facility readiness towards NCDs. Some further in-depth research and the outcomes of that research might point policymakers in the right path when it comes to taking the required actions.\n\n\nConclusions\n\nIn summary, there are significant deficiencies in essential categories of facility preparation, such as recommendations on diagnosing and treating diabetes and CVDs. These deficiencies need to be addressed as soon as possible. There is also a lack of skilled workers for services that are diabetes and CVD specific. The supply of medicines for diabetes and CVD is also inadequate. This study has compared the readiness score for diabetes and CVD over two separate survey data in 2014 and 2017. Our analysis concluded that no statistically significant development occurred during the targeted years regarding facility readiness. Since there has been no rise in the number of qualified workers throughout this period, services for diabetes and CVD have been ignored. Therefore, the crucial actions that need to be made are to ensure guidelines on the diagnosis and treatment of illnesses, the capacity to conduct diagnostics, and the capability to have sufficient medication and pharmaceuticals. These steps will help facilities be ready and help provide health coverage to the population. The information presented in this research might assist in the generation of scientific evidence that could be used by policymakers and other relevant stakeholders in establishing policies and programs that would benefit both the institutions and the population.", "appendix": "Data availability\n\nData used in this study are from the DHS VI and DHS VII datasets of the Bangladesh 2014 and 2017 Standard DHS and SPA, available from the Demographic and Health Survey (DHS) website https://dhsprogram.com/data/available-datasets.cfm. Access to the dataset requires registration and is granted only for legitimate research purposes. 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Publisher Full Text\n\nHanif AAM, Hasan M, Khan SA, et al.: Ten-years cardiovascular risk among Bangladeshi population using non-laboratory-based risk chart of the World Health Organization: Findings from a nationally representative survey. PLoS One. 2021 May 1; 16(5): e0251967. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBasu S, Andrews J, Kishore S, et al.: Comparative Performance of Private and Public Healthcare Systems in Low- and Middle-Income Countries: A Systematic Review. PLoS Med. 2012; 9(6): e1001244. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCockcroft A, Andersson N, Milne D, et al.: What did the public think of health services reform in Bangladesh? Three national community-based surveys 1999-2003. Health Res. Policy Syst. 2007 Feb 26; 5(1): 1–7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPakhare A, Kumar S, Goyal S, et al.: Assessment of primary care facilities for cardiovascular disease preparedness in Madhya Pradesh, India. BMC Health Serv. Res. 2015 Sep 23; 15(1): 408. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "206265", "date": "26 Oct 2023", "name": "Dian Sidik Arsyad", "expertise": [ "Reviewer Expertise Cardiovascular disease and risk factors epidemiology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn overall, the authors present an important study which demonstrate trends for the availability and readiness of the health care facility to deliver CVD and diabetes care in Bangladesh between 2014 and 2017. However, there are some areas that warrant further clarifications and corrections.\nAbstract\nIn conclusion, the first and second sentences are contradictory, and the words \"this improvement\" in the second sentence should be replaced or rephrased for more clear meaning.\n\nIntroduction\nThe introduction are too long, few of the sentences could be excluded for more concise and easy to read (for example 2nd and 3rd paragraph).\n\nTwo sentences in the first paragraph need citations : The World Health Organization (WHO) estimates that more than 15 million people between the ages of 30 and 69 years die every year from an NCD worldwide, with low-to-middle-income countries (LMICs) accounting for three-fourths (77%) of all early fatalities. According to the WHO, CVDs cause the death of 17.9 million people every year, whereas diabetes claims the lives of 1.5 million individuals each and every year.\n\nThe author need to clearly state the objective or aim of the study.\nMethods:\nThe author mentioned that they use BHFS data source in their study. Please clarify and mention what data from the original BHFS data source are extracted and included for analysis. For example equipment and essential drugs for CVD and diabetes care.\n\nPlease add references for information provided in the Data source section (SPA from USAID).\n\nIs there any information on how the study calculate the sample size?\n\nThere was a change (increase) in population/sampling frame of BHFS between 2014 and 2017, but there was a decrease in sample size from 2014 to 2017 BHFS waves, can the author explained what is causing the reduced sample size?\n\nPlease provide additional information on the excluded number and reason for exclusion in the total number of health facilities interviewed and actual sample size analyzed in Figure 1 and Figure 2.\n\nConsider adding some information to the \"Data management and analysis\" section to provide information on how these readiness domains were produced. I assume they are derived from a summary of inventory items?\n\nMore detailed information regarding data analysis will help readers to understand the steps for deriving the results in the tables.\nResults:\nThe descriptive results derived from inventory/tracer items in table 1 are missing from the results. I suggest to add the table to describe percentage of each of health facility levels that own every particular tracer items.\n\nInformation regarding basic readiness of health care facilities such as basic amenities, equipment, laboratory capacity, etc. are not presented in the results whilst it is provided in the service provision assessment questionnaire used in BHFS study (mentioned in the study design and settings). Can author explained about this?\n\nOne reference from Tuhin Biswas et al. regarding the readiness of health facilities for diabetes and cardiovascular services in Bangladesh using BHFS 2014 data showing a different results in some of the readiness index with this study while using the same data. For example, the readiness index of trained staff for Diabetes service at district hospital in 2014 is 30.5 (Biswas et.al) vs 62.71 (this study). and many other different results of 2014 data. Can author explained why there are differences?1\nDiscussion:\nThe author should state the main findings of the study and the answer of the research objective mentioned previously in the introduction section as the first paragraph in the discussion section.\n\nMissing reference for information stated in the first two sentences in paragraph 6 at discussion section.\n\nConclusion:\nThe conclusion mainly repeating what is already mentioned in both results and discussion. The author should rewrite the conclusion into more interpretable sentences, what is the study findings suggest, and what are the implications towards health care, especially for DM and CVDs.\n\nGeneral comments:\nThe language is well written, although could be improved more by rephrasing some of the unclear sentences.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "209886", "date": "30 Nov 2023", "name": "Rashmi Maharjan", "expertise": [ "Reviewer Expertise Non communicable disease", "epidemiology", "nursing", "healht systems", "needs assessment", "implementation science", "qualitative research" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIntroduction: I am not sure about the guideline of this journal for introduction but the introduction section for this paper is too long, over 800 words. Typically journals allow introduction for 250-350 word count. Authors should reduce the word count for the introduction section and make it concise and clear. References are missing in the introduction section. Some of them are hyperlinked but not numbered or cited in the reference section. Reference no 5 and a couple of others are not appropriate. Introduction section is not convincing enough, I don't see cohesion and requires extensive revision. For instance “Despite the fact that it is vital to understand the preparedness of the healthcare system in Bangladesh, particularly for services connected to diabetes and CVDs.”\nI do not understand this sentence. The gap and significance for this study is not well illustrated.\nI am not sure of the audience for this paper but it needs a revision from a native speaker, there are many redundant sentences and phrases and grammatical errors.\nAuthors have not stated why they are comparing 2014 and 2017 data, was there any huge reform in between or was this just their choice?\nLabels of figures and tables are not appropriate.\nSampling is not explained with detail.\nTable 1 can be added in supplementary file only; this should not be presented in the main body.\nAuthors need to elaborate in their methods section how they scored the readiness, calculated readiness index, and software they used for data analysis.\nAuthors also need to work on discussion section, I rarely see any academic discussion\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] } ]	1	https://f1000research.com/articles/12-898
https://f1000research.com/articles/12-437/v1	24 Apr 23	{ "type": "Method Article", "title": "Modelling host-Trypanosoma brucei gambiense interactions in vitro using human induced pluripotent stem cell-derived cortical brain organoids", "authors": [ "Praveena Chandrasegaran", "Agatha Nabilla Lestari", "Matthew C. Sinton", "Jay Gopalakrishnan", "Juan F. Quintana", "Praveena Chandrasegaran", "Agatha Nabilla Lestari", "Matthew C. Sinton", "Jay Gopalakrishnan" ], "abstract": "Background: Sleeping sickness is caused by the extracellular parasite Trypanosoma brucei and is associated with neuroinflammation and neuropsychiatric disorders, including disruption of sleep/wake patterns, and is now recognised as a circadian disorder. Sleeping sickness is traditionally studied using murine models of infection due to the lack of alternative in vitro systems that fully recapitulate the cellular diversity and functionality of the human brain. The aim of this study is to develop a much-needed in vitro system that reduces and replaces live animals for the study of infections in the central nervous system, using sleeping sickness as a model infection. Methods: We developed a co-culture system using induced pluripotent stem cell (iPSC)-derived cortical human brain organoids and the human pathogen T. b. gambiense to model host-pathogen interactions in vitro. Upon co-culture, we analysed the transcriptional responses of the brain organoids to T. b. gambiense over two time points. Results: We detected broad transcriptional changes in brain organoids exposed to T. b. gambiense, mainly associated with innate immune responses, chemotaxis, and blood vessel differentiation compared to untreated organoids. Conclusions: Our co-culture system provides novel, more ethical avenues to study host-pathogen interactions in the brain as alternative models to experimental infections in mice. Future work is required to increase the complexity of the organoids (e.g., addition of microglia and vasculature). We envision that the adoption of organoid systems will be beneficial to researchers studying mechanisms of brain infection by protozoan parasites. Furthermore, organoid systems have the potential to be used to study other parasites that affect the brain, including neurocysticercosis, significantly reducing the number of animals undergoing moderate and/or severe protocols associated with the study of neuroinflammation and brain infections.", "keywords": [ "Brain organoids", "sleeping sickness African trypanosomes", "brain infection", "in vitro culture" ], "content": "\n\n\n\nScientific benefit(s)\n\n\n\n• Human-derived brain organoids can be used to study neuropathogenesis during Trypanosoma infection. This has been challenging to study in human tissues due to ethical implications and lack of complex in vitro culture systems.\n\n• Evaluation of putative human brain cell populations associated with innate responses to protozoan pathogens.\n\n3Rs benefit(s)\n\n\n\n• Adoption of stem cell-derived 3D organoids can reduce ~47% of the mice used to study trypanosome infection, which would typically undergo protocols considered moderate or severe.\n\n• Further ~20% reduction of donor mice required to generate infectious parasites, which are moderate-to-severe procedures.\n\nPractical benefit(s)\n\n\n\n• Possible to effectively introduce mutations of interest into the organoids without the need to established complex and expensive breeding schemes.\n\n• Reductions in the number of animals required for in vivo work reduces breeding and husbandry costs.\n\nCurrent applications\n\n\n\n• Evaluation of global responses to a human pathogen.\n\nPotential applications\n\n\n\n• Screening for drugs acting on the CNS for treatment of infectious diseases.\n\n• Can be combined with additional organoids, cell type/s of interest (“building blocks”), and/or organic matrices or scaffolds to generate more complex tissues/organs.\n\n• Potential to manipulate genes/pathways (e.g., CRISPR-Cas9 gene editing) to assess their function in pathogenesis to infection.\n\n\nIntroduction\n\nNeurotropic pathogens encompass a wide range of parasitic organisms, from viruses to protozoan parasites, and are the causative agents of debilitating conditions affecting the central nervous system (CNS), often resulting in life-long impairments and death if left untreated. To date, most of these infections are studied using murine models of infection. Although these infection models often recapitulate the clinical outcomes observed in humans, there are serious ethical and biological implications associated with in vivo host-pathogen interaction studies. For instance, there are intrinsic differences in the immune response between hosts (e.g., mouse vs. human) that pose limitations for translational science. More recently, the generation of organoids developed in vitro from human stem cells have provided novel insights into developmental biology, and their potential application as alternative models to study host-pathogen interactions is starting to be recognised. These models offer an opportunity to interrogate human tissues that are difficult to access, such as CNS tissue. Indeed, human brain organoids comprising the diversity of cell types representative of the complex neuroepithelium are an increasingly attractive model system to interrogate how human nervous cells respond to infection. Currently, in vitro brain organoid systems are being used to study infections from ZIKA and SARS-CoV-2,1–4 and have proven insightful for understanding other parasitic infections, including toxoplasmosis and malaria.5,6 However, these in vitro systems have not been used to explore the pathogenesis of human African trypanosomiasis, a parasitic infection traditionally known for its devastating neurological effects.7–10\n\nHere, we explored whether human brain organoids can be used to model host-trypanosome interactions in vitro. Using bulk RNA sequencing, we observed that the human cortical brain organoids transcriptionally respond to the human pathogen T. brucei gambiense by upregulating gene pathways associated with innate immune functions, amongst others. Some of the upregulated genes are proposed to have antimicrobial properties, suggesting that human brain organoids are able to sense and respond to pathogens in the absence of innate immune cells (e.g., microglia). Using this novel in vitro system, we estimate a direct reduction of ~47% of animals required to achieve similar conclusions, and ~20% of animals used as donors to generate infectious parasites. The methods and results presented here have the potential to open new research avenues for the adoption of human brain organoids to model host-pathogen interactions with important implications for the 3Rs principles—replacement, refinement, and reduction.\n\n\nMethods\n\nThis work was conducted jointly at the Heinrich-Heine-Universität and the University of Glasgow.\n\n1. IMR90 human induced pluripotent embryonic stem cells (IPS(IMR90)-2 (RRID:CVCL_C435)), maintained at 80% confluency, were seeded at ~10,000 cells per well in mTeSR1 (Stem Cell Technologies, Vancouver, Canada) in 24-well, Matrigel-precoated plates (Corning, NY, USA). Cells were incubated at 37°C and 5% CO2 with medium changed daily.\n\n2. Colonies were observed to form after 7-10 days.\n\n3. To detach colonies, mTeSR1 media was removed and the wells were washed once with 1 ml of 1X D-PBS without Calcium and Magnesium (Stem Cell Technologies) at 37°C.\n\n4. PBS was removed and discarded. A total of 1 ml ReLeSR™ at 37°C temp (Stem Cell Technologies) was added per well.\n\n5. Plates were incubated for 5-7 minutes at 37°C, after which 1ml TeSR™ was added to each well and the plates were vortexed for 2-3 minutes at room temperature (17-22°C) until the cultures were fully detached. Note that the mean aggregate size should be approximately 50-200 μm.\n\n6. Cell pellets were resuspended in 500 μl AggreWell medium and 10% Clone R (Stem Cell Technologies) and seeded at 9,000 cells per well in round-bottom 96-well plates (in ~200 ml) and incubated at 37°C and 5% CO2.\n\n7. After two days, the medium was replaced with fresh AggreWell without Clone R, and the cells were incubated for an additional three days at 37°C and 5% CO2. The medium was changed by gently placing the plate in a 45° angle to medium change.\n\n8. On day six, the medium was replaced with neural induction medium (NIM) containing DMEM/F12, N2 supplement (Thermo Fisher Scientific, Waltham, MA, USA), minimum essential medium-nonessential amino acids (MEM-NEAAs), GlutaMAX (Thermo Fisher Scientific) and 1 μg/ml heparin (Sigma, MO, USA), and the cells incubated for five days 37°C and 5% CO2.\n\n9. After the NIM medium was changed, embryoid bodies (EBs) were transferred by pipette onto Matrigel droplets (Corning) that were 3 mm in diameter on the inner part of a 75 mm petri dish. The EBs should appear as located at the centre of the droplet. These droplets were incubated for 1 hour at 37°C, transferred to 24-well plates and maintained in cerebral organoid differentiation medium (CORD) containing DMEM/F12 and Neural Basal Medium (in 1:1 ratio), supplemented with 1:200 N2 (Thermo Scientific), 1:100 l-glutamine (Stem Cell Technologies), 1:100 B27 without vitamin A (Thermo Scientific), 100 U/ml penicillin, 100 μg/ml streptomycin, 23 μM insulin (Sigma-Aldrich), 0.05 mM MEM non-essential amino acids (NAA), and 0.05 mM β-mercaptoethanol (Life Technologies) was used to differentiate the Matrigel embedded droplets. The medium was replaced every three days until usage.\n\n\n\n1. Culture-adapted bloodstream slender forms of Trypanosoma brucei gambiense Eliane strain (MHOM/CI/52/ITMAP 2188)11 were used in all experiments. This strain, originally isolated from an infected patient in Côte d’Ivoire (Ivory Coast)11 was previously adapted in the laboratory to grow in HMI-9 culture medium supplemented with 20% foetal calf serum (FCS).\n\n2. Cultures were maintained at 37°C in humidified atmosphere containing 5% CO2. Pleomorphic parasites were typically maintained at a density of 105 and 106 parasites/ml at 37°C and 5% CO2.\n\n\n\n1. A total of 105 parasites at log-phase of growth were co-cultured with the brain organoids on 12 well plates (Final ratio of 1 organoid:105 parasites per well) for a period of 24 or 72 hours in HMI-9 media diluted 50:50 with CORD media at 37°C and 5% CO2 in round-bottomed 96-well plates. These two time points were chosen to mimic acute (24 hours) and chronic (72 hours) responses and we determined that parasites grew well under these conditions, at least during the first 72 hours in culture (Figure 1B).\n\n2. In parallel, organoids cultured in HMI-9 media diluted 50:50 with CORD media at 37°C and 5% CO2 but without parasites were also seeded in round-bottomed 96-well plates and were included as controls to assess the effect of diluted media on the organoids transcriptome. As controls, we included organoids kept in 50:50 HMI-9:CORD organoid media alone.\n\n3. After 24 or 72 hours, some organoids were fixed in 4% PFA for 24 hours at room temperature and preserved as paraffin-embedded blocks for immunohistochemistry analysis. The rest of the organoids were processed for bulk transcriptomics.\n\nA) Schematic representation of the experimental design developed for this study. B) Growth curve assay for T. b. gambiense in HMI-9 alone (teal) or diluted 50:50 with CORD media (magenta). The arrow indicates a dilution step to bring the parasite cultures down to 102 parasites/ml. Data shown as mean ± standard deviation from three independent experiments. C) Representative H&E staining and MAP 2 Immunohistochemistry from naïve (top) and T. brucei gambiense-infected (bottom) organoid after 72 hours of in vitro co-culture. Scale bar = 50 μm. D) Principal component analysis of the samples including the bulk RNA sequencing analysis. Volcano plot of differentially expressed genes between untreated organoids and after (E) 24 hours and (F) 72 hours in culture with T. brucei gambiense. Dotted line represents the significance (-0.5 < Log2FC > 0.5 and p adjusted value < 0.05). Pathway analysis of the genes dysregulated at (G) 24 hours and (H) 72 hours in culture with T. brucei gambiense. The adjusted p value (Q value) for each of the enriched pathways is included. MAP 2, microtubule associated protein 2.\n\n\n\n1. Paraformaldehyde-fixed organoid were processed into paraffin blocks for long-term maintenance.\n\n2. We prepared 5 μm thick paraffin sections, which were placed on Superfrost Plus™ slides (Fisher Scientific) and stained with Mayer’s haematoxylin Solution (Sigma-Aldrich), Bluing Buffer (Dako) for 5 minutes and 1:10 dilution of Eosin Y solution (Sigma-Aldrich) in 0.45 M of Tris-acetic acid buffer, pH 6.0, for 5 minutes in distilled water, with 3-4 washing steps in ultrapure water between each step. All solutions were kept at room temperature. The H&E staining was conducted using a Dako Autostainer Link 48 (Dako) with all the incubation steps at room temperature (17-22°C).\n\n3. For staining with the monoclonal neuron-specific microtubule associated protein 2 (MAP 2, Clone M13, Thermo Fisher Scientific Cat. No. 13-1500. RRID: AB_2533001), 5 μm thick paraffin sections were treated in a pressure cooker (~140°C) for 5 minutes in citrate buffer pH 6.0, followed by staining with the monoclonal NSE antibody (Cell Signalling Technologies, clone E2H9X, Cat. No. 24330. RRID: AB_2868543) diluted in 1:1,000 in 1× blocking buffer (Dako) and incubated overnight at 4°C. Staining was conducted using a goat anti-Rabbit antibody coupled to Horseradish peroxidase (1:1,000, Thermo Fisher Scientific Cat. No. A16104. RRID: 2534776) for 1 hour at room temperature.\n\n4. The samples were mounted in VECTASHIELD Antifade Mounting Media with DAPI (Vectorlabs, Cat. No. H-1200. RRID: AB_2336790) and visualised on a Axio Imager 2 instrument (Zeiss. RRID: SCR_018876).\n\n\n\n1. Before proceeding with the RNA extraction step, all the pipettes and surfaces were thoroughly cleaned with RNAZap (Thermo) to remove RNAses. For this protocol, we used sterile filtered tips.\n\n2. At the selected time points, brain organoids were harvested and washed in 500 μl of 1X PBS at 4°C twice. The washes were conducted by letting the organoids settle at the bottom of a 1.5 ml Eppendorf tube before removing the supernatant.\n\n3. Once washed, the organoids were resuspended in 500 μl of Qiazol (Qiagen) and dissociated firmly by pipetting up and down using a wide bore p1000 pipette tip.\n\n4. The dissociated tissue was then subjected to total RNA extraction using the mRNeasy kit (Qiagen), following the recommended volume of chloroform. All the solutions were kept at room temperature (17-22°C) unless indicated otherwise by the manufacturer. All the centrifugation steps were conducted at 4°C. We eluted the total RNA from brain organoids in 50 ml of EB buffer (Qiagen). On average, we detected a recovery of ~100 μg/ml of total RNA, as quantified by Qubit.\n\n5. The quality of the RNA was assessed on a Bioanalyzer RNA Pico chip (Agilent). We considered an RNA Integrity Number (RIN) value >8.0 to be ideal for bulk RNA sequencing. All the samples analysed here consistently had a RIN value >8.0.\n\n6. Once assessed, 1 μg of total RNA per sample was submitted to the Beijing Genomic Institute (BGI; RRID: SCR_011114) for RNA sequencing and processed for 150 bp paired-end sequencing on the DNBSeq platform (RRID: SCR_017981).\n\n7. Once sequenced, raw reads were filtered using SOAPnuke (RRID:SCR_015025) software (v1.5.2) developed by BGI, allowing for the removal of reads containing adapters, reads with N content >5%, or with a base quality score <15.\n\n8. Clean reads were then aligned the to the human genome using the package Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT) (RRID:SCR_015530) (v2.0.4) and Bowtie 2 (RRID:SCR_016368) (v2.2.0), with default parameters using the Genome reference consortium Human Build 38 patch release 12 (GRCh38.p12).\n\n9. Subsequent downstream analysis, including differential gene expression and pathway analysis using Gene Ontology (RRID: SCR_002811), were conducted on the Dr. Tom analysis suite built by BGI. For gene expression analysis, differentially expressed genes were considered significant if the adjusted p value < 0.05, and Log2 fold change of -2< or >2.\n\n\nResults\n\nAfrican trypanosomes cause extensive neurological changes resulting in neuropsychiatric disorders and culminating in death if not treated adequately. Although this disease is frequently modelled using experimental infections in mice, for ethical reasons around the use of animals in research, we were motivated to explore the utility of induced pluripotent stem cell (iPSC)-derived human cortical brain organoids to model brain-trypanosome interactions in vitro as alternatives to in vivo infections. Thus, using an in vitro co-culture system, we set out to characterise the transcriptional responses of the iPSC-derived human brain organoids to the human pathogen T. brucei gambiense (Figure 1A),22,23 compared to organoids that were not incubated with the parasites. These time points were selected to evaluate early (24 hours) and late (72 hours) responses, in an attempt to gain as much insight as possible into the temporal dynamics associated with tissue responses to infection. Importantly, we did not detect significant morphological or histological changes in the organoids exposed to the parasites based on H&E staining and MAP 2 staining (Figure 1C), suggesting that T. brucei gambiense does not elicit tissue damage over a 72 hour culture period. Principal component analysis demonstrates that at a transcriptional level, the samples segregate mainly based on infection status and experimental time point, but with limited transcriptional variation between samples harvested at 24 and 72 hours (Figure 1D). In these brain cortical organoids, we identified a total of 6,157 dysregulated genes at 24 hours (3,234 and 2,923 downregulated and upregulated genes, respectively) and 6,677 dysregulated genes at 72 hours (3,468 and 3,209 downregulated and upregulated genes, respectively) (Figure 1E and 1F, and Table S1 in Underlying data),22,23 defined as genes with an adjusted p value < 0.05 and a Log2 Fold change of -2< or >2. To obtain a broad overview of immune related pathways, we examined cytokine, chemokine, and immune receptors that were significantly dysregulated in brain organoids exposed to T. b. gambiense. We detected several genes with canonical immune functions such as CD274, that encodes for Programme death ligand 1(PD-L1), the complement factor C4B, and the glial fibrillary acidic protein (GFAP), typically associated with gliosis during CNS inflammation12 (Table 1 and Table S2 in Underlying data).22,23 Additionally, we detected the expression of several interleukins and chemokines such as interleukin-34 (IL34) that promotes monocyte and macrophage survival and differentiation,13 the chemokine CXCL14 involved in immune cell recruitment,14 transforming growth factor beta 1 (TGFB1), and the alarmin IL33, which is a critical mediator of innate immune responses and inflammation15 (Table 1 and Table S2 in Underlying data).22,23 We also detected significant expression of the interleukin-17 receptor subunit A and D (IL17RA and IL17RD, respectively), interleukin-10 receptor subunit a (IL10RA), and the Interferon gamma receptor 1 (IFNGR1) (Table 1 and Table S2 in Underlying data),22,23 indicating that these organoids are primed to sense and respond to IL-17, IL-10, and IFNγ signalling upon exposure to T. brucei gambiense. Furthermore, we also detected genes involved in angiogenesis and endothelial function, including the vascular endothelium growth factor subunit c (VEGFC), epithelial cell adhesion molecule (EPCAM), cadherin 5 (CDH5), the integrin associated protein CD47, and von Willebrand factor (VWF) (Table 1 and Table S2 in Underlying data),22,23 suggesting that co-culture with T. b. gambiense also induces the expression of genes associated with vasculogenesis and vascular repair. Some of these genes showed a temporal expression dynamic, with some genes involved in immune sensing, recruitment and tissue repair (e.g., CXCL14, VWF, TLR4, IL4R) being exclusively detected after 72 hours of exposure to T. b. gambiense compared to naïve controls.\n\nTo gain a better understanding of the broad transcriptional responses triggered in the human brain organoids to T. b. gambiense infection, we performed Gene Ontology analysis on genes significantly dysregulated. After 24 hours of exposure to T. b. gambiense, the iPSC-derived human brain organoids upregulate genes associated with blood vessel and vasculature development, signalling, and chemotaxis, with a concomitant reduction in genes associated with response to hypoxia, defence response against viruses, and protein ubiquitination (Figure 1G). At 72 hours, the pathways overrepresented in the organoids transcriptome were associated with glial cell differentiation, positive regulation of CD8+ T cells, chemotaxis, and vascular and blood vessel differentiation, and a significant reduction of gene pathways associated with cell cycle progression, protein transport and proteasome-mediated protein degradation (Figure 1H). Taken together, these data suggest that T. b. gambiense trigger a broad innate-like immune response in the iPSC-derived human brain organoids accompanied by upregulation of genes involved in vascular development, immune chemotaxis, and cytokine-mediated immune signalling.\n\nSimilar approaches have been recently implemented to study host-pathogen interactions in the context of viral infections and protozoan infections, including toxoplasmosis and malaria, in vitro. We anticipate that our detailed protocol can be used to explore further interactions between T. brucei and iPSC-derived human brain organoids in more detail, including novel effects of T. brucei on the function of human neurons, which remains unexplored. We additionally anticipate that the protocol provided here can be leveraged to study potential cytotoxic side effects of novel antiparasitic compounds.\n\n\nDiscussion and outlook\n\nIn this study, we tested the possibility of using stem cell-derived human brain organoids as an in vitro system as an alternative mode to live animals to study host-trypanosome interactions, in line with the 3Rs principles. We firstly set up an in vitro co-culture system whereby iPSC-derived human brain organoids were co-cultured with the human pathogen T. b. gambiense and assessed the response of these organoids to the pathogen using histology and transcriptomics as a proxy for global responses to the pathogen. The data presented here demonstrate that iPSC-derived human brain organoids trigger a transcriptional programme associated with an innate-like immune response when exposed to T. brucei gambiense. Bulk transcriptomics has enabled us to identify that the brain organoids specifically respond to T. brucei gambiense in vitro by upregulating several genes with putative immune functions such as CXCL14, the alarmin IL33, the complement component C4B, as well as vasculogenesis and vascular repair such as VEGFC, and EPCAM. CXCL14 is a potent antimicrobial cytokine secreted in response to inflammatory processes and is critical for human neutrophil recruitment,14,16,17 which have been proposed as important players in controlling CNS infections.18,19 Similarly, the upregulation of several genes critical for angiogenesis and development of vascular beds, including VEGFA, VEGFB, and VWF, suggests that they may potentially support vasculogenesis in the presence of this pathogen. All of these observations require further testing at the protein and functional level but provide an initial robust framework to dissect the relevance of these 3D culture systems to model brain-trypanosome interactions.\n\nOur work provides an initial approach to explore the utility of complex 3D culture systems to study host-Trypanosoma interactions in vitro, adding African trypanosomes to the compendium of pathogens that have been tested to model host-pathogen interactions using brain organoids. However, there are many challenges and considerations that need to be addressed for the full implementation of these in vitro systems, with the aim of replacing animal models of infection. One of the critical hurdles is to generate fully mature organs in vitro, encompassing all the cell types typically identified in vivo, including microglia and vasculature cells,20 which are likely to be the main drivers of and/or responders to infection. The incorporation of additional organoids (e.g., vascular or choroid plexus organoids1) or inclusion of additional cell types (e.g., endothelial cells, microglia), referred to as “building blocks”,21 will support the development of mature cortical brain organoids that could faithfully recapitulate the immunological responses observed in vivo. Given these technical and biological limitations, we are unable to examine the role of these cell types using our in vitro host-pathogen culture system. Future work addressing these key challenges will improve the quality of these organoids to model CNS infections in vitro, facilitating the reduction and/or replacement of animals in research. Our work provides a wealth of data that can be further mined to design, refine, or implement in vitro experiments (e.g., using stem-cell derived astrocytes) as alternatives for in vivo work, and provides a foundation for future work in this area.\n\nIn summary, we delivered an initial proof-of-concept framework for future adoption of these in vitro systems for neuro-immunology research, motivated by the need to reduce and/or fully replace to use animals to study brain-pathogen interactions, in line with the 3Rs principles under the Animals (Scientific procedure) Act, 1986. Based on our estimations, with this model in place, animals used to study brain infections with African trypanosomes, typically considered to be moderate to severe procedures, would have been reduced by ~47%, with an additional ~27% reduction in the number of immunocompromised mice used as donors to generate infectious parasites.", "appendix": "Data availability\n\nGene Expression Omnibus: Modelling host-Trypanosoma brucei gambiense interactions in vitro using human induced pluripotent stem cell-derived cortical brain organoids. Accession number GSE220766; https://identifiers.org/geo:GSE220766. 22\n\nFigshare: Modelling host-Trypanosoma brucei gambiense interactions in vitro using human induced pluripotent stem cell-derived cortical brain organoids. https://doi.org/10.6084/m9.figshare.22491100. 23\n\nThis project contains the following underlying data:\n\n‐ Table S1 (Quality control and summary of the bulk transcriptomics analysis obtained from the iPSC-derived human brain organoids co-culture with T. b. gambiense)\n\n‐ Table S2 (List of differentially dysregulated genes in iPSC-derived human brain organoids at 24 h and 72 h in co-culture with T. b. gambiens)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nPellegrini L, et al.: SARS-CoV-2 Infects the Brain Choroid Plexus and Disrupts the Blood-CSF Barrier in Human Brain Organoids. Cell Stem Cell. 2020; 27: 951–961.e5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRamani A, et al.: SARS-CoV-2 targets neurons of 3D human brain organoids. EMBO J. 2020; 39: e106230.\n\nQian X, Nguyen HN, Jacob F, et al.: Using brain organoids to understand Zika virus-induced microcephaly. Dev. Camb. Engl. 2017; 144: 952–957. Publisher Full Text\n\nGarcez PP, et al.: Zika virus impairs growth in human neurospheres and brain organoids. Science. 2016; 352: 816–818. PubMed Abstract \| Publisher Full Text\n\nSeo H-H, et al.: Modelling Toxoplasma gondii infection in human cerebral organoids. Emerg. Microbes Infect. 2020; 9: 1943–1954. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarbuzariu A, et al.: Modelling heme-mediated brain injury associated with cerebral malaria in human brain cortical organoids. Sci. Rep. 2019; 9: 19162. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRodgers J, Steiner I, Kennedy PGE: Generation of neuroinflammation in human African trypanosomiasis. Neurol. Neuroimmunol. Neuroinflammation. 2019; 6: e610. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKennedy PGE, Rodgers J: Clinical and Neuropathogenetic Aspects of Human African Trypanosomiasis. Front. Immunol. 2019; 10: 39. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHuman African trypanosomiasis - The Lancet. http\n\nThe Burden of Human African Trypanosomiasis\|PLOS Neglected Tropical Diseases. 10.1371/journal.pntd.0000333\n\nRadwanska M, et al.: Novel primer sequences for polymerase chain reaction-based detection of Trypanosoma brucei gambiense. Am. J. Trop. Med. Hyg. 2002; 67: 289–295. PubMed Abstract \| Publisher Full Text\n\nQuintana JF, et al.: Single cell and spatial transcriptomic analyses reveal microglia-plasma cell crosstalk in the brain during Trypanosoma brucei infection. Nat. Commun. 2022; 13: 5752. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFoucher ED, et al.: IL-34 induces the differentiation of human monocytes into immunosuppressive macrophages. antagonistic effects of GM-CSF and IFNγ. PLoS One. 2013; 8: e56045. Publisher Full Text\n\nLu J, Chatterjee M, Schmid H, et al.: CXCL14 as an emerging immune and inflammatory modulator. J. Inflamm. 2016; 13: 1. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCayrol C, Girard J-P: IL-33: an alarmin cytokine with crucial roles in innate immunity, inflammation and allergy. Curr. Opin. Immunol. 2014; 31: 31–37. PubMed Abstract \| Publisher Full Text\n\nDai C, et al.: CXCL14 displays antimicrobial activity against respiratory tract bacteria and contributes to clearance of Streptococcus pneumoniae pulmonary infection. J. Immunol. Baltim. Md. 1950. 2015; 194: 5980–5989.\n\nTsujihana K, et al.: Circadian protection against bacterial skin infection by epidermal CXCL14-mediated innate immunity. Proc. Natl. Acad. Sci. U. S. A. 2022; 119: e2116027119. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStock AJ, Kasus-Jacobi A, Pereira HA: The role of neutrophil granule proteins in neuroinflammation and Alzheimer’s disease. J. Neuroinflammation. 2018; 15: 240. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKanashiro A, et al.: The role of neutrophils in neuro-immune modulation. Pharmacol. Res. 2020; 151: 104580. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSabate-Soler S, Bernini M, Schwamborn JC: Immunocompetent brain organoids—microglia enter the stage. Prog. Biomed. Eng. 2022; 4: 042002. Publisher Full Text\n\nHofer M, Lutolf MP: Engineering organoids. Nat. Rev. Mater. 2021; 6: 402–420. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChandrasegaran P, et al.: Modelling host-Trypanosoma brucei gambiense interactions in vitro using human induced pluripotent stem cell-derived cortical brain organoids. [Dataset]. Gene Expression Omnibus. Reference Source\n\nQuintana J: Modelling host-Trypanosoma brucei gambiense interactions in vitro using human induced pluripotent stem cell-derived cortical brain organoids. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "170892", "date": "03 May 2023", "name": "David Smith", "expertise": [ "Reviewer Expertise Organoids", "parasitology", "host:parasite interactions", "protozoa", "helminths" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 from Chandrasegaran et al., reports the application of iPSC-derived cerebral organoids as a model for neurological T. b. gambiense infection. Organoids are increasingly powerful in vitro models that better represent in vivo tissues compared to simpler cell culture systems. This is allowing researchers to address research questions at a level of precision and detail that is difficult to achieve in vivo. It also greatly reduces reliance on animals to experimentally address specific research questions. Overall, the methods in this manuscript are very clear (some minor points to be addressed stated below) which, importantly, provides an accessible protocol for other researchers to follow for the cultivation of iPSC-derived cerebral organoids (for which the authors are commended). In the results, the authors demonstrate infection of cerebral organoids by T. b. gambiense parasites and the differential gene expression determined between uninfected organoids and organoids infected with T. b. gambiense for 24 or 72 hours. A large number of genes are differentially up and down regulated and the author’s inclusion of GO analysis is helpful to provide broader context to these transcriptomics differences. This report is overall very clear (with some minor points to address below) and will provide a valuable addition to the literature. There is minimal modification necessary before this manuscript is suitable for indexing.\nHow long were the cerebral organoids cultivated for before challenge with parasites? Were the consistently matured to the same started point? What is the timescale for “maturing” the cerebral organoids?\n\nPoint 1 under “Immunohistochemistry”(methods) should read “storage” instead of “maintenance”.\n\nThe results section indicates 3 experimental replicates were used in the RNA-seq analysis for each test group. Please make this clear in the associated methods section.\n\nPerhaps there is not sufficient read depth, but if it is possible it would be interesting to map the parasite RNA-seq reads from the 24h and 72h group to determine any differences, potentially informing on how the parasite is adapting to co-culture and infection in the cerebral organoids and whether this is similar to what would be expected/observed in vivo. If this is possible, it would have been useful to have a test group of parasites in the RNA-seq analysis representative of parasites immediately prior to organoid challenge (to better assess how the parasite itself is responding to co-culture with the organoids) – this is just a point for future consideration for the authors. It would be useful in future experiments to see how long a chronic infection can persist in the organoids (i.e. how far beyond 72 hours post-challenge can the cultures be maintained?).\n\nHow did the authors determine the predicted reduction in animal usage by replacement with organoids.\n\nFigure legend 1C should say (left) and (right) instead of (top) and (bottom)? Also use arrows in panel C to indicate parasites for non-specialists.\n\nDid the authors quantify parasite burden in the cerebral organoids at 24 and 72 hours post-challenge, relative to the 105 parasites used to challenge organoids at the start of the experiment.\n\nAre a suitable application and appropriate end-users identified? Yes\n\nAre the 3Rs implications of the work described accurately? Yes\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": "9944", "date": "28 Jul 2023", "name": "Juan Quintana", "role": "Author Response", "response": "This manuscript from Chandrasegaran et al., reports the application of iPSC-derived cerebral organoids as a model for neurological T. b. gambiense infection. Organoids are increasingly powerful in vitromodels that better represent in vivo tissues compared to simpler cell culture systems. This is allowing researchers to address research questions at a level of precision and detail that is difficult to achieve in vivo. It also greatly reduces reliance on animals to experimentally address specific research questions. Overall, the methods in this manuscript are very clear (some minor points to be addressed stated below) which, importantly, provides an accessible protocol for other researchers to follow for the cultivation of iPSC-derived cerebral organoids (for which the authors are commended). In the results, the authors demonstrate infection of cerebral organoids by T. b. gambiense parasites and the differential gene expression determined between uninfected organoids and organoids infected with T. b. gambiense for 24 or 72 hours. A large number of genes are differentially up and down regulated and the author’s inclusion of GO analysis is helpful to provide broader context to these transcriptomics differences. This report is overall very clear (with some minor points to address below) and will provide a valuable addition to the literature. There is minimal modification necessary before this manuscript is suitable for indexing. Authors: We sincerely thank this reviewer for taking the time to provide feedback on our methods article. We hope the comments below clarify their questions. How long were the cerebral organoids cultivated for before challenge with parasites? Were the consistently matured to the same started point? What is the timescale for “maturing” the cerebral organoids? Authors: The cortical brain organoids used in this study were ~2 months old, to ensure a minimum level of maturation, as reported in references 2 and 4. Point 1 under “Immunohistochemistry”(methods) should read “storage” instead of “maintenance”. Authors: We have amended the text accordingly. The results section indicates 3 experimental replicates were used in the RNA-seq analysis for each test group. Please make this clear in the associated methods section. Authors: We have clarified this in the methods section, in step 2 under “Bulk RNA sequencing and data analysis”. Perhaps there is not sufficient read depth, but if it is possible it would be interesting to map the parasite RNA-seq reads from the 24h and 72h group to determine any differences, potentially informing on how the parasite is adapting to co-culture and infection in the cerebral organoids and whether this is similar to what would be expected/observed in vivo. If this is possible, it would have been useful to have a test group of parasites in the RNA-seq analysis representative of parasites immediately prior to organoid challenge (to better assess how the parasite itself is responding to co-culture with the organoids) – this is just a point for future consideration for the authors. It would be useful in future experiments to see how long a chronic infection can persist in the organoids (i.e. how far beyond 72 hours post-challenge can the cultures be maintained?). Authors: Indeed, we agree with this reviewer, and this is something we plan to consider in future experiments. We had financial constraints that limited our ability to explore how the parasites responded to the co-culture system. It is important to note that in our hands, we did not see parasites penetrating the organoids per se, and so we decided to wash the organoids with 1X PBS to remove as many parasites as possible. This has now been clarified in the methods section, in step 3 under “Trypanosoma brucei gambiense – human brain organoids co-culture system”. How did the authors determine the predicted reduction in animal usage by replacement with organoids. Authors: The figures presented in the current version of the manuscript were based on a prediction assuming full adoption of this method, and the number of animals that undergo similar procedures (e.g., brain responses to infection) over the past 5 years of our current Home Office license. In this case, we determined that on a typical year of our license, 47/100 animals undergo moderate-to-severe procedures involving evaluating brain responses to infection that could be fully replaced with a suitable in vitro brain organoids system. To generate those infections, we also typically require donor mice from which we obtain infective trypanosomes, which we estimated to be reduced by about 1/5 with the organoids system in place. Figure legend 1C should say (left) and (right) instead of (top) and (bottom)? Also use arrows in panel C to indicate parasites for non-specialists. Authors: We have amended the figure legend as suggested. Unfortunately, we did not detect parasites inside the organoids by any means, and so the images in panel 1C are showing the integrity of the organoids post-culture compared to untreated organoids, and the staining for neurons using MAP2. Did the authors quantify parasite burden in the cerebral organoids at 24 and 72 hours post-challenge, relative to the 105 parasites used to challenge organoids at the start of the experiment. Authors: In short, we did not. We had originally intended to inoculate the parasites inside the organoids using microinjections, but this was not feasible for various reasons (e.g., access to adequate microinjection platforms, size of the organoids, etc). Thus, we decided to co-culture the parasites with the organoids instead. Before doing so, we ensured that the parasite remained viable under the culture conditions (50:50 organoids:HMI9 media) using a growth curve approach, as shown in figure 1B." } ] }, { "id": "170807", "date": "18 May 2023", "name": "Maria Bernabeu", "expertise": [ "Reviewer Expertise 3D brain bioengineered models", "host-parasite interactions", "malaria", "vascular engineering" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this manuscript, Chandrasegaran et al., use for the first-time in vitro brain organoids to understand Trypanosoma brucei gambiense pathogenesis. This is an important topic, as brain organoids have already become as a valid strategy to study disease mechanisms. Although the team led by Juan Quintana is already a leader in animal models of T. brucei, I would like to praise their efforts on using alternative disease modelling tools that could reduce the number of research animals and overcome differences between mouse and humans. The authors show differential gene expression after brain organoid incubation with T, brucei gambiense after a 24h and 72h incubation. The manuscript is timely, and overall, scientifically sound and well written. I support the article indexing after the introduction of some modifications on the text.\nMajor\nAlthough the methods section is very clear, I couldn’t find any reference on how long the brain organoids were grown. This is important because brain organoids are grown for long periods of time (up to a year) and depending on the maturation time, they acquire different brain developmental stages. I would suggest that the authors include this information in the methods section, as well as on the results or discussion section, as it is important for interpretation of the results.\n\nHow does the 24h and 72h time point or the parasite concentration used compare with the life cycle of T. brucei gambiense in the brain? This information could be useful for an audience not familiar with T. brucei.\n\nThe authors couldn’t find any brain damage markers on Fig 2C after staining with two different markers. However, other non-used markers could be affected. Although the sentence in the result section mildly implies that (\"Importantly, we did not detect significant morphological or histological changes in the organoids exposed to the parasites based on H&E staining and MAP 2 staining (Figure 1C), suggesting that T. brucei gambiense does not elicit tissue damage over a 72 hour culture period.”), I would suggest to rephrase to make it more obvious. Furthermore, did the author quantify for differences in expression on MAP2, or is the analysis mostly qualitative?\n\nThe increased expression of endothelial markers is intriguing, taking into account that brain organoids present minimal presence of endothelial cells. This is important because vascularization of brain organoids is one of the main challenges in the bioengineering field, and the presence of vasculature in these models could be used to study the molecular mechanisms of T. brucei crossing through the brain microvasculature. Did the authors checked for the presence of blood vessels by immunostaining. In a similar topic, I would like to clarify that EPCAM is not an endothelial marker, so I would recommend to delete any reference to EPCAM in the figures/tables, results and discussion section.\nMinor\nAbstract “Future work is required to increase the complexity of the organoids (e.g., addition of microglia and vasculature). We envision that the adoption of organoid systems will be beneficial to researchers studying mechanisms of brain infection by protozoan parasites.” Although it is important to showcase the limitations of the model, the second part of the sentence has somehow a negative connotation on the validity of the current results. In this paper, the authors validate the use of organoids systems to study T. brucei infection and the authors should highlight that they already represent an alternative to animal models.\n\nResearch highlights (3Rs benefit(s)) and results page 3: Which methodology did you use to measure the reduction in animal models that could be used to study trypanosomiasis?\n\nThere seems to be a reference missing in: “For instance, there are intrinsic differences in the immune response between hosts (e.g., mouse vs. human) that pose limitations for translational science.”\n\nResults Page 7: “We also detected significant expression of the interleukin-17 receptor subunit A and D (IL17RA and IL17RD, respectively), interleukin-10 receptor subunit a (IL10RA), and the Interferon gamma receptor 1 (IFNGR1) (Table 1 and Table S2 in Underlying data),22, indicating that these organoids are primed to sense and respond to IL-17, IL-10, and IFNγ signalling upon exposure to T. brucei gambiense” - I would recommend to rephrase to something similar to “these organoids are prime to sense and response to T. brucei gambiense by activating IL-17, IL-10 and IFNg pathways.”\n\nAre a suitable application and appropriate end-users identified? Yes\n\nAre the 3Rs implications of the work described accurately? Yes\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": "9945", "date": "28 Jul 2023", "name": "Juan Quintana", "role": "Author Response", "response": "In this manuscript, Chandrasegaran et al., use for the first-time in vitro brain organoids to understand Trypanosoma brucei gambiense pathogenesis. This is an important topic, as brain organoids have already become as a valid strategy to study disease mechanisms. Although the team led by Juan Quintana is already a leader in animal models of T. brucei, I would like to praise their efforts on using alternative disease modelling tools that could reduce the number of research animals and overcome differences between mouse and humans. The authors show differential gene expression after brain organoid incubation with T, brucei gambiense after a 24h and 72h incubation. The manuscript is timely, and overall, scientifically sound and well written. I support the article indexing after the introduction of some modifications on the text. We sincerely thank this reviewer for their positive assessment of our work. We are always motivated to explore novel and more ethical ways to conduct our research and are indeed excited by the possibility of implementing organoids and “organ-on-a-chip” approaches to study brain responses to infection. Major Although the methods section is very clear, I couldn’t find any reference on how long the brain organoids were grown. This is important because brain organoids are grown for long periods of time (up to a year) and depending on the maturation time, they acquire different brain developmental stages. I would suggest that the authors include this information in the methods section, as well as on the results or discussion section, as it is important for interpretation of the results. Authors: We apologise for this issue. The cortical brain organoids used in this study were ~2 months old, to ensure a minimum level of maturation, as reported in references 2 and 4. We have included this in the methods section of the revised manuscript. How does the 24h and 72h time point or the parasite concentration used compare with the life cycle of T. brucei gambiense in the brain? This information could be useful for an audience not familiar with T. brucei. Authors: This is a great question, but a challenging one to address. Gambiense HAT is typically mild, lasting for years before the clinical symptoms associated with the second stage of the disease (e.g., sleep disturbances) become patent. Unfortunately, there is no clinical data indicating how many parasites there are in the brain at any given points during gambiense HAT, but CSF from second stage gambiense HAT patients can report anywhere tens to hundred parasites per ml of CSF (https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(22)00558-8/fulltext for reference). In our own experience infecting mice with T. b. gambiense, we typically observed around 102-104 parasites/gram of brain tissue (unpublished data), but we are unsure at this stage how comparable this is to the in vitro system we set out to develop here. We will focus on these aspects in future work. The authors couldn’t find any brain damage markers on Fig 2C after staining with two different markers. However, other non-used markers could be affected. Although the sentence in the result section mildly implies that (\"Importantly, we did not detect significant morphological or histological changes in the organoids exposed to the parasites based on H&E staining and MAP 2 staining (Figure 1C), suggesting that T. brucei gambiense does not elicit tissue damage over a 72 hour culture period.”), I would suggest to rephrase to make it more obvious. Furthermore, did the author quantify for differences in expression on MAP2, or is the analysis mostly qualitative? Authors: We thank this reviewer for this useful suggestion. We have rephrased the text to highlight that we are basing our observations of a limited number of morphological markers (H&E and MAP2), as follow: Importantly, we did not detect significant morphological or histological changes in the organoids exposed to the parasites based on the morphological aspects observed upon H&E staining and MAP2 staining ( Figure 1C), suggesting that T. brucei gambiense does not seem to elicit tissue damage over a 72 hour culture period, at least not with the markers used in this study. It is important to note that we originally intended to keep some of these organoids to run western blotting for quantification of markers of interest (e.g., MAP2) but were unable to do so due to limited availability. We plan to dissect this aspect in more detail as part of future work. The increased expression of endothelial markers is intriguing, taking into account that brain organoids present minimal presence of endothelial cells. This is important because vascularization of brain organoids is one of the main challenges in the bioengineering field, and the presence of vasculature in these models could be used to study the molecular mechanisms of T. brucei crossing through the brain microvasculature. Did the authors checked for the presence of blood vessels by immunostaining. In a similar topic, I would like to clarify that EPCAM is not an endothelial marker, so I would recommend to delete any reference to EPCAM in the figures/tables, results and discussion section. Authors: We agree with this reviewer. We were also surprised to see an upregulation of genes typically found in the endothelial compartment as these organoids do not typically contain vasculature, as this reviewer states. It is important to note that we failed to detect positive staining for VWF and CDH5 by immunohistochemistry, but there might be technical limitations to consider (e.g., antibody compatibility, detection level, etc) before we can confidently support or exclude the presence of a vasculature-like cell population in our dataset in response to T. b. gambiense exposure/co-culture. Although intriguing and exciting, we decided to err on the side of caution and limit our interpretations to present the transcriptional features, without concluding that these organoids in fact contain vasculature. Also, as suggested by this reviewer, we have removed references to Epcam from the text/table. Minor Abstract “Future work is required to increase the complexity of the organoids (e.g., addition of microglia and vasculature). We envision that the adoption of organoid systems will be beneficial to researchers studying mechanisms of brain infection by protozoan parasites.” Although it is important to showcase the limitations of the model, the second part of the sentence has somehow a negative connotation on the validity of the current results. In this paper, the authors validate the use of organoids systems to study T. brucei infection and the authors should highlight that they already represent an alternative to animal models. Authors: We agree with this reviewer. As suggested, we have amended the abstract accordingly as follow: Although our data support the use of brain organoids to explore and model host-pathogen interactions in the context of T. brucei infection as an alternative to in vivo models, future work is required to increase the complexity of the organoids ( e.g., addition of microglia and vasculature). We envision that the adoption of organoid systems is beneficial to researchers studying mechanisms of brain infection by protozoan parasites. Research highlights (3Rs benefit(s)) and results page 3: Which methodology did you use to measure the reduction in animal models that could be used to study trypanosomiasis? Authors: The figures presented in the current version of the manuscript were based on a prediction assuming full adoption of this method, and the number of animals that undergo similar procedures (e.g., brain responses to infection) over the past 5 years of our current UK Home Office license. In this case, we determined that on a typical year of our license, 47/100 animals undergo moderate-to-severe procedures involving evaluating brain responses to infection that could be fully replaced with a suitable in vitro brain organoids system. To generate those infections, we also typically require donor mice from which we obtain infective trypanosomes, which we estimated to be reduced by about 1/5 with the organoids system in place. There seems to be a reference missing in: “For instance, there are intrinsic differences in the immune response between hosts (e.g., mouse vs. human) that pose limitations for translational science.” Authors: We have removed this sentence from the manuscript. Results Page 7: “We also detected significant expression of the interleukin-17 receptor subunit A and D (IL17RA and IL17RD, respectively), interleukin-10 receptor subunit a (IL10RA), and the Interferon gamma receptor 1 (IFNGR1) (Table 1 and Table S2 in Underlying data),22, indicating that these organoids are primed to sense and respond to IL-17, IL-10, and IFNγ signalling upon exposure to T. brucei gambiense” - I would recommend to rephrase to something similar to “these organoids are prime to sense and response to T. brucei gambiense by activating IL-17, IL-10 and IFNg pathways.” Authors: We have rephrased the manuscript as suggested as follow: indicating that these organoids are primed to sense and respond to T. brucei gambiense by activating IL-17, IL-10, and IFNγ signalling pathways" } ] } ]	1	https://f1000research.com/articles/12-437
https://f1000research.com/articles/9-1221/v1	09 Oct 20	{ "type": "Research Article", "title": "Upcoming Christmas jump in LIBOR", "authors": [ "Vikenty Mikheev", "Serge E. Miheev", "Serge E. Miheev" ], "abstract": "Background: London Interbank Offered Rate (LIBOR) exists since 1986 as a benchmark interest rate. Methods: Using two-layer linear regression method, we found a pattern of shortterm nature in LIBOR behaviour. Results: To wit, 2-month LIBOR experiences a jump after Xmas for the last two decades. The direction and size of the jump depend on the data trend on 21 days before Xmas. Conclusions: The obtained results can be used to build a winning strategy on the Swap Market.", "keywords": [ "LIBOR", "short term approximation", "pattern", "swap market", "Christmas jump", "linear regression" ], "content": "Introduction\n\nIn 1986, a new benchmark interest rate was introduced, named the London Interbank Offered Rate (LIBOR). At LIBOR, major banks of the world lend to one another in the international interbank market for short-term loans. From a mathematical point of view, LIBOR is a sequence of daily changing real values. LIBOR data is in open access and can be found on multiple web-sites, for example, here1.\n\nIn Figure 1, one can see a large scale sample of 2-month LIBOR for loans in USD. In Figure 2, the values of 2-month LIBOR 21 days before Xmas and 6 days after from 2004–2019 years were put together.\n\nLIBOR has a crucial role in the Swap Market, where people exchange their loan interests and can win or lose money depending on their right or wrong predictions of LIBOR dynamics. For example, person P got a one-million-dollar loan with 5% interest and person E borrowed the same amount but with the interest 2%+LIBOR. After some time, they decide to exchange their interest rates because P thinks that LIBOR will go lower than 3% but E believes that it will go higher than 3%. Both their opinions are based on some prediction methods, even if it is just an intuition. We intend to bring another prediction tool into the game. A curious reader may find more complex models and measures on LIBOR for different problems2–5.\n\nThus, here we are not interested to LIBOR nature per se but in its volatility. More precisely, we study the behavior of LIBOR after Christmas from December 26 to December 31. Examples of such data are in Figure 3 and Figure 4.\n\nAlthough LIBOR itself is going to disappear in 20216,7, and one can apply our results only for Xmas 2020, we think that the model we introduce here might be useful for short-term analysis in other problems.\n\nSo, how does Christmas affect dynamics of LIBOR until the next holiday?\n\n\nMethods\n\nThe research we conducted indicates convincingly that a jump does exist. But what is a jump in a discrete sequence of numbers? The following seems to be the most acceptable:\n\nDefinition 1. There are a real number x¯ and a real discrete function given tabularly\n\n\n\nwhere x1 < x2 < ... < xn and xk<x¯<xk+1 for some natural k ∈ [2,n − 2]. One chooses approximant A : Rr × R1 → R1 among functions having continuous derivative by second argument notated as A′2 and chooses some quality criterion Q(z,A(p, ·) to minimize by parameter vector p ∈ Rr. Then we appoint\n\n\n\nand consider the approximation problem with the criterion Q(z0,A(p,·)) → minp∈Rr. Let its solution be denoted as A¯(z0,x). Then we consider the next problem\n\n\n\nLet its solution be denoted as A¯(z1,x). Then the difference A¯(z0,x¯)−A¯(z1,x¯) is the jump at x¯.\n\nIn other words, the jump at x¯ of a discrete function given by a tabular is the difference at x¯ between the obtained solutions of two approximation problems of the same type, the first problem is formulated on the left part of the table, the second problem is formulated on the right part of the table and must keep at x¯ trend (i.e. derivative) of the first problem solution. The left part corresponds to the nodes less than x¯, the right part corresponds to the nodes greater than x¯.\n\nIn our case, x¯ =Dec 25).\n\nIt is easy to see that the so-defined jump depends on the type of approximation and on the amount of the input data. On top of that, we have to decide the amount of input data in z0. Notice that the amount of the data in z1 is only three pairs (date, LIBOR of this date) because there are exactly three working banking days between Xmas and New Year’s Eve (NYE). The data source is available in 1 or in many other sources.\n\nVariability of the data due to random factors leads to the choice of the simplest approximation. We use linear approximating functions, which coefficients may be found by linear regression with its own quality criterion. We restrict ourselves to LIBOR data for the last 22 years, because it is natural to expect the evolution of LIBOR behavior over the years.\n\nSo, for year j in set J taken sequentially with no gaps from {1997, ..., 2019} data are taken for 15 banking days x′−15,...,x′−1 (corresponding to 21 calendar days) preceding Xmas of year j. Since all the days are in December, we may refer to them just by number without problem of passing days to another month: x′−15,...,x′−1 ⊂ {4,...,24}. Moreover, for simplicity of following constructions we may decrease them by 25, i.e. xi:=x′i−25, i = −15,...,−1. Therefore, x−15,...,x−1 ⊂ {−21,...,−1}. Each xi corresponds to yi, which is the annual interest rate of LIBOR for 2 months on day xi. Using them we build a linear regression\n\n\n\nor yi=y^(x)+εi, where x is a December day minus 25 and εi is the error.\n\nThat is, in terms of Definition 1, A¯(z0,x)=aj(z0)x+bj(z0). Since the current trend of LIBOR (meaning the rate of growth or decrease) does not change a lot over a short time interval, it is almost the same before and after Xmas. Therefore, we seek an approximation after Xmas in the following form: y^(x)=a′jx+b′j, where x is a December day decreased by 25 and a′j=aj=A¯(z0,x¯). Hence, the second approximation has only one unknown parameter, b′j. It can also be found by linear regression or can be calculated simply as the average of values yi − ajxi, where i runs 1,2,3 and xi ∈ {27 − 25,...,31 − 25} = {2,...,6} (There are exactly three bank days between Xmas and New Year.) The examples of such approximations are seen in Figure 5 and Figure 6.\n\nNotice that on the last Figure 5 and Figure 6 with data for 2012 and 2004 years and their regressions, the y-axes have different scales.\n\nThus, for each selected year j there is a relationship (bj,aj)→b^j. According to Definition 1 the difference Δj:=b^j-bj is the jump we have been looking for. Having such connections over 23 years, one can try to find a pattern. To do that, we turn to linear-quadratic regression on two-dimensional nodes. This time the approximating function has the form:\n\n\n\nwith an approximation table FJ (aj,bj) ≈ Δj, j ∈ J ⊂ {1995,...,2019}. Sub index J at F points at which subset of years over the past 23 has been chosen to construct the regression. The remaining years will be used to verify the statistical reliability of the result.\n\nOn one hand, we want as much data for our approximation as possible. On the other hand, the longer the time interval, the less accurate the trend on the end of the interval. Someone could say: ”Why don’t you take a more complex approximant to capture more complicated futures of the time series?” Well, that would require even more data for statistical power of such approximant. Since we want to detect a short-term pattern, we should avoid such approach. It made sense to take a number of days before Xmas divisible by 5, so each week day would appear evenly. After trying 25, 20, 15, 10, 5, we found the model worked best with 15 days.\n\nRegarding 3 LIBOR days after Xmas, the same logic explained above is applicable here too. Again, empirically we have found that 3 days work the best. Notice every year has exactly 3 LIBOR days between Xmas and NYE. It is possible that NYE plays a big role in that.\n\n\nResults\n\nWe conducted the process above for several different numbers of years for F regression (from 5 to 20 years), different LIBOR data (overnight, 1 month, 2 months, etc.). The most convincing results have been obtained with the following setups: 21 calendar day regression for each year from 15-year intervals; 2-month-loan values of LIBOR.\n\nObserve the results in the Table 1.\n\nSo, our prediction for the jump formula after Xmas 2020 are:\n\n\n\nThe 95%-confidence intervals for the coefficients β0,β1,β2,β3 in (3) are (-0.00217, 0.01171), (-9.77318, -8.75835), (-0.00536, 0.00066) and (1.72466, 2.31286), respectively.\n\nIt may be activated at Dec 24 2020 as following:\n\nAt this day extract data {yi} from 1 for bank days {x′i} since Dec 21 till Dec 24 (in 2020, of course). Build 15 pairs (xi,yi), i = −15,...,−1, where xi=x′i−25. Put them into any program to find linear regression, for example, into our code in R, which is available as Extended data8. The result of the regression is two numbers: that corresponding to free term is b2020, the other is a2020. Substitution of them to (3) yields the jump.\n\nThe prediction of the jump can be used to predict the mean LIBOR after Xmas and before NYE (Ljmean). Let us show some formulas.\n\nAccording to Definition 1 the jump with approximations above is Δj=b^j-bj, where b^j = arg minb {∑i=13(ajxi+b−yi)2}, which is equivalent to b^j=13∑i=13(yi−ajxi). Hence\n\n\n\nNotice that the last term in (4) is just a predicted mean value of LIBOR between Xmas and NYE (L^jmean), according to the regression for j-th year. Thus,\n\n\n\nIf as estimate of Ljmean we take L^jmean+Δ^j, then its absolute error is equal to Δ^j−Δj.\n\nThe latter difference according to our calculations for years 2015, 2016, 2017, 2018, 2019 was always less by absolute value than \|Δ^j\|.\n\n\nConclusion\n\nWe have found a short-term pattern in LIBOR dynamics. Namely, the 2-month LIBOR experiences a jump after Xmas. The sign and size of the jump depends on data trend on 21 days before Xmas. The results are obtained in the form of the jump per se and as mean predicted value of LIBOR between Xmas and NYE. A swap market player may try to use this information to predict behaviour of LIBOR to do a better game on his part. For Xmas of 2020, on a date of Dec 24, one can compute a and b according to (1) on 21 calendar days and use the formula (3) to predict the jump after Xmas.\n\nIn the pre-print9 of this paper, one can find our predictions for the jump after Xmas of 2019 and see that later data from the event confirmed it.\n\n\nData availability\n\nAll data used in this paper can be found at IBORate (http://iborate.com/usd-libor/)1.\n\nThe code used to develop the model is available at: https://github.com/keshmish/Chistmas-Jump-in-LIBOR/.\n\nArchived code at time of publication: https://doi.org/10.5281/zenodo.39771338.\n\nLicense: MIT License.", "appendix": "Acknowledgements\n\nWe would like to show our gratitude to the Institute for Mathematics and its Applications (https://ima.umn.edu/node), U. of Minnesota for organizing Math-to-Industry Boot Camp IV, where Fadil Santosa and Daniel Spirn suggested to search for some patterns in LIBOR behaviour around national holidays. We thank Davood Damircheli, Anthony Nguyen and Samantha Pinella for discussions and participation in the first attempts to detect the pattern.\n\n\nReferences\n\nIBORate: LIBOR database. Cited 15 Jan 2020. Reference Source\n\nJamshidian F: LIBOR and swap market models and measures. Financ Stoch. 1997; 1: 293–330. Publisher Full Text\n\nSchoenmakers J: Robust Libor Modelling and Pricing of Derivative Products. Chapman and Hall/CRC, New York. 2005. Reference Source\n\nMoreni N, Pallavicini A: Parsimonious HJM modelling for multiple yield-curve dynamics. Quant Finance. Routledge, 2014; 14(2): 199–210. Publisher Full Text\n\nHinch M, McCord M, McGreal S: LIBOR and interest rate spread: sensitivities of the Australian housing market. Pac Rim Prop Res J. Routledge, 2019; 25(1): 73–99. Publisher Full Text\n\nHeltman J: Libor is going dark in 2021, and some banks aren’t ready. American Banker. 2018. Cited 15 Jan 2020. Reference Source\n\nFarrar D: You might have heard that LIBOR is going away.... Consumer Financial Protection Bureau. 2019. Cited 15 Jan 2020. Reference Source\n\nMikheev V: Code in R for Xmass Jump in Libor. http://www.doi.org/10.5281/zenodo.3977133\n\nMikheev V, Miheev SE: Christmas Jump in LIBOR. Arxiv. 2019. Reference Source" }	[ { "id": "123668", "date": "02 Mar 2022", "name": "Victor Malyutin", "expertise": [ "Reviewer Expertise Mathematical statistics" ], "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 behavior of LIBOR after Christmas from December 26 to December 31 is studied in the paper. The Authors use linear regression to find the regression coefficients for data before Xmas and jump after Xmas for each selected year. To get the jump prediction formula the linear-quadratic regression on two-dimensional nodes is used. The prediction of the jump can be used to predict the mean LIBOR after Xmas and before NYE. Presented results demonstrate that predicted results approximate real values well.\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": "127765", "date": "30 May 2022", "name": "FAUZIA MUBARIK", "expertise": [ "Reviewer Expertise Financial Economics", "Islamic Finance" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article has a good readability and qualifies to be approved with reservations. This article has an interesting way forward to identify and recognize the most recent developments in the Alternative Reference Rates (ARR); Secured Overnight Financing Rate (SOFR) of United States, Sterling Overnight Index Average (SONIA) of England, Euro Short-Term Rate (ESTR) of European Union, Swiss Average Rate Overnight (SARON) of Switzerland and Tokyo Overnight Average Rate (TONAR) of Japan introduced in the global financial market as the successors to LIBOR.\nThe article can be published after incorporating the following suggestions/recommendations;\nThe in-text citations are missing. The results can be strengthened through empirical support. 2021 and 2020 were big years for LIBOR research, please cite some of this research – or conduct more of your own – to strengthen your results. See this Congressional Report, this from KKR Investments, and this from the Bank for International Settlements, for example. The researcher may explain whether any windows are created to study the jumps. Is it a two step study, first of 21 days and 6 days; second of 15 days and 3 days? Is the prediction in the jump studied through mean of the regression method?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "9342", "date": "28 Apr 2023", "name": "Vikenty Mikheev", "role": "Author Response", "response": "1. If you could specify where exactly those missing citations were supposed to be, it would help us a lot. 2. The articles you mentioned are talking about LIBOR transition, which is a little unrelated to our topic. Unfortunately, adding data after 2020 is hard since the LIBOR got mostly shut down in 2021. There above, you mentioned similar to LIBOR data where the proposed here method could be tried on. This is a very useful hint. Thanks! 3. We hope that the section \"Why 15 week days before and 3 week days after Xmas?\" explains this very reasonable question. 4,5. \"Two-step\" in our research stays for two-step regression. First, we find (by a regression) the parameters of a function for each year from 1997 to 2019. Second, we do another regression, this time on those found parameters to predict the next year." } ] } ]	1	https://f1000research.com/articles/9-1221
https://f1000research.com/articles/12-895/v1	27 Jul 23	{ "type": "Research Article", "title": "A randomized interventional clinical trial assessing the safety and effectiveness of PeaNoc XL tablets in managing joint pain and inflammation in arthritis patients", "authors": [ "Nandakumar Kadanangode Narayanaswam", "Eric Caston", "Rajappan Chandra Satish Kumar", "Thangavel Mahalingam Vijayakumar", "Vishagan Sulur Vanangamudi", "Negi Pankaj", "Abdul Sukkur", "Eric Caston", "Rajappan Chandra Satish Kumar", "Thangavel Mahalingam Vijayakumar", "Vishagan Sulur Vanangamudi", "Negi Pankaj", "Abdul Sukkur" ], "abstract": "Background: Globally, alternative medicine is used widely by most patients for several health challenges. To evaluate the effectiveness and safety of PeaNoc XL Tablet in managing pain and inflammation, a randomized clinical trial and systematic study was designed. PeaNoc XL Tablet has been widely utilized for pain and inflammation management, but no previous studies have examined its efficacy and safety. The aim of this study was to determine the clinical effectiveness and safety profile of PeaNoc XL in patients with arthritis experiencing joint pain and inflammation. Methods: A randomized, controlled, and an open-label trial was conducted. A total of 155 patients (18 to 60 years) with arthritis were enrolled for participation. Using computer-generated random sequences, the study population was divided into two groups in a randomized manner. Group A received Standard therapy and Group B received Standard therapy with PeaNoc XL Tablet 400mg (two tablets OD after food). Results: Out of 155 patients, a total of 83 individuals were excluded from the study, leaving 72 patients who were randomly assigned to either Group A (n=36) or Group B (n=36). The administration of PeaNoc XL as an adjunct to standard therapy resulted in a significant reduction in levels of TNF-α (P<0.01), IL-1β (P<0.001), IL-6 (P<0.01), and CRP (P<0.01) in arthritis patients experiencing joint pain and inflammation. Conversely, no notable differences were observed from the baseline in the standard therapy group. Conclusions: After 12 weeks of supplementation of PeaNoc XL tablets, as an add-on therapy helps in the reduction of pain score, joint stiffness, and physical stiffness. Trial registration: CTRI/2022/10/046693.", "keywords": [ "arthritis", "pain", "palmitoylethanolamide", "astaxanthin", "inflammation", "joint pain" ], "content": "Introduction\n\nAlternative medicine, encompassing herbal medicines, phytonutrients, ayurvedic products, and nutraceuticals, is commonly employed by a substantial number of patients worldwide to address diverse health conditions. According to available data, approximately 80% of the global population relies on herbal products as their primary choice of treatment for various ailments. The utilization of alternative medicines, including classical herbal products, has exhibited a consistent and notable upward trend over the past few decades.1\n\nPeaNoc XL Tablet is extensively utilized for the purpose of pain and inflammation management. PeaNoc XL Tablet is a combination of palmitoylethanolamide 400mg and astaxanthin 1mg.\n\nPalmitoylethanolamide (PEA) is an endogenous fatty acid amide belonging to the class of lipid mediators and the family of N-acylethanolamines (NAEs). It shares similarities with the endocannabinoid anandamide (AEA). PEA demonstrates inhibitory effects on the release of pro-inflammatory mediators from activated mast cells and diminishes mast cell activation at nerve injury sites.2 These mechanisms are associated with the alleviation of allodynia and hyperalgesia in the neuropathic pain model.\n\nAstaxanthin is a carotenoid primarily present in natural sources and marine organisms, including microalgae, salmon, trout, krill, shrimp, crayfish, and crustaceans.3 Carotenoids, including astaxanthin, are recognized for their antioxidant properties and have gained significant attention for their therapeutic advantages in conditions related to aging and various diseases.\n\nTo the best of our knowledge, there is no scientific study investigating the efficacy and safety of PeaNoc XL in arthritis patients. Therefore, a clinical trial was conducted to assess the clinical efficacy and safety of PeaNoc XL specifically in arthritis patients experiencing joint pain and inflammation.\n\n\nObjectives\n\n\n\n1. To evaluate the efficacy of PeaNoc XL tablets on biochemical parameters in arthritis patients with joint pain and inflammation.\n\n2. To evaluate the efficacy of PeaNoc XL tablets on inflammatory cytokines in arthritis patients with joint pain and inflammation.\n\n3. To assess the efficacy and safety of PeaNoc XL tablets in relation to the arthritis Index (WOMAC) in arthritis patients with joint pain and inflammation.\n\n4. To evaluate adverse drug reactions in the study period.\n\n\nMethods\n\nA randomized, controlled, open-labelled trial was conducted at a SRM Medical College Hospital and Research Centre in Tamil Nadu.\n\nThe study adhered to the guidelines set forth by the International Committee on Harmonization on Good Clinical Practice and followed the revised version of the Declaration of Helsinki. Approval for the study protocol was obtained from the institutional human ethics committee of SRM Medical College Hospital and Research Centre on March 25, 2022, with Ethics Clearance No: 8275/IEC/2022. The study is registered with the Clinical Trials Registry India (CTRI) under the reference number CTRI/2022/10/046693.\n\nPeaNoc XL Tablet contains astaxanthin (1mg) + palmitoylethanolamide (400mg)\n\nDirection: two tablets once daily (OD)\n\n\n\n• Eligible participants diagnosed with arthritis, regardless of sex, in the age range of 18 to 60 years (inclusive).\n\n• Patients with a DAS 28 (Disease Activity Score) score greater than or equal to 3.2\n\n• Voluntary willingness to provide written informed consent for participation.\n\n• Ability to comprehend the nature and objectives of the study and demonstrate a willingness to adhere to study procedures.\n\n\n\n• Participants taking other non-steroidal anti-inflammatory drugs (NSAIDs)/painkillers other than standard drug\n\n• Abnormal results on liver function test\n\n• Patients with diabetic neuropathy\n\n• Patients with severe renal, hepatic, cardiac, gastrointestinal, neurological, hematological, or respiratory disorder\n\n• Patients with a psychiatric disorder\n\n• BMI >35 kg/m2 or <20 kg/m2\n\n• Participants who were likely to have surgery during the study period\n\n• Participants who have partaken in any clinical study or clinical trial in the previous 12 weeks\n\n• Known hypersensitivity to the study drugs\n\n• Patients with severe infection\n\n• History of intake of any ayurvedic/herbal/homeopathic/dietary supplements in the last two months\n\n• Pregnant or nursing mothers and women of childbearing age refusing to use contraceptives\n\nIn this pilot study conducted over a duration of nine months, a sample size of 30 patients was divided into two groups. Group A received standard therapy for the specified condition, while Group B received standard therapy in addition to PeaNoc XL Tablet 400mg, taken orally after food.\n\nGroup A: Standard therapy\n\nGroup B: Standard Therapy + PeaNoc XL Tablet 400mg (2 Tablets OD after food)\n\nStudy Duration - nine months\n\nSample size - Pilot sample (30 patients in each group) as per WHO guidelines\n\nThe included study populations based on study criteria were randomized into two groups by using a computer-generated random sequence in R software. Group A received Standard therapy and Group B received Standard therapy with PeaNoc XL Tablet 400mg (two tablets OD after food).\n\nThe hematology, liver, and kidney functions were evaluated for both groups. The levels of inflammatory cytokines, including TNF-α, IL-1β, IL-6, and CRP, were measured using the enzyme-linked immunosorbent assay (ELISA) technique. Western Ontario and McMaster Universities Arthritis Index (WOMAC)4 questionnaire was assessed subjectively before and after the treatment to evaluate the efficacy of the PeaNoc XL supplementation.\n\nMorning blood samples of 5mL were collected via venous puncture from participants who had fasted overnight, specifically between the hours of 8:00 a.m. and 10:00 a.m. Following collection, centrifugation was performed using an Eppendorf Centrifuge 5430R. The resulting samples were divided into aliquots and stored at -20°C until analysis. All biochemical tests were conducted using a fully automated clinical chemistry analyzer (EM 360; Transasia, ERBA Diagnostics [Transasia]) with ERBA diagnostics kits (ERBA Diagnostics Mannheim GmbH).\n\nThe levels of TNF-α, IL-6, IL-1β, and CRP were quantified utilizing a two-step sandwich-type immunoassay known as the Human Leptin Quantikine ELISA Kit, which incorporates enzymatic amplification.\n\nThe WOMAC pain scale is extensively used in the evaluation of hip and knee osteoarthritis (OA). It is a self-managed questionnaire consisting of 24 items divided into three subscales, as follows:\n\n1. Pain (five items): while walking, using stairs, in bed or rest, sitting or lying, and standing upright\n\n2. Stiffness (two items): after the first walk and later in the day\n\nPhysical Function (17 items): climbing stairs, walking, rising from a sitting position, standing, bending down, moving in or out of a vehicle, shopping, putting on or taking off socks, rising from bed, lying in bed, getting in or out of the bath, getting on or off the toilet, doing heavy domestic duties, or light domestic duties.5\n\nThe results of the questions are scored on a 0-4 scale:\n\n▪ None (0),\n\n▪ Mild (1),\n\n▪ Moderate (2),\n\n▪ Severe (3), and\n\n▪ Extreme (4)\n\nThe scores for each subscale are added up, with a possible score range of\n\n▪ 0-20 for Pain,\n\n▪ 0-8 for Stiffness, and\n\n▪ 0-68 for Physical Function.\n\nHigher scores on the WOMAC signify worse pain, stiffness, and functional limitations.\n\n\nResults\n\nA total number of 155 patients were assessed for admissibility, while 83 patients were excluded. In the end, 72 patients were included and were randomized into two groups. Group A received Standard therapy and Group B received standard therapy with PeaNoc XL (Figure 1). The baseline characteristics for both groups are mentioned in Table 1.\n\nIn the Standard therapy group (Group A), two patients were lost to follow-up due to non-response to phone calls. In the Standard therapy group + PeaNoc XL group (Group B), one patient was lost to follow-up due to migration. Thus, 34 patients’ data were analyzed in Group A and 35 patients’ data were analyzed in Group B (Figures 2 and 3).6\n\nThe values are presented as mean±SD, and the level of significance is indicated as follows: P<0.01* (significant), P<0.05 (significant), and P<0.001* (highly significant).\n\nPatient demographics were recorded for both groups after receiving informed consent. In the baseline assessment, no significant differences (P>0.05) were observed between age, BMI, hip circumference, waist circumference, platelets, blood, and biochemical parameters among the groups (Table 1).\n\nBlood samples were obtained from the patients at the beginning of the study (baseline) and at the end of the three-month period for both study groups. These samples were collected to conduct liver and kidney function tests, which included the analysis of various parameters such as total bilirubin, direct bilirubin, total protein, albumin, globulin, serum glutamic-oxaloacetic transaminase (SGOT), serum glutamic pyruvic transaminase (SGPT), gamma-glutamyl transferase (GGT), alkaline phosphatase (ALP), and serum creatinine.\n\nResults showed that PeaNoc XL tablets did not influence any of the parameters. Thus, the safety of the PeaNoc XL is established with the biochemical parameters as shown in Table 2.\n\nThe values are presented as mean±SD. Significance levels are denoted as follows: P<0.01* (significant), P<0.05 (significant), and P<0.001* (highly significant).\n\nThe levels of inflammatory cytokines, including TNF-α, IL-6, IL-1β, and CRP, were assessed using the ELISA technique. The addition of PeaNoc XL to standard therapy resulted in a significant reduction in the levels of TNF-α (P<0.01), IL-6 (P<0.01), IL-1β (P<0.001), and CRP (P<0.01) among patients experiencing joint pain and inflammation. In contrast, the standard therapy group did not exhibit any notable difference compared to the baseline levels of these cytokines.\n\nWOMAC questionnaire has three main areas such as pain score, joint stiffness, and physical stiffness. The addition of PeaNoc XL as an adjunct therapy demonstrated significant reductions in pain (P<0.001), joint stiffness (P<0.01), and physical stiffness (P<0.001) compared to baseline among patients with joint pain and inflammation. In contrast, standard therapy did not exhibit statistically significant differences in these parameters in the same patient population.\n\nSafety assessment\n\nFollowing a 12-week treatment with PeaNoc XL therapy, all hematological and biochemical safety parameters remained within normal ranges. No severe adverse side effects were reported during the study period, and none of the patients withdrew their consent due to adverse drug reactions.\n\n\nDiscussion\n\nPEA is a bioactive lipid mediator resembling endocannabinoids that falls within the NAE fatty acid amide family. It is ubiquitously present in various tissues, including the brain. PEA is thought to be synthesized in response to cellular injury as a pro-homeostatic protective mechanism and its production is enhanced in disease conditions. PEA exhibits diverse effects, encompassing anti-inflammatory, analgesic, antimicrobial, antipyretic, antiepileptic, immunomodulatory, and neuroprotective properties.7\n\nThe multifaceted mechanisms of action exhibited by PEA offer potential therapeutic advantages in various disorders, including allergic reactions, the common cold, chronic pain, joint pain, and neurodegenerative conditions. Additionally, PEA has been shown to enhance muscle recovery and improve cognition, mood, and sleep.7\n\nPEA presents itself as a promising alternative for the relief of joint pain. A clinical trial employing a triple-blind, randomized, parallel-arm design revealed that PEA exhibited superior efficacy in reducing temporomandibular joint (TMJ) OA pain when compared to ibuprofen.8\n\nIn a double-blind, randomized, placebo-controlled trial, the efficacy of PEA in patients with mild to moderate knee OA was established. Over the course of an eight-week clinical study, patients who received a high-bioavailability form of PEA demonstrated dose-dependent improvements in joint pain, stiffness, and function, as evaluated using the WOMAC questionnaire. Notably, joint pain decreased by 40% with a 300 mg PEA dosage and by 49.5% with a 600 mg PEA dosage, accompanied by a significant decrease in the use of rescue medication by the end of the eighth week. These findings highlight the potential of PEA as a novel treatment for alleviating pain and related symptoms associated with knee OA.9\n\nThe available studies, along with the existing literature, highlight the intriguing potential of PEA as an alternative treatment for addressing joint pain.\n\nAstaxanthin, a red carotenoid pigment present in diverse plant and marine organisms like shrimps and salmon, exhibits a range of biological functions. Notably, it is recognized for its potent antioxidant, anti-inflammatory, and anti-cancer properties.10\n\nA study has provided evidence supporting the potential beneficial effects of astaxanthin in the context of OA. Notably, astaxanthin demonstrated significant reductions in the activities of MMP-1, MMP-3, and MMP-9, as well as inhibited the expression of MMP-1, MMP-2, MMP-9, and MMP-13 in various cell types. These findings are particularly valuable in terms of inhibiting matrix degradation. Consequently, the study suggests that astaxanthin holds promise as an agent with anti-osteoarthritic properties.10\n\n\nKey findings\n\nThe findings of the present randomized, open-label interventional trial showed that PeaNoc XL tablets help in the reduction of pain, joint stiffness, and physical stiffness (WOMAC questionnaire).\n\nInflammatory levels of TNF-α, IL1-β, IL-6, and CRP levels in patients with joint pain and inflammation were significantly reduced in PeaNoc XL add-on treatment as compared to baseline and standard therapy.\n\nA 12- week supplementation of PeaNoc XL add-on therapy was effective in arthritis patients with joint pain and inflammation.\n\nPeaNoc XL was well-tolerated as an add-on oral therapy, suggesting its safety and efficacy.\n\n\nConclusions\n\nThis randomized study showed that adding PeaNoc XL Tablet to standard therapy effectively reduced pain, joint stiffness, and physical stiffness in arthritis patients. It also resulted in significant reductions in inflammatory markers. PeaNoc XL Tablet demonstrates potential as a safe and effective option for managing joint pain and inflammation in arthritis patients.\n\n\nAuthor contributions\n\nAll authors, including K. N. Nandakumar, Dr. E. Caston, Dr. R. C. Satish Kumar, Dr. T.M. Vijayakumar, S. V. Vishagan, Pankaj Negi, and A. Sukkur, made equal contributions to this report. They had full access to all the data in the study and took responsibility for ensuring the integrity and accuracy of the data analysis.\n\nStudy design: K. N. Nandakumar, Dr. E. Caston, Dr. R. C. Satish Kumar, Dr. T.M. Vijayakumar, S. V. Vishagan, Pankaj Negi, and A. Sukkur.\n\nStudy supervision: K. N. Nandakumar, Dr. E. Caston, Dr. R. C. Satish Kumar, Dr. T.M. Vijayakumar, S. V. Vishagan, Pankaj Negi, and A. Sukkur.\n\nAcquisition, analysis, or interpretation of data: K. N. Nandakumar, Dr. E. Caston, Dr. R. C. Satish Kumar, Dr. T.M. Vijayakumar, S. V. Vishagan, Pankaj Negi, and A. Sukkur.", "appendix": "Data availability\n\nFigshare: master sheet peanoc xl 2.xlsx, https://doi.org/10.6084/m9.figshare.23641023. 11\n\nFigshare: CONSORT checklist for “A randomized interventional clinical trial assessing the safety and effectiveness of PeaNoc XL tablets in managing joint pain and inflammation in arthritis patients”, https://doi.org/10.6084/m9.figshare.23641023. 11\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nMedical writing support for the manuscript was provided by DocMode Health Technologies Ltd., Mumbai. The researchers express their gratitude to the staff members of Pharmacy Practice & IIISM, Pharm D students, volunteers, nurses, and doctors who have made valuable contributions to this research.\n\n\nReferences\n\nEkor M: The growing use of herbal medicines: issues relating to adverse reactions and challenges in monitoring safety. Front. Pharmacol. 2014 Jan 4; 4: 177. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDimou T, Spanomanoli A; Michelis SESRA19-0249: The use of palmitoylethinolamide (PEA) in FBSS for chronic pain management. Reg. Anesth. Pain Med. 2019; 44: A168.\n\nMedhi J, Kalita MC: Astaxanthin: An algae-based natural compound with a potential role in human health-promoting effect: An updated comprehensive review. J. App. Biol. Biotech. 2021; 9(1): 114–123.\n\nRiddle DL, Perera RA: The WOMAC Pain Scale and Crosstalk From Co-occurring Pain Sites in People With Knee Pain: A Causal Modeling Study. Phys. Ther. 2020 Sep 28; 100(10): 1872–1881. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStratford PW, Kennedy DM: Does parallel item content on WOMAC's pain and function subscales limit its ability to detect change in functional status? BMC Musculoskelet. Disord. 2004 Jun 9; 5: 17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKumar SR, Vijayakumar TM: Clinical Study Report, A Randomized Open-Label Interventional Clinical Study to Evaluate the Safety and Efficacy of PeaNoc XL Tablets on Arthritis Patients with Joint Pain and Inflammation.2022.\n\nClayton P, Hill M, Bogoda N, et al.: Palmitoylethanolamide: A Natural Compound for Health Management. Int. J. Mol. Sci. 2021 May 18; 22(10): 5305. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarini I, Bartolucci ML, Bortolotti F, et al.: Palmitoylethanolamide versus a nonsteroidal anti-inflammatory drug in the treatment of temporomandibular joint inflammatory pain. J. Orofac. Pain. 2012 Spring; 26(2): 99–104. PubMed Abstract\n\nSteels E, Venkatesh R, Steels E, et al.: A double-blind randomized placebo-controlled study assessing safety, tolerability, and efficacy of palmitoylethanolamide for symptoms of knee osteoarthritis. Inflammopharmacology. 2019 Jun; 27(3): 475–485. PubMed Abstract \| Publisher Full Text\n\nChen WP, Xiong Y, Shi YX, et al.: Astaxanthin reduces matrix metalloproteinase expression in human chondrocytes. Int. Immunopharmacol. 2014 Mar; 19(1): 174–177. PubMed Abstract \| Publisher Full Text\n\nNandakumar K: master sheet peanoc xl 2.xlsx. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "194026", "date": "06 Sep 2023", "name": "Shovan Kumar Rath", "expertise": [ "Reviewer Expertise pain 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\nAdding PeaNoc XL Tablet to standard therapy effectively reduced pain, joint stiffness, and physical stiffness in arthritis patients. It must be supplemented for all backpain & arthritis patients. This study adequately shows the effectiveness of PeaNoc XL tablets as an adjunct for chronic pain management in arthritis patients. PeaNoc XL tablets, as an add-on therapy helps in the reduction of pain score, joint stiffness, and physical stiffness.\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": "194023", "date": "15 Sep 2023", "name": "Arnab Karmakar", "expertise": [ "Reviewer Expertise Orthopaedics", "pain 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 paper is done very accurately and very useful for clinical practice. Pain relief is very important, this paper reflects the proper usage of peanoc-xl and the potency of the medication. The generated data will be useful for future doctors to use the medicine in treating different chronic painful conditions.\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/12-895
https://f1000research.com/articles/12-643/v2	27 Jul 23	{ "type": "Research Article", "title": "Impact of sodium fluoride and nano silver fluoride-based varnishes on remineralisation of enamel caries: an in-vitro study", "authors": [ "Pranjali Vilas Deulkar", "Nilesh Rathi", "Nilima Thosar", "Meghana Ajay Deshpande", "Sphurti Pramod Bane", "Nilesh Rathi", "Nilima Thosar", "Meghana Ajay Deshpande", "Sphurti Pramod Bane" ], "abstract": "Background: The aim of this study was to perform a comparative evaluation of 5% Sodium fluoride varnish, neutral nano silver fluoride (NSF) varnish and acidulated nano silver fluoride varnish in remineralising artificially induced enamel caries of primary teeth. Methods: 39 primary anterior teeth were sectioned 2mm below the cemento-enamel junction (CEJ) and mounted in acrylic resin blocks. Incipient enamel caries were induced on the samples artificially and primary Vicker’s surface microhardness (SMH) was assessed. Samples were divided equally and applied varnishes; Group 1: 5% Sodium fluoride varnish; Group 2: Neutral NSF varnish, and Group 3: Acidulated NSF varnish. A pH cycling protocol of 7 days was followed, and second Surface microhardness (SMH) testing was carried out. One sample from each group was observed for Scanning electron microscopy and Energy Dispersive Spectroscopy (SEM EDS). Statistical analysis was conducted using HSD Tukey and one way ANOVA tests. Results: There was a statistically significant difference between the pre-treatment and post-treatment values of all three groups. The difference in SMH after applying 5% Sodium fluoride varnish and acidulated NSF varnish was statistically significant (p<0.01). Similarly, neutral NSF varnish and acidulated NSF varnish also showed statistical significance (p<0.01). However, SMH after application of 5% Sodium fluoride varnish and neutral NSF varnish was statistically not significant. The SEM EDS analysis revealed the presence of an even fine granular layer of minerals on the surface of treated enamel in the acidulated NSF group whereas other groups showed uneven deposits of minerals. EDS showed fluoride and silver in groups containing NSF. Conclusions: Acidulated NSF varnish has the highest efficacy followed by neutral NSF varnish and 5% Sodium fluoride in remineralisation of enamel caries in primary teeth.", "keywords": [ "REMINERALISATION", "NANO SILVER FLUORIDE", "SODIUM FLUORIDE", "INCIPIENT CARIES" ], "content": "Introduction\n\nThe professional application of topical fluoride varnishes remains the most preferred method for treatment of demineralisation. Regularly available topical fluoride varnishes are sodium fluoride, stannous fluoride, acidulated phosphate fluoride.1 However, these remineralising agents have their shortcomings. Sodium fluoride varnish has to be applied four times at weekly intervals. Stannous fluoride varnish may cause brownish discoloration of the teeth and adjacent tissues and reversible tissue irritation. It has a sour taste and needs to be prepared freshly before use.2\n\nSilver diamine fluoride (SDF) is an effective agent in remineralising initial carious lesions and arresting advanced caries. Annual application of SDF has shown successful results in caries prevention. However, staining caused by SDF on the tooth and adjacent structures is a significant drawback.3 A substituted silver-based preparation, nano silver fluoride (NSF), was developed by Targino AG et al. to overcome SDF’s limitations.4 The potency of NSF in arresting carious lesions is owed to the synergistic action of silver nanoparticles and fluoride. It is currently mulled over silver diamine fluoride to arrest caries without discoloring the permeable dental tissues dark.5\n\nIn recent times, the use of low pH fluoride delivery systems is on an upheaval. In the year 1988, Saxegaard et al. asserted that acidic pH improves the deposition of calcium fluoride.6 Cruz et al. in 1992 further studied this fact and emphasized on the crystalline change that occurs to enhance ion incorporation.7 Various studies comparing the remineralising potential of acidulated phosphate fluoride gel (APF) and sodium fluoride varnish suggested better results with APF gel.8,9 Olympio et al. suggested that low pH dentifrices increase fluoride concentration in saliva and delay its salivary clearance.10\n\nThus, this research was conducted to assess the remineralising potential of 5% Sodium fluoride varnish, neutral nano silver fluoride and acidulated nano silver fluoride in artificially induced enamel caries of primary teeth.\n\n\nMethods\n\nThe in vitro study was carried out in the Department of Pediatric and Preventive Dentistry in the year 2020 after obtaining approval from the Institutional Ethical Committee (DMIMS/DU/IEC/2018-19/4799) on September 30th 2018. The sample size was calculated using 95% probability, showing a statistically significant difference using the alpha level and power 80% by using N master software. According to this software, the minimum sample size calculated was 12 for each group and total 36 samples were taken. The teeth included in the study were caries free primary anterior teeth without any cracks or defects near to exfoliation obtained from healthy children between 5 to 7 years of age. The teeth of children with any systemic condition and teeth with cracks, caries or any defect were excluded from the study. The parents were informed about the procedure and a written consent was obtained. The parents and patients were explained how the teeth will be extracted after application of topical anaesthetic agent and injecting local anaesthetic agent in the required region. The tooth was then extracted and bleeding was stopped by applying finger pressure to the socket using gauze piece. After giving post-operative instructions the patients were sent home. The extracted samples were stored in 0.1% thymol solution at 4°C and were utilised for the study within three months.\n\nThe primary anterior teeth were placed in 5.25% sodium hypochlorite for 1 minute for cleaning, and scaling using Woodpecker ultrasound scaler (UDS-J) on the surface for 2 minutes. The samples were stored in 0.1% thymol solution at 4°C for not more than three months. The teeth samples were sliced 2 mm below the cemento-enamel junction (CEJ) and mounted in self-cure acrylic resin, and polished using silicon carbide paper sequentially. The samples were then cleaned using distilled water for 20 seconds. An area of 5 × 5 mm was exposed on the buccal surface of all the samples and two coats of nail varnish were applied on the remaining portion of the teeth.\n\nFive grams of nano silver fluoride powder was manufactured by wet chemical route synthesis at Nano Research Elements, Haryana, India. Nano silver fluoride varnish was prepared by dispersing 4.16% NSF in a colophony base. The pH was adjusted to 7 for the neutral varnish and 4 for the acidulated varnish using ascorbic acid. Further, both the varnish were separately stored in amber colored glass bottles at room temperature.\n\nDemineralisation solution was prepared using 2.2 mM calcium chloride (CaCl2), 2.2 mM potassium dihydrogen phosphate (KH2PO4), 0.05 M acetic acid and 0.25 ppmF, and stirred on a magnetic stirrer. After which, 1M KOH was added to the solution for adjusting the pH at 4.5. The remineralising solution consisted of 20 mMol l−1 HEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), 130 mM potassium chloride (KCl),1.5 mM calcium chloride (CaCl2), 0.9 mM potassium dihydrogen phosphate (KH2PO4) and 1 mM sodium azide (NaN3). Potassium hydroxide (KOH) was used to adjust the pH at 7. Each sample was immersed in 30 ml of demineralisation solution for three days to induce incipient caries. Next, the samples were washed with distilled water for 20 seconds.\n\nPrimary surface microhardness (SMH) of the samples was tested by Vickers micro hardness testing machine (MITUTOYA, 810-401 D) under a load of 50 grams for 10 seconds, at 3 different sites. The mean surface microhardness value was calculated for each sample. The samples were washed with distilled water, dried and remineralising agents were applied on them as follows:\n\nGroup 1: Sodium fluoride varnish was dispensed on the paper pad and applied on the exposed enamel surface unidirectionally using an applicator brush.\n\nGroup 2: Two drops of neutral nano silver fluoride varnish applied on the exposed enamel surface unidirectionally using an applicator brush.\n\nGroup 3: Two drops of acidulated nano silver fluoride varnish applied on the exposed enamel surface unidirectionally using an applicator brush.\n\nSimulation of the oral condition was accomplished by following a 7 day pH cycling protocol.11 Samples were immersed in remineralising solution for 21 hours and then in the demineralising solution for 3 hours. This cycle was repeated for 7 days. The solutions were changed on every third day. The samples were washed with distilled water and subjected to post treatment SMH testing, same as before.\n\nOne sample representative of each group was prepared to carry out Scanning electron microscopy and Energy Dispersive Spectroscopy (SEM EDS).\n\nScanning electron microscope (JEOL JSM-6380A) was used to examine the surface changes after 7 days of remineralising agent application. The samples were coated with platinum sputter in the Auto fine coater (JEOL JFC-1600) for better visualization. The samples were scanned at 50×, 500× and 1000× magnification and photomicrographs were taken.\n\nEnergy-dispersive X-ray spectroscopy (JEOL JSM-6380A) was used to analyse the elemental concentration in the teeth samples. The concentrations of silver, fluoride, calcium and phosphorus ions were assessed in the sample after application of the remineralising agents. The proportion of the individual concentration of elements present on the enamel surface were measured in weight percentage.\n\nDescriptive and inferential statistics were to be obtained from the data. Student’s paired t-test was used to compare the mean surface microhardness values before and after application of each test materials. Comparison of difference in mean surface microhardness values after application of 5% Sodium fluoride varnish, neutral nano silver fluoride and acidulated nano silver fluoride using one way ANOVA. Whereas, comparison of difference in the p values of mean surface microhardness values after application using 5% Sodium fluoride varnish, neutral nano silver fluoride and acidulated nano silver fluoride using HSD Tukey test. Software used for the analysis were SPSS 24.0 and GraphPad Prism 7.0 version, and P<0.05 is considered as level of significance.\n\n\nResults\n\nThere was a significant difference (HSD Tukey) in all the groups after demineralisation and after remineralisation, showing that all the agents increased the surface microhardness values (Table 1).35–37\n\nThe effectiveness of all the remineralisaing agents differed (One Way ANOVA). The highest increase in the surface microhardness was observed in group 3 followed by group 2 and group 1. The mean difference between group 1 and group 2 was statistically insignificant. Whereas, the mean difference between group 1 and group 3 and also, group 2 and group 3 was statistically significant (P<0.01) (Table 2).\n\nThe elemental composition of enamel surface after application of 5% sodium fluoride varnish, neutral nano silver fluoride and acidulated nano silver fluoride in Wt% is suggestive of increase in the concentration of fluoride in all the three samples and presence of silver in group 2 and 3 (Table 3).\n\n\nDiscussion\n\nSodium fluoride (NaF) varnish is the most widely used topical fluoride agent containing 22,600ppm fluoride.12 On application, NaF varnish reacts with hydroxyapatite crystals and deposits a layer of calcium fluoride over the HAP lattice and its choking off phenomenon provides a sustained fluoride release.13,14 Sodium fluoride varnishes are easy to apply and have moisture tolerance.15 According to a systematic review, 5% sodium fluoride varnish demonstrated acceptable remineralising ability and is considered as the gold standard.16\n\nUnder the broad umbrella of nanotechnology, silver nanoparticles have emerged as a promising tool and this is attributed to two major properties; quantum size effect which is elicited because of the small size, providing a larger surface area for interactions and quantum tunnelling effect which depicts the ability of the particle to cross any barrier to cause membrane disintegration and show antibacterial property.17 Augmentation of broad range of interaction and molecular reactions, modify the physical properties of materials by re-organization of the particles.18,19 The positive results of AgNPs encouraged its incorporation in various dental materials for diagnostic and therapeutic purposes.20\n\nRecent studies have emphasized the synergistic action of silver nanoparticles with high fluoride concentration in prevention of spread of dental caries.21,22 A new compound, nano silver fluoride was introduced by Targino AG. et al. for anticariogenic action.4 This new agent has a high safety index and amalgamates the antibacterial properties of silver and remineralising efficacy of fluoride.\n\nIn the present study, the remineralising efficacy of 5% sodium fluoride varnish was evaluated before and after varnish application. Baseline value was not assessed to avoid damage to the samples and mean ranging from 320 to 350 VHN mentioned in literature was considered.23 The results depicted a significant increase in the surface microhardness of carious lesion (Table 1) The remineralisation of samples can be attributed to the formation of fluorapatite which has a low solubility and increases the precipitation of calcium and phosphate ions on the teeth surface as mentioned by Shen C. et al.24 and Vicente A. et al.25\n\nTwo indigenously prepared varnishes of nano silver fluoride in neutral and acidulated forms were used in the current study at a concentration of 4.16% conforming its minimum inhibition concentration and minimum bactericidal concentration.26,27 Neutral nano silver fluoride group showed a statistically significant difference in the remineralising efficacy before and after its application (Table 1). The increase in surface microhardness of the carious lesion can be attributed to the deposition of fluoride and silver nano particles, which precipitated into the demineralised lesion, and is in congruence with the study conducted by Nozari A et al.23 According to Zhi QH et al., silver fluoride promotes remineralisation by getting incorporated into the crystalline lattice. It also suggests increased calcium fluoride formation when more than 100 ppm of fluoride is present in the delivery system, which tilts the demineralising curve towards remineralisation. This favours the results of the present study.\n\nOn comparing the remineralising efficacy of neutral NSF and 5% sodium fluoride, it was observed that the mean microhardness of samples treated with neutral NSF was more but the difference was statistically insignificant (P=0.356674). These results are in equivalence with the studies carried out by Silva A. et al.26 and Nozari A. et al.23 These studies stated that as silver nanoparticles are inherently stable, they penetrate deep into the demineralized structures without interfering with the action of fluoride. In a study conducted Burns J. et al., NSF was applied showed improved efficacy than water.6 The results of a trial conducted by Tirupathi S. et al. concluded that 5% NSF showed better efficacy in caries reduction as compared to 38% SDF when applied annually due to the higher concentration of fluoride used in NSF group.5\n\nIn our study, statistically significant increase was obtained in the mean value of the surface microhardness of enamel caries after applying acidulated NSF. Under the influence of acid, hydroxyapatite released calcium, aiding the formation of calcium fluoride. Alongside this, the nano size of the particles improved the penetration of NSF into the enamel as suggested by Alves K. et al.27\n\nA comparison between 5% Sodium fluoride and acidulated NSF was revealed a statistically significant difference (P=0.001005) with 188.46 VHN in 5% Sodium fluoride group and 202.66 VHN in acidulated nano silver fluoride group, in our study. However, a study comparing the remineralising potential of acidic NSF and NaF claimed better results after application of NaF varnish. The difference in the results can be attributed to chitosan coating over the NSF particles, which precluded the ionic bonding between NSF and hydroxyapatite.28 In the present study, NSF was produced by wet chemical route synthesis without chitosan. Another reason making a difference in the results, can be the amount of fluoride used in the formulation. Akylidiz M. et al. used 10,147 ppm of fluoride28 whereas, in our study 1,45,000 ppm of fluoride is NSF was used, which improved the efficacy of the experimental formulations.\n\nA comparison between neutral NSF and acidulated NSF was also carried out in the present study. The mean surface microhardness of acidulated NSF statistically more (P=0.002056) than neutral NSF with 194.26 VHN. Similarly, in a study conducted Lee Y. et al. neutral sodium fluoride and acidulated phosphate fluoride was evaluated and acidulated phosphate fluoride showed better efficacy. This study’s results are owed to the fact that acidic pH etched the surface of the teeth and assisted deeper incorporation of fluoride ions. Although the fluoride concentration was less in APF gel than neutral sodium fluoride, it showed better results.29 Thus, the acidulated formulations of topical fluorides augment the fluoridation of teeth.6\n\nResearchers have attempted to decode the mechanism by which nano silver fluoride acts on the dental tissues and have suggested that caries prevention occurs by the virtue compound supplementary action of silver and fluoride.30 Literature suggests that there is precipitation of silver ions on the tooth surface, increasing the microhardness.31 Noronha et al. proposed a hypothesis that silver nanoparticles in NSF have inherent ionic stability, which prevents it from interfering with the action of fluoride.32 A striking revelation has been made by Zhi QH et al. regarding the mechanism of NSF in remineralisation, which suggests the formation of silver apatite. On application of silver fluoride, there may be precipitation of silver salts that decrease the permeability and aids in calcification of the teeth.21\n\nA study conducted by Zhao et al. mentions that the interaction between the hydroxyapatite lattice and the fluoride compounds used depends on fluoride concentration. A high concentration of fluoride leads to the formation of calcium fluoride, whereas at lesser concentration, fluorapatite is formed.33 According to this, presence of calcium fluoride can be anticipated after NSF application.\n\nThe positive results of the surface microhardness assessment encouraged us to investigate their clinical applicability further. A qualitative correlation of the results was carried out by analysing the samples under scanning electron microscope (SEM). The 5% sodium fluoride sample depicts a fine granular layer of precipitated minerals. Some amount of the deposits is retained, but cracks are still visible, representing a partially mineralized structure (Figure 1). The sample treated with neutral nano silver fluoride illustrates irregular polyhedral deposits with a fine layer of precipitated minerals (Figure 2). The application of acidulated nano silver fluoride shows presence of polyhedral deposits in abundance, depicting a mineral phase precipitation without any debris, owed to the acidic pH (Figure 3). An extra sample was prepared to obtain SEM image on the 3rd day after application of acidulated nano silver fluoride for evaluating initial remineralisation (Figure 4). The image depicts polyhedral deposits of mineral phase with a flower-field like appearance depicting initial remineralisation phase, as suggested by Gjorgievska et al.34\n\nThe sample displays flower-field appearance in few regions. This represents an initial phase of remineralisation.\n\nThe present study’s Energy dispersive X-ray spectrophotometry (EDS) analysis detected fluoride concentration of 5.45 wt% in the 5% Sodium fluoride group without any silver content. The neutral nano silver fluoride group showed 14.64% of fluoride and 13.57% of silver. The acidulated nano silver fluoride group values were approximately in the same range as neutral nano silver fluoride with 14.94% of fluoride and 16% of silver. These fluoride and silver values on the teeth surface confirm the deposition of minerals on the tooth surface, initiating the process of remineralisation.\n\nThe results of the study prove the superiority of acidulated nano silver fluoride followed by neutral nano silver fluoride and 5% sodium fluoride in remineralisation of enamel caries in primary teeth.\n\n\nConclusion\n\nAll the remineralising agents were capable to remineralise the enamel of primary teeth. However, acidulated nano silver fluoride varnish depicted more efficacy than others; whereas, 5% sodium fluoride and neutral nano silver fluoride varnish had close results.", "appendix": "Data availability\n\nFigshare: IMPACT OF SODIUM FLUORIDE AND NANO SILVER FLUORIDE-BASED VARNISHES ON REMINERALISATION OF ENAMEL CARIES: AN IN-VITRO STUDY. https://doi.org/10.6084/m9.figshare.22800479.v1. 35\n\nThis project contains the following underlying data:\n\n- SEM.pdf (Raw unedited uncropped images)\n\nFigshare: IMPACT OF SODIUM FLUORIDE AND NANO SILVER FLUORIDE-BASED VARNISHES ON REMINERALISATION OF ENAMEL CARIES: AN IN-VITRO STUDY. https://doi.org/10.6084/m9.figshare.22592200.v1. 36\n\nThis project contains:\n\n- MASTERCHART.xlsx (Microhardness data)\n\nFigshare: IMPACT OF SODIUM FLUORIDE AND NANO SILVER FLUORIDE-BASED VARNISHES ON REMINERALISATION OF ENAMEL CARIES: AN IN-VITRO STUDY. https://doi.org/10.6084/m9.figshare.22827947.v1. 37\n\nThis project contains the following underlying data:\n\n- energy-dispersive x-ray spectroscopy data for all 3 groups\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nRobinson C, Shore RC, et al.: The chemistry of enamel caries. Crit. Rev. Oral Biol. Med. 2000; 11(4): 481–495. Publisher Full Text\n\nMarinho VC, Worthington HV, Walsh T, et al.: Fluoride varnishes for preventing dental caries in children and adolescents. Cochrane Database Syst. Rev. 2013; 7. Publisher Full Text\n\nRosenblatt A, Stamford TCM, Niederman R: Silver diamine fluoride: A caries “silver-fluoride bullet”. J. Dent. Res. 2009; 88(2): 116–125. PubMed Abstract \| Publisher Full Text\n\nTargino AGR, Flores MAP, dos Santos Junior VE , et al.: An innovative approach to treating dental decay in children. A new anti-caries agent. J. Mater. Sci. Mater. Med. 2014 Aug; 25(8): 2041–2047. PubMed Abstract \| Publisher Full Text\n\nTirupathi S, Nirmala SVSG, Rajasekhar S, et al.: Comparative cariostatic efficacy of a novel Nano-silver fluoride varnish with 38% silver diamine fluoride varnish a double-blind randomized clinical trial. J. Clin. Exp. Dent. 2019; 11: e105–e112. PubMed Abstract \| Publisher Full Text\n\nSoekanto SA, Marpaung LJ, Ushohwah H, et al.: Efficacy of propolis fluoride and nano silver fluoride for inhibition of streptococcus mutans and enterococcus faecalis biofilm formation. Int. J. Appl. Pharm. 2018 Jan 1; 9: 51. Publisher Full Text\n\nBrighenti FL: Effect of Low Fluoride Acidic Dentifrices on Dental Remineralization. Braz. Dent. J. 2013; 24(1): 35–39. PubMed Abstract \| Publisher Full Text\n\nShashikiran ND, Reddy VVS, Patil R: Evaluation of fluoride release from teeth after topical application of NaF, SnF2 and APF and antimicrobial activity on mutans streptococci. J. Clin. Pediatr. Dent. 2006; 30(3): 239–245. PubMed Abstract \| Publisher Full Text\n\nDelbem ACB, Brighenti FL, Vieira AEM, et al.: In vitro comparison of the cariostatic effect between topical application of fluoride gels and fluoride toothpaste. J. Appl. Oral Sci. 2004; 12(2): 121–126. PubMed Abstract \| Publisher Full Text\n\nOlympio KPK: Low-Fluoride Dentifrices with Reduced pH: Fluoride Concentration in Whole Saliva and Bioavailability. Caries Res. 2007; 41: 365–370. PubMed Abstract \| Publisher Full Text\n\nTen Cate JM, Buijs MJ, Damen JJM: PH cycling of enamel and dentin lesions in the presence of low concentrations of fluoride. Eur. J. Oral Sci. 1995; 103: 362–367. PubMed Abstract\n\nSeppa L: Fluoride varnishes in caries prevention. Proc. Finn. Dent. Soc. 1982; 78 Suppl 8: 1–50.\n\nOgaard B: The cariostatic mechanism of fluoride. Compend. Contin. Educ. Dent. 1999; 20(1 Suppl): 10–17.\n\nKhanduri N, Kurup D, Mitra M: Quantitative evaluation of remineralizing potential of three agents on artificially demineralized human enamel using scanning electron microscopy imaging and energy-dispersive analytical X-ray element analysis: An in vitro study. Dent. Res. J. 2020; 17: 366–372. Publisher Full Text\n\nSeppa L, Tolonen T: Caries preventive effect of fluoride varnish applications performed two or four times a year. Scand. J. Dent. Res. 1990; 98: 102–105. PubMed Abstract\n\nGao SS, Zhang S, Mei ML, et al.: Caries remineralisation and arresting effect in children by professionally applied fluoride treatment – a systematic review. BMC Oral Health. 2016; 16: 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang W, Liao S, Zhu Y, et al.: Recent Applications of Nanomaterials in Prosthodontics. J. Nanomater. 2015; 2015: 1–8. Publisher Full Text\n\nSlenters TV, Hauser IG, Daniels AU, et al.: Silver coordination compounds as light-stable, nanostructured and anti-bacterial coatings for dental implant and restorative materials. J. Mater. Chem. 18(44): 5359–5362. Publisher Full Text\n\nDamm C, Munstedt H, Rosch A: Long-term antimicrobial polyamide 6/silver-nanocomposites. J. Mater. Sci. 2007; 42(15): 6067–6073. Publisher Full Text\n\nPercival SL, Bowler PG, Russell D: Bacterial resistance to silver in wound care. J. Hosp. Infect. 2005; 60(1): 1–7. Publisher Full Text\n\nZhi QH, Lo EC, Kwok AC: An in vitro study of silver and fluoride ions on remineralization of demineralized enamel and dentine. Aust. Dent. J. 2013; 58(1): 50–56. PubMed Abstract \| Publisher Full Text\n\nBawden JW: Fluoride varnish: a useful new tool for public health dentistry. J. Public Health Dent. 1998; 58: 266–269. PubMed Abstract \| Publisher Full Text\n\nNozari A: Impact of Nano Hydroxyapatite, Nano Silver Fluoride and Sodium Fluoride Varnish on Primary Enamel Remineralization: An in vitro Study. J. Clin. Diagn. Res. 2017; 12(3): 38–43.\n\nShen C, Autio-Gold J: Assessing fluoride concentration uniformity and fluoride release from three varnishes. J. Am. Dent. Assoc. 2002; 133: 176–182. PubMed Abstract \| Publisher Full Text\n\nVicente A, Ortiz Ruiz AJ, González Paz BM, et al.: Efficacy of fluoride varnishes for preventing enamel demineralization after interproximal enamel reduction. Qualitative and quantitative evaluation. Remuzzi G, editor. PLoS One. 2017 Apr 21; 12(4): e0176389. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSilva A, Teixeira J, Júnior P, et al.: Remineralizing Potential of Nano-Silver-Fluoride for Tooth Enamel: An Optical Coherence Tomography Analysis.\n\nAlves KM, Pessan JP, Brighenti FL, et al.: In vitro evaluation of the effectiveness of acidic fluoride dentifrices. Caries Res. 2007; 41: 263–267. Publisher Full Text\n\nAkyildiz M: Comparison of Remineralising Potential of Nano Silver Fluoride, Silver Diamine Fluoride and Sodium Fluoride Varnish on Artificial Caries: An in vitro Study. Oral Health Prev. Dent. 2017; 7: 5.\n\nLee YE, Baek HJ, Choi YH, et al.: Comparison of remineralization effect of three topical fluoride regimens on enamel initial carious lesions. J. Dent. 2010 Feb; 38(2): 166–171. PubMed Abstract \| Publisher Full Text\n\nNagireddy VR, Reddy D, Kondamadugu S, et al.: Nanosilver Fluoride—A Paradigm Shift for Arrest in Dental Caries in Primary Teeth of Schoolchildren: A Randomized Controlled Clinical Trial. Int. J. Clin. Pediatr. Dent. 2019; 12(6): 484–490. PubMed Abstract \| Publisher Full Text\n\nAl-Nerabieah Z, Arrag EA, Rajab A: Cariostatic efficacy and children acceptance of nano-silver fluoride versus silver diamine fluoride: a randomized controlled clinical trial.2020; 8.\n\nNoronha VT, Amauri JP, Durán G, et al.: Silver nanoparticles in dentistry. Dent. Mater. 2017; 33(10): 1110–1126. Publisher Full Text\n\nZhao IS, Yin IX, Mei ML, et al.: Remineralising Dentine Caries Using Sodium Fluoride with Silver Nanoparticles: An in vitro Study. Int. J. Nanomedicine. 2020 Apr; 15: 2829–2839. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGjorgievska ES, Nicholson JW, Slipper IJ, et al.: Remineralization of demineralized enamel by toothpastes: A scanning electron microscopy, energy dispersive X-ray analysis, and three-dimensional stereo-micrographic study. Microsc. Microanal. 2013 Jun; 19(3): 587–595. PubMed Abstract \| Publisher Full Text\n\nDeulkar PV, Rathi N, Thosar N, et al.: IMPACT OF SODIUM FLUORIDE AND NANO SILVER FLUORIDE-BASED VARNISHES ON REMINERALISATION OF ENAMEL CARIES: AN IN-VITRO STUDY. [Dataset]. figshare. 2023. Publisher Full Text\n\nDeulkar PV, Rathi N, Thosar N, et al.: IMPACT OF SODIUM FLUORIDE AND NANO SILVER FLUORIDE-BASED VARNISHES ON REMINERALISATION OF ENAMEL CARIES: AN IN-VITRO STUDY. [Dataset]. figshare. 2023. Publisher Full Text\n\nDeulkar PV, Rathi N, Thosar N, et al.: IMPACT OF SODIUM FLUORIDE AND NANO SILVER FLUORIDE-BASED VARNISHES ON REMINERALISATION OF ENAMEL CARIES: AN IN-VITRO STUDY. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "200519", "date": "29 Aug 2023", "name": "Abdulkadeer Jetpurwala", "expertise": [ "Reviewer Expertise Pediatric Dentistry", "Dental Caries", "Dental Materials" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nPage 3\nSample preparation:\nWhat was the grit of silicon carbide used sequentially?\nPage 4\nSurface microhardness assessment\nWas the surface microhardness assessment done prior to demineralization of the enamel?\nThe effect of various agents to restore the hardness of enamel after demineralization when presented in percentile change would provide a better comparison between groups compared to absolute values and mean scores, as the baseline microhardness scores of the samples would be variable.\nTable 1: legend should read ‘HSD Tukey test’\nPage 5:\nBaseline VHN was not done to prevent damage to the sample,\nThis could be countered by increasing the available area of enamel (not covered by nail varnish) for analysis.\nVHN causes very small indentation on the surface of the sample. The damage to the sample thus occurred would be minimal or insignificant in comparison the to data obtained by baseline VHN. This data would be very helpful in comparisons of microhardness before and after application of test agents. The ability of the test agents to restore the VHN values according to baseline could also be assessed.\nThe assumption that the VHN at baseline would be 320-350 as per literature can also be questioned as the enamel surfaces were abraded with silicon carbide due to which the matured surface layer of enamel would be lost\nThe post application values of VHN for NaF, NSF and aNSF at 186, 194 and 212 respectively are significantly lesser (>30%) of assumed VHN scores\nFIG 1,2,3:\nThe legend does not mention the agent used for treating the surface in each figure\nPage 9\nRef 18: Year not mentioned\nRef 26 incomplete\nRef 31 incomplete\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "10193", "date": "22 Sep 2023", "name": "Pranjali Deulkar", "role": "Author Response", "response": "Page 3 Sample preparation: What was the grit of silicon carbide used sequentially? - Silicon carbide paper of 200, 600, 800, and 1200-grit sequentially Surface microhardness assessment Was the surface microhardness assessment done prior to demineralization of the enamel? - No The effect of various agents to restore the hardness of enamel after demineralization when presented in percentile change would provide a better comparison between groups compared to absolute values and mean scores, as the baseline microhardness scores of the samples would be variable. - Continuous data was collected for the said parameters. So we have calculated mean and SD for the same. Categorical data was not available to calculate percentiles. Table 1: legend should read ‘HSD Tukey test’ Page 5: Baseline VHN was not done to prevent damage to the sample, This could be countered by increasing the available area of enamel (not covered by nail varnish) for analysis. VHN causes very small indentation on the surface of the sample. The damage to the sample thus occurred would be minimal or insignificant in comparison the to data obtained by baseline VHN. This data would be very helpful in comparisons of microhardness before and after application of test agents. The ability of the test agents to restore the VHN values according to baseline could also be assessed. The assumption that the VHN at baseline would be 320-350 as per literature can also be questioned as the enamel surfaces were abraded with silicon carbide due to which the matured surface layer of enamel would be lost The post application values of VHN for NaF, NSF and aNSF at 186, 194 and 212 respectively are significantly lesser (>30%) of assumed VHN scores - Each microhardness test constitutes of 2 indentations and a gap between each indentation is required for proper placement of the jig. Thus, to avoid damage to the samples, baseline microhardness testing was not performed. Thus, not covering the enamel surface with nail varnish also wouldn't have provided enough area. - The post application values of VHN was less then the assumed baseline score as the enamel surface was sequentially polished with carbide paper to obtain a smooth surface for microhardness testing. This process removes some amount enamel which in turn reduces the microhardness value of the enamel surface. Thus, the values obtained post treatment are less than the assumed baseline values. FIG 1,2,3: The legend does not mention the agent used for treating the surface in each figure - The group number mentioned in the legends has been specified in the figure. Page 9 Ref 18: Year not mentioned - Slenters TV, Hauser-Gerspach I, Daniels AU, Fromm KM. Silver coordination compounds as light-stable, nano-structured and anti-bacterial coatings for dental implant and restorative materials. Journal of Materials Chemistry. 2008;18(44):5359-62. Ref 26 incomplete - Teixeira JD, Melo PC, Lima MG, Mota CC, Lins EC, Pereira JR, Gomes AS, Targino AG, Rosenblatt A. Remineralizing potential of nano-silver-fluoride for tooth enamel: an optical coherence tomography analysis. Pesquisa Brasileira em Odontopediatria e Clínica Integrada. 2019;19. Ref 31 incomplete - Al-Nerabieah Z, Arrag E, Rajab A. Cariostatic efficacy and children acceptance of nano-silver fluoride versus silver diamine fluoride: A randomized controlled clinical trial. Journal of Stomatology. 2020;73(3):100-6." } ] } ]	2	https://f1000research.com/articles/12-643
https://f1000research.com/articles/12-891/v1	26 Jul 23	{ "type": "Research Article", "title": "Racial disparities in major cardiovascular and cerebrovascular adverse events in breast cancer survivors: A nationwide analysis", "authors": [ "Akhil Jain", "Rupak Desai", "Ibrahim Ahmed", "Kingsley Amakye", "Maharshi Raval", "Sagar Patel", "Kanishka Uttam Chandani", "Vidit Majmundar", "Siddharth Pravin Agrawal", "Labdhi Sanghvi", "Monika Garg", "Darsh Patel", "Mohammad Hamza", "Raphael Bonita", "Sunil Dhar", "Rupak Desai", "Ibrahim Ahmed", "Kingsley Amakye", "Maharshi Raval", "Sagar Patel", "Kanishka Uttam Chandani", "Vidit Majmundar", "Siddharth Pravin Agrawal", "Labdhi Sanghvi", "Monika Garg", "Darsh Patel", "Mohammad Hamza", "Raphael Bonita", "Sunil Dhar" ], "abstract": "Background: Improved survival outcomes in breast cancer has brought attention to major cardiovascular and cerebrovascular adverse events (MACCE). Racial disparities in these events among breast cancer survivors are understudied. Methods: Using National Inpatient Sample datasets (October 2015-December 2017, ICD-10-CM), we investigated racial disparities in the hospitalized breast cancer survivors for MACCE. They were further sub-categorized on the basis of prior chemotherapy or radiation therapy (CT/RT). Results: Of 1,301,320 breast cancer survivor women, 75.8% were White, 11.3% were Black, and 16.1% had prior CT/RT. All-cause in-hospital mortality was highest in Asian or Pacific Islanders (3.2%) in the whole breast cancer survivor population; and in Native Americans (4.7%) in CT/RT subgroup. Native Americans (4.1%) had the highest incidence of acute myocardial infarction (AMI) in the overall population, whereas White patients (2.9%) predominated in CT/RT subgroup. White patients (29.6%) had the highest prevalence of arrhythmia, regardless of the prior CT/RT. For strokes, Asian or Pacific Islanders (3.9%) and Black patients (3.8%) had a higher prevalence. All-cause mortality, AMI, arrhythmia, and stroke had the highest adjusted odds in Asian or Pacific Islanders (1.19), Native Americans (1.31), White patients (1), and Black patients (1.12) respectively. Black patients had the lowest quartile income and a longer median stay. White patients had the highest transfer to nursing facilities, whereas Asian or Pacific Islanders had the highest mean hospital expenditures. Conclusions: Racial disparities exist in MACCE among breast cancer survivors. Further research, especially pooling and analyzing real-world data is needed on the prevalence of MACCE in breast cancer survivors, particularly in subgroups with different cancer-related treatments.", "keywords": [ "breast cancer", "survivors", "prior history", "racial disparities", "major adverse cardiac and cerebrovascular events (MACCE)", "cardiovascular", "mortality" ], "content": "Introduction\n\nWith the improving survival of breast cancer patients, cardiovascular adverse events in this population group have been gaining increasing attention. For women diagnosed with breast cancer between 2010 to 2016, the 5-year relative survival rate for nonmetastatic invasive breast cancer was reported to be 84%.1 Of note, the prognosis of breast cancer has been improving over the years. Since 2007, the number of women 50 years and older who have died of breast cancer has continued to decline. The number of women younger than 50 who have died of breast cancer has remained consistent. From 2013 to 2018, the death rate for women with cancer dropped by 1% each year.2 Racial disparities in cardiovascular morbidities among breast cancer survivors are not well studied.3\n\nWe conducted this national population-represented sample-based study to investigate major cardiovascular and cerebrovascular adverse events in breast cancer survivors and how they might differ among the various ethnicities. Breast cancer and its treatment has been shown to have an association with cardiovascular morbidity and mortality. Anthracycline is used in both early and advanced stages. Anthracycline-related irreversible cardiomyopathy has been of concern since the initial years of its use as a part of chemotherapy regimens.4 Black and Hispanic patients have a higher incidence of heart failure following anthracycline treatment compared to other ethnic groups.5 Ethnic variation in the incidence of breast cancer has been well-established for decades.2 Incidence is known to be higher among white women. However, survival rates have been reported to be varying among different races, and black women are known to have poorer outcomes.6 The choice of categories in our study was based on the previous studies, as noted above, that evaluated the racial differences in the incidence and survival of breast cancer. As the differences are not studied for major cardiovascular and cerebrovascular adverse events, we decided to conduct this study. There were no funding agencies involved and no rules of human categorization were required for this study.\n\n\nMethods\n\nWe used National Inpatient Sample datasets (NIS) from October 2015 to December 2017. These datasets are publicly available under the Healthcare and Utilization Project of the Agency for Healthcare Research and Quality (AHRQ).7 Datasets of each year contain 20% stratified sample of discharges from community hospitals (excluding rehabilitation and long-term acute care institutions). Statistical weighted analysis of these datasets yields national estimates of inpatient hospitalizations, utilization, access, costs, and outcomes for the United States. We did not need Institutional Review Board approval because NIS contains de-identified data. To minimize the potential for bias, comprehensive multivariable regression analysis was performed.\n\nWe used ICD10 codes to identify adult hospitalizations with breast cancer survivors (i.e., with prior history of breast cancer - Z85.3) and with and without a history of chemotherapy (CT, Z9221) or radiotherapy (RT, Z923). The Clinical Classifications Software Refined (CCSR) aggregates ICD-10-CM/PCS diagnostic and procedural codes into clinically meaningful categories.8 Using CCSR outcomes of interest were generated. AHRQ comorbidity software-generated comorbidities measures (binary variables) were used in the analysis.\n\nUsing the algorithm as shown in Figure 1, all adult admissions with history of breast cancer, above the age of 18 years, were identified. This cohort was further divided into two sub groups; patients who had received some form of chemotherapy (CT) and/or radiotherapy (RT) and those without exposure to CT/RT. A subsequent sub-cohort of the population whose racial data was available were identified. These cohorts were then further stratified by race to study outcomes of interest, including cardiovascular disease (CVD) burden, major adverse cardiovascular and cerebrovascular events (MACCE), and healthcare resource utilization. The patient population whose data pertaining to race was not available were excluded from the study.\n\nAge in a continuous fashion and other variables (race, admission type, hospital characteristics including hospital bed size (small, medium, or large), location/teaching status (rural, urban non-teaching or urban teaching), region, median household income quartiles, and payer status, disposition type, death as an outcome) in categorical fashion were used for statistical analysis.\n\nWe included all-cause in-hospital mortality, acute myocardial infarction (AMI), arrhythmia, and stroke as major adverse cardiovascular and cerebrovascular events (MACCE) for the outcomes. All-cause in-hospital mortality was available as NIS has an in-build variable “died” corresponding to in-hospital deaths. Other outcomes were extracted from discharge diagnosis using clinical classification software for all-cause mortality, acute myocardial infarction (AMI, CCS 100), arrhythmia (CCS 106), and stroke (CCS 109). NIS has an in-built variable “race”, with the categories: White, Black, Hispanic, Asian or Pacific Islander, Native American, and other. MACCE was compared among these races. Racial disparities for MACCE were also assessed for breast cancer survivor subgroups with and without prior CT/RT.\n\nIn SPSS V24.0 (IBM Corp., Armonk, NY, USA), data on national estimates were examined using sampling weights and complex sample modules. Discharge records with missing data for race (<5%) were excluded from the final analysis. Baseline characteristics including demographics, comorbidities; and MACCE outcomes were compared among races using chi-square (statistical significance determined as a two-sided p-value 0.05) for categorical or student’s t-test for continuous data. Besides extracted breast cancer survivor sample population, these were also compared for sub-populations with and without prior CT/RT. The adjusted odds ratios (aOR) of MACCE were estimated with whites as the reference group using multivariate logistic regression, correcting for relevant confounders such as sociodemographic factors, cardiac and extracardiac comorbidities, and prior CT/RT.\n\n\nResults\n\nWe identified 1,301,320 nationwide hospitalizations with a prior history of breast cancer in women, 83.9% (1,092,280) without, and 16.1% (209,040) with prior CT/RT. Of the admissions with a prior history of breast cancer with exposure to CT/RT (209,040), those whose data pertaining to race was not available, were also excluded, resulting in a final cohort of 201,965 patients. Discharge records with missing data for race (<5%) were excluded from the final analysis. The majority of hospitalizations were distributed between White (151, 510 patients, 75.8%) and Black patients (27, 885 patients, 11.3%), followed by Hispanic patients (12,190 patients, 6.04%), Asian/Pacific Islander patients (4,765 patients, 2.35%), Native American patients (750 patients, 0.37%) and patients of other races (4,865 patients, 2.4%). Breast cancer survivors had a higher mean age for White patients, followed by Asian or Pacific Islander, Black patients, Hispanic patients, and Native American patients at hospitalization (75, 72, 69, 69, 69, and 69 years, respectively Table 1). Breast cancer survivors without prior CT/RT maintained a similar pattern to the overall study population, but breast cancer survivors with prior CT/RT had lower mean age for all races; White, Asian or Pacific Islander, Black, Hispanic, Native American (71, 66, 64, 63, 63 years, respectively Table 2). Non-elective admissions were highest in Black patients (82.9%), followed by Native American patients (80.6%), Hispanic pateints (80.3%), Asian or Pacific Islander patients (78.9%), and White pateints (77.4%), with a similar pattern observable in both subgroups i.e., with and without prior CT/RT (Table 3).\n\n# Represents a quartile classification of the estimated median household income of residents within the patient’s zip code, https://www.hcup-us.ahrq.gov/db/vars/zipinc_qrtl/nrdnote.jsp.\n\n§ The bed size cutoff points divided into small, medium, and large have been done so that approximately one-third of the hospitals in a given region, location, and teaching status combination would fall within each bed size category. https://www.hcup-us.ahrq.gov/db/vars/hosp_bedsize/nrdnote.jsp.\n\n~ A hospital is considered to be a teaching hospital if it has an American Medical Association-approved residency program. https://www.hcup-us.ahrq.gov/db/vars/hosp_ur_teach/nrdnote.jsp.\n\nThe prevalence of comorbidities was assessed. Hypertension was the most common condition in the two sub-populations of breast cancer survivors, and among all races; with Black patients having the highest prevalence (83.3%), followed by White patients, Native American patients, Asian/Pacific Islander patients, and Hispanic patients (71.3, 70.4, 69. 68.8 percent, respectively). Overall and in both cohorts, diabetes mellitus (DM) was prevalent in Native American patients (41.1%) followed by Black patients (37.8%), and it was lowest in White patients (22.6 percent). In the whole breast cancer survivor population and prior CT/RT subgroup, White patients had a higher prevalence of dyslipidemia (45%, 42.2%), followed by Asian or Pacific Islander patients (44.8%, 39.3%) and Black patients (42.3%,37.8%). Smoking was prevalent in the whole breast cancer survivor sample population and two subgroups, with Native American patients smoking the most, followed by White and Black patients. Obesity, renal failure, congestive heart failure, and pulmonary circulation disorder were the most common conditions in Black patients; chronic pulmonary illness and coagulopathy were the most common conditions in Native American patients; and depression was the most common condition among White patients.\n\nThe prevalence and adjusted odds ratios of MACCE among racial groupings were our outcomes of interest (Figure 2). Prevalence of in-hospital deaths was the highest among Asian or Pacific Islander patients in the whole breast cancer survivor population (3.2%) and in those without prior CT/RT (3.2%), followed by Native American patients (3%) whereas Native American patients (4.7%) had higher in-hospital deaths as compared to Asian or Pacific Islander patients (3.5%) in those with prior CT/RT. Asian or Pacific Islander patients (aOR 1.19, 95% CI 1.10, 1.28, p0.001), Hispanic patients (aOR 1.14, 95% CI 1.09, 1.20, p0.001), and Black patients (aOR 1.10, 95% CI 1.06, 1.20, p0.001) had significantly higher odds of all-cause mortality than White patients, whereas Native American patients had non-significant difference. The incidence of AMI was the greatest among Native American patients (4.7%) among the whole breast cancer survivor population, followed by White patients (3.2%) and Black patients (3.1%). In the prior CT/RT subgroup, White patients had 2.9% AMI incidence, followed by Asian or Pacific Islander patients (2.8%), Native American patients (2.7%), Black patients (2.6%), and Hispanic patients (1.9%). When compared to White patients, Native American patients had higher odds of having an AMI (aOR 1.31, 95% CI 1.12, 1.53, p=0.001), but other races had statistically significantly lower odds. In the whole breast cancer survivor population, the incidence of arrhythmia was highest among White patients (29.6%), followed by Asian/Pacific Islander patients (23%), and Black patients (21.6%). In both the CT/RT and non-CT/RT subgroups, the incidence of arrhythmia followed a similar pattern. All races had considerably lower odds of developing arrhythmia than White patients, with Native American patients having the lowest odds ratio (aOR 0.62, 95% CI 0.57, 0.68, p0.001) (Table 4). Amongst all the breast cancer survivors, stroke was most common among Asian or Pacific Islander patients (3.9%) and Black patients (3.8%), followed by White patients (3.3%), with a similar pattern observed across both subgroups. With White patients as referents, Black patients had statistically significant odds (aOR 1.12, 95% CI 1.08,1.15, p0.001), while Hispanic patients had significantly reduced odds (aOR 0.89, 95% CI 0.85, 0.94, p0.001) of stroke. Though Asian or Pacific Islander patients had a higher trend toward strokes, the adjusted odds ratio did not reach statistical significance.\n\nHospitalizations were greater in large bed-size and urban teaching institutions in the whole breast cancer survivor population and subgroups with and without CT/RT (more than 50 percent across all racial groups) than smaller-size and other non-teaching institutions. Black patients, Hispanic patients, and White patients had higher hospitalizations in the Southern region of the US, whereas Western region hospitals had higher hospitalizations for Asian or Pacific Islander patients and Native American patients. Though Medicare was a major primary payer across all races, it covered hospitalization costs of 78% White patients versus 68% Black patients and 67% Native American patients. In the whole breast cancer survivor population, Black patients (51.3%) were highest in the lowest quartile (0-25th) median household income, followed by Native American patients (41.3%) and Hispanic patients (35.4%); the pattern was comparable in two subgroups. The median length of stay in the hospital was four days for Black patients, compared to three for the other races. Routine discharges were lowest among White patients, whereas transfers to skilled facilities were highest. For the whole breast cancer survivor population and subgroups, Asian or Pacific Islander patients had the highest mean total expenditure, followed by Hispanic patients and White patients.\n\n\nDiscussion\n\nPrevious research has found racial disparities in the incidence of breast cancer, anthracycline-related cardiac outcomes, and cardiovascular risk factors.2,5,6 This research looks at the racial disparities in MACCE in breast cancer survivors along with the results being reported for two subgroups, i.e., with and without prior CT/RT, from the largest nationally representative national database. We discovered that three-quarters of the sample population was White, and about three-eighths was Black, followed by other races. Asian or Pacific Islander patients had the highest all-cause in-hospital mortality in the whole breast cancer survivor population whereas Native American patients had the highest all-cause in-hospitality in the prior CT/RT subgroup. Native American patients had the highest incidence of AMI in the overall population, but White patients had predominated in the prior CT/RT subgroup for AMI. White patients also had the highest incidence rate of arrhythmia regardless of treatment status. For strokes, Asian or Pacific Islander patients and Black patients had a higher prevalence than others. All-cause mortality, AMI, arrhythmia, and stroke had the highest odds in Asian or Pacific Islander patients, Native American patients, White patients, and Black patients respectively. Black patients had a lower socioeconomic position and a longer median stay than the others. White patients had a higher transfer to nursing facilities, whereas Asian or Pacific Islander patients had the highest mean hospital expenditures.\n\nCardiovascular disease is common among patients with cancer and coexists with other risk factors such as diabetes, obesity, etc.9 This can be attributed to underlying systematic inflammation however, cardiovascular disease also results from anti-cancer therapies.9,11 With the introduction of personalized medicine and providing patient-centered care, there is a trend of developing strategies for early diagnosis and treatment of disease and treatment-related complications such as cardiovascular disease and cerebrovascular disease. The ethnic disparities among patients continue to be a challenge to providing optimal care as race, a complex variable, could act as a proxy for various factors like socioeconomic status, culture, and discrimination.6 It is also implicated to act as a surrogate for differences in tumor and host biology impacting hormone receptor status, tumor grade, and S-phase fraction, which could lead to more aggressive tumor in certain races making treatment challenging.6\n\nHypertension is a modifiable risk factor that has been linked with an increased risk of breast cancer and cardiovascular diseases.12 Soler et al. (1999) reported OR of 1.44 for breast cancer risk associated with treated hypertension in women with BMI >25 kg/m^2.13 This link is not fully understood; however, few mechanisms have been proposed – namely that hypertension and breast cancer share similar pathophysiological pathways leading to a state of chronic inflammation, perhaps from an abundance of adipose tissue, leading to both hypertension and breast cancer. Another mechanism is exposure to steroid hormone factors e.g. estradiol has been implicated in the development of breast cancer and hypertension.14 Furthermore, those with hypertension have a 45% increased risk of mortality in metastatic breast cancer patients. Therefore, hypertension contributes to increased mortality risk in breast cancer, which in part, explains the increased mortality risk in Black patients compared to White patients. Black individuals are known to have a high incidence of cardiovascular risk factors such as HTN, DM, and obesity,12 which can subsequently lead to a higher incidence of cerebrovascular events.12\n\nThere are several causes of increased incidence of cardiovascular risk factors and disease in breast cancer patients. There are mainly three explanations. Firstly, breast cancer and cardiovascular disease share similar risk factors – older age, obesity, diet, family history, hormone replacement, physical activity, and tobacco use.9 Our results are aligned with CDC in 2019 reported that the highest incidence of hypertension and obesity were in African American and dyslipidemia in Caucasians.10 Obesity has been linked to the development of CVD, including atherosclerosis, abdominal aortic aneurysm, and heart failure, as well as breast cancer through chronic low-grade inflammation, which accelerates the onset or progression of carcinogenesis.11\n\nWhite patients were noted to have higher rates of arrhythmias and AMI in this study. This is in accordance with the data reported by Chi. et al. (2020) reported the highest rates of AMI in White patients, followed by African American patients, Hispanic patients, and Asian or Pacific Islander patients.15 This study showed, however, that between 2000 and 2014, the absolute burden (the number of people hospitalized) of AMI declined in the White population. It also showed that the absolute burden of AMI increased for Hispanic population and Asian or Pacific Islander population over the same study period, which is likely explained by rapid growth in population size for these demographics and slower growth for the White population.15 It has been shown in several studies that the White population has an increased risk for arrhythmia's such as atrial fibrillation regardless of concurrent cardiovascular risk factors, particularly when compared to African American population.16 The reasons are unclear as African American patients tends to have higher rates of cardiovascular risk factors, but it could be related to genetic factors or environmental exposures related to race.\n\nAs mentioned above, the use of cardiotoxic chemotherapeutic agents such as anthracyclines, alkylating agents, and taxanes is also notorious for causing cardiovascular diseases in cancer patients. Cardiotoxicity is defined as the presence of symptoms of HF with an ejection-fraction reduction ≥5% to <55% or the absence of symptoms with an ejection-fraction reduction ≥10% to <55%.17 There are four main mechanisms of medication-induced damage to the heart 1) direct cytotoxic effects (alkylating agents, anthracyclines, interferon alfa, monoclonal antibodies), 2) cardiac ischemia (antitumor antibiotics, fluorouracil, topoisomerase inhibitors), 3) cardiac arrhythmias (anthracyclines), 4) pericarditis (bleomycin, cyclophosphamide, cytarabine).18 Cardiotoxicity can be reversible/irreversible, acute/chronic, early-onset/late-onset. As per our study, the breast cancer survivor subgroup that received CT/RT has a lower prevalence of acute myocardial infarctions, arrhythmias, and stroke as compared to patients who did not receive CT/RT. It is difficult to ascertain what mechanisms are responsible for our study results as details of chemotherapeutic regimens, dosages, and duration of treatment were not available.\n\nThere are disparities in cardio-oncology contributing to the higher morbidity and mortality of African American patients. For example, a retrospective study in 2004 showed that African American patients had a 3-fold higher risk of cardiotoxicity with doxorubicin compared to non-African American patients.19 A second study showed that African American women were more than 2-fold likely to develop cardiotoxicity from trastuzumab and had a much higher likelihood of not completing therapy compared to White women.20 These findings could possibly explain the findings in our study, where Black patients were shown to have higher all-cause mortality.\n\nAll-cause mortality, when adjusted for demographic confounders, was found to be higher in Black than in White individuals. This is in line with several published studies and can be explained by the following. African American women have more aggressive forms of tumors – triple-negative breast cancers – when they are discovered.6 African American pateints, in general, have lower socioeconomic status, which translates into less access to healthcare facilities and primary care clinics as well as preventative visits, causing lower rates of screening mammography and late-stage diagnosis.21 Underserved communities are less likely to have equipped facilities for screening or the appropriate expertise available. Lower socioeconomic status also means less access to health insurance; in fact, studies have shown African American women are twice as likely to be uninsured and depend on public insurance as compared to White American women.22 Lower Socioeconomic Status directly correlates to lower educational attainment,6 and therefore patients may not understand the importance of early detection of breast cancer.6 Furthermore, there is a lack of diversity in clinical trials for multiple reasons, such as cultural or language barriers to informed consent, and most cardiotoxicity studies do not report race-specific data on cardiotoxicity prevalence.23\n\nIn our study, Native American pateints with breast cancer with and without prior CT/RT were found to have the highest prevalence of diabetes mellitus, smoking, chronic pulmonary disease, and coagulopathy. A 2015 population study estimated the prevalence of diabetes mellitus to be 5.5% in breast cancer patients.24 At present, there is no literature on the prevalence of diabetes in Native American pateints with breast cancer with/without prior CT/RT. The presence of diabetes has been linked to increased mortality and a worse prognosis of breast cancer.24 Multiple mechanisms have been proposed to explain this link. Hyperinsulinemia has been shown to promote cell proliferation, reduced apoptosis, angiogenesis, and metastases of breast cancers by activating insulin growth-like factor 1 (IGF-1R) signalling pathways.25,26 Insulin resistance and hyperinsulinemia are linked to decreased rates of recurrence-free survival.27\n\nSmoking is also a modifiable risk factor contributing to cardiovascular disease in cancer patients.28 In our study, smoking was found to have the highest prevalence (36.8%) in Native American patients with breast cancer with and without prior CT/RT, followed by White patients (34) and Black patients (33.2). The Indian Health Service reported that Native American individuals had the highest smoking prevalence compared to the other racial groups in general, with 23.2% in both Native American men and women.28 This can be contrasted with the lower smoking prevalence in White (21.1% and 17.2%) and African American (22.8% and 15.4%) men and women, respectively.28 There are several possible explanations for the high smoking prevalence in the Native American community. Tobacco is used for ceremonial or medicinal purposes and has a high cultural and spiritual importance. Secondly, the average smoker begins smoking in early adolescence (age 14.7), and thirdly quitting rates are relatively lower compared to other racial groups.29,30 The CDC also reports that tobacco is extensively promoted and marketed to the Native American communities; however, the effect and impact of this are difficult to measure.29 Smoking has been associated with a higher risk of breast cancer-specific and all-cause mortality, as well as poorer prognosis.31 It has also been shown that African American women with ER Negative breast cancer who smoke have higher mortality compared to non-African American women.32\n\nOur study was conducted using the National Inpatient Sample. The study could only be conducted in a cross-sectional manner, without allowing for further analysis of results. The “Others” race cannot be elaborated upon owing to missing information on races in this class. The details of chemotherapeutic drugs or regimes, number of chemotherapy cycles, types of radiation therapy, and details of comprehensive cancer regimes are not known in National Inpatient Sample. Duration since the completion of oncology treatment is not available. Despite this, we provide contemporary data for the racial disparities in the MACCE in the patients who had survived breast cancer which is of large significance in designing comprehensive screening programs for high-risk populations.\n\n\nConclusions\n\nOur study shows that there are significant differences in MACCE events in breast cancer survivors of different races. All-cause mortality is lowest in whites even though the incidence of AMI and arrhythmias were higher. There appears to be a complex interplay of factors influencing clinical outcomes in breast cancer patients of various races. These factors are poorly understood, and further basic science research is warranted for a better understanding of why different conditions are more common in different racial populations. This will provide a gateway into major clinical research on cancer therapies oriented based on race, targeting specific morbidities from which that race is more prone to have an adverse outcome. Our results also emphasize the need for tailoring the screening programs differently for different races to prevent cardiovascular events.", "appendix": "Data availability\n\nOur study examined racial disparities for major cardiovascular and cerebrovascular events in hospitalized breast cancer survivors using discharge data from the National Inpatient Sample and the Nationwide Inpatient Sample (NIS), Healthcare Cost and Utilization Project (HCUP), Agency for Healthcare Research and Quality. We used the 2015-2017 datasets which size over 100 GBs. It is the largest inpatient care database of the United States and contains data on over 7 million hospital stays. Data can be accessed from the website of Agency for Healthcare Research and Quality.\n\n\nReferences\n\nSurvival rates for breast cancer: Accessed April 15, 2022. Reference Source\n\nBreast cancer - statistics. CancerNet: Published June 25, 2012. Accessed April 15, 2022. Reference Source\n\nGuha A, Fradley MG, Dent SF, et al.: Incidence, risk factors, and mortality of atrial fibrillation in breast cancer: a SEER-Medicare analysis. Eur. Heart J. 2022; 43(4): 300–312. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHenriksen PA: Anthracycline cardiotoxicity: an update on mechanisms, monitoring and prevention. Heart. 2018; 104(12): 971–977. PubMed Abstract \| Publisher Full Text\n\nZhang L, Song J, Clark R, et al.: Abstract 13090: Racial and Ethnic Differences in Anthracycline Cardiotoxicity. [Abstract taken from Circulation. 2021;144:A13090].November 16, 2021; Vol 144(Suppl_1).\n\nPolite BN, Cirrincione C, Fleming GF, et al.: Racial differences in clinical outcomes from metastatic breast cancer: a pooled analysis of CALGB 9342 and 9840—Cancer and Leukemia Group B. JCO. 2008; 26(16): 2659–2665. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHCUP National Inpatient Sample (NIS): Healthcare Cost and Utilization Project (HCUP). Rockville, MD: Agency for Healthcare Research and Quality; 2015-2017. Reference Source\n\nClinical classifications software refined (CSSR): Accessed April 15, 2022. Reference Source\n\nMehta LS, Watson KE, Barac A, et al.: Cardiovascular disease and breast cancer: where these entities intersect: a scientific statement from the American heart association. Circulation. 2018; 137(8): e30–e66. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nInfographics - health, united states - products: Published January 2, 2020. Accessed April 15, 2022. Reference Source\n\nGuha A, Wang X, Harris RA, et al.: Obesity and the bidirectional risk of cancer and cardiovascular diseases in African Americans: disparity vs. Ancestry. Front Cardiovasc Med. 2021; 8: 8. Publisher Full Text\n\nHan H, Guo W, Shi W, et al.: Hypertension and breast cancer risk: a systematic review and meta-analysis. Sci. Rep. 2017; 7(1): 44877. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSoler M, Chatenoud L, Negri E, et al.: Hypertension and hormone-related neoplasms in women. Hypertension. 1999; 34(2): 320–325. PubMed Abstract \| Publisher Full Text\n\nLargent JA, McEligot AJ, Ziogas A, et al.: Hypertension, diuretics and breast cancer risk. J. Hum. Hypertens. 2006; 20(10): 727–732. PubMed Abstract \| Publisher Full Text\n\nChi GC, Kanter MH, Li BH, et al.: Trends in acute myocardial infarction by race and ethnicity. J. Am. Heart Assoc. 2020; 9(5): e013542. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDewland TA, Olgin JE, Vittinghoff E, et al.: Incident atrial fibrillation among Asians, Hispanics, blacks, and whites. Circulation. 2013; 128(23): 2470–2477. Publisher Full Text\n\nCsapo M, Lazar L: Chemotherapy-induced cardiotoxicity: pathophysiology and prevention. Med. Pharm. Rep. 2014; 87(3): 135–142. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGeorgia SAT: PharmD, BCOP Assistant Professor of Pharmacy Practice Philadelphia College of Osteopathic Medicine School of Pharmacy Georgia Campus Suwanee. Chemotherapy agents that cause cardiotoxicity.\n\nHasan S, Dinh K, Lombardo F, et al.: Doxorubicin cardiotoxicity in African Americans. J. Natl. Med. Assoc. 2004; 96(2): 196–199. PubMed Abstract \| Free Full Text\n\nLitvak A, Batukbhai B, Russell SD, et al.: Racial disparities in the rate of cardiotoxicity of HER2-targeted therapies among women with early breast cancer: Cardiotoxicity of HER2-Targeted Therapy. Cancer. 2018; 124(9): 1904–1911. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDoescher MP, Saver BG, Fiscella K, et al.: Racial/ethnic inequities in continuity and site of care: location, location, location. Health Serv. Res. 2001; 36(6 Pt 2): 78–89. PubMed Abstract \| Free Full Text\n\nThomasson MA: Racial differences in health insurance coverage and medical expenditures in the united states: a historical perspective. Soc. Sci. Hist. 2006; 30(4): 529–550. Publisher Full Text\n\nFazal M, Malisa J, Rhee J-W, et al.: Racial and ethnic disparities in cardio-oncology: a call to action. JACC CardioOncology. 2021; 3(2): 201–204. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu AH, Kurian AW, Kwan ML, et al.: Diabetes and other comorbidities in breast cancer survival by race/ethnicity: the california breast cancer survivorship consortium (Cbcsc). Cancer Epidemiol. Biomark. Prev. 2015; 24(2): 361–368. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFerguson RD, Novosyadlyy R, Fierz Y, et al.: Hyperinsulinemia enhances c-Myc-mediated mammary tumor development and advances metastatic progression to the lung in a mouse model of type 2 diabetes. Breast Cancer Res. 2012; 14(1): R8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAhmadieh H, Azar ST: Type 2 diabetes mellitus, oral diabetic medications, insulin therapy, and overall breast cancer risk. ISRN endocrinology. 2013; 2013: 181240. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGoodwin PJ, Ennis M, Pritchard KI, et al.: Fasting insulin and outcome in early-stage breast cancer: results of a prospective cohort study. J. Clin. Oncol. 2002; 20(1): 42–51. PubMed Abstract \| Publisher Full Text\n\nTobacco prevention: Promotion/Disease Prevention. Accessed April 15, 2022. Reference Source\n\nCDCTobaccoFree: American indian and alaska native people and commercial tobacco. Centers for Disease Control and Prevention.\n\nHodge F, Nandy K: Factors associated with American Indian cigarette smoking in rural settings. Int. J. Environ. Res. Public Health. 2011; 8(4): 944–954. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBérubé S, Lemieux J, Moore L, et al.: Smoking at time of diagnosis and breast cancer-specific survival: new findings and systematic review with meta-analysis. Breast Cancer Res. 2014; 16(2): 3402. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nParada H, Sun X, Tse C-K, et al.: Active smoking and survival following breast cancer among African American and non-African American women in the Carolina Breast Cancer Study. Cancer causes & control: CCC. 2017; 28(9): 929–938. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "198874", "date": "07 Sep 2023", "name": "Zhengyi Deng", "expertise": [ "Reviewer Expertise epidemiology", "cancer", "survivors", "racial disparity" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 used National Inpatient Sample datasets to investigate the racial/ethnic disparities in the major cardiovascular and cerebrovascular adverse events among the hospitalized breast cancer survivors. This is an interesting topic but there are multiple major concerns that need to be addressed.\nOverall, please avoid abbreviations as most are unnecessary and confusing.\nMethods:\nPlease provide more information about the datasets, for example, which country and areas in this country these datasets covered.\n\nIs it possible that a patient could have multiple prior cancers? Is the prior breast cancer the first cancer? Is the CT/RT for the prior breast cancer?\n\nIt is unclear why the authors did the analyses stratified by CT/RT status. Please clarify the motivation.\n\nWhy and how were those variables chosen to be included in the statistical model?\n\nIs there information on prior breast cancer, including age at diagnosis and tumor characteristics (tumor stage, grade, size, lymph node status, molecular subtype)? These variables are important to be included in the model as they could explain the observed racial/ethnic disparities.\n\nI would suggest running several logistic regression models that adjust for different set of variables. Model 1 could adjust for demographics only, model 2 could further adjust for other variables, and model 3 could further adjust for characteristics of the prior breast cancer, if available. These stepwise models could help evaluate whether these variables could explain the observed racial disparities.\n\nStudent t-test is used to test two groups. You have 6 racial/ethnic groups, so t-test is not the appropriate method. ANOVA could be a more reasonable approach in your case. Then you need to include p-value in your table 1-3. However, I would not suggest conducting statistical tests across multiple groups, as p-value is less meaningful.\n\nResults:\nThese sentences are confusing: “Obesity, renal failure, congestive heart failure, and pulmonary circulation disorder were the most common conditions in Black patients; chronic pulmonary illness and coagulopathy were the most common conditions in Native American patients; and depression was the most common condition among White patients.” Taking depression as an example, I think you mean depression was more prevalent in White than other groups. However, the sentence reads like depression was the most common condition among all conditions in White patients, which is not correct, as hypertension was the most common condition.\n\nThe authors present three tables on the admitting characteristics, comorbidities, and outcomes among breast cancer survivors and by history of CT/RT. It seems a bit redundant, as the patterns are similar across three groups. The authors need to provide justifications on presenting these tables.\n\nIt is unclear why the authors did not stratify table 4 by history of CT/RT, given that they did this stratification for all other analyses.\n\nThe authors mentioned that CT/RT could be risk factors of MACCE. I would be interested in whether survivors with a history of CT/RT had increased risk of MACCE than those without the treatment.\n\nDiscussion:\nOverall, this discussion lacks a discussion on existing studies on the racial/ethnic disparities in CVD among breast cancer survivors. The authors should make a comprehensive summary of existing evidence and state the novelty of this study.\n\nPlease spell out HTN and DM in the third paragraph.\n\nThe authors mentioned “There are several causes of increased incidence of cardiovascular risk factors and disease in breast cancer patients. There are mainly three explanations. Firstly, breast cancer and cardiovascular disease share similar risk factors – older age, obesity, diet, family history, hormone replacement, physical activity, and tobacco use.”. I don’t think tobacco use is a strong risk factor for breast cancer. The influence of obesity on breast cancer differs by menopausal status. You mentioned three explanations but why only discussed one of them? You have already mentioned some explanations, including treatment and hypertension, in the second and third paragraph. These paragraphs seem disorganized. In summary, I would suggest reorganizing these paragraphs to make it flow in a more logic way.\n\nThe authors mentioned “As per our study, the breast cancer survivor subgroup that received CT/RT has a lower prevalence of acute myocardial infarctions, arrhythmias, and stroke as compared to patients who did not receive CT/RT. It is difficult to ascertain what mechanisms are responsible for our study results as details of chemotherapeutic regimens, dosages, and duration of treatment were not available.”. The authors made this conclusion based on crude comparison of prevalence between two groups, which could be largely biased. As is shown in table 1 and table 3, patients with CT/RT were much younger, and this could explain the lower prevalence of CVD in this group. That is why I think a regression model that compares patients with versus without treatment while adjusting for potential confounders would be necessary.\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": "209718", "date": "20 Oct 2023", "name": "Amanda Leiter", "expertise": [ "Reviewer Expertise Health services research", "cancer survivorship", "endocrinology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 explores a highly relevant and interesting topic using a large US national dataset. There are known racial disparities in breast cancer outcomes and I think it’s very interesting to look specifically at cardiovascular outcomes in breast cancer survivors. Concerns below - I want to highlight that I’m concerned about how breast cancer treatment was classified and defined - I do not think this is appropriate with the National Inpatient Sample. I also think that lack of information about breast cancer diagnosis and treatment is a major limitation with this dataset. I also think that the intro and discussion need to review the literature on this topic more in-depth and need to be rewritten for clarity.\nIntro:\nThe last sentence of paragraph 1 does not link well to the rest of the paragraph and the importance of studying cardiovascular events needs to be elucidated more - should restructure order of information in intro.\n\nWould define anthracycline as a chemotherapy upfront - can also mention that radiation may be implicated in heart disease especially since looking at a patient population who received radiation. I would also mention that trastuzumab is also very high linked with cardiomyopathy, and that hormone therapy (aromatase inhibitors) have shown an association with cardiovascular mortality - there are many papers and references describing this.\n\nIn general the introduction needs to be restructured to introduce why studying racial disparities in cardiovascular events in breast cancer patients is important - some elements are there but this does not logically flow.\n\nMethods and Results:\nThe use of the Z codes to stratify patients by history of receiving chemotherapy or radiation certainly underestimates those exposed - these codes are not often used in clinical practice. The number of patients who received these treatments seems very low (16%) - around 50% of BC survivors receive radiation (Bryant et al., 20171). I would reconsider stratifying these patients by treatment status - this dataset does not seem appropriate to classify treatment type in cancer survivors, or would give further justification as to why this was done. There is also an issue that they could have received treatment for another cancer type. I would consider excluding patients with another primary cancer.\n\nCould consider heart failure exacerbation as a cardiac outcome to measure (especially since cardiomyopathy is a complication of chemo and radiation).\n\nFor comparing continuous variables I would use ANOVA or Wilcoxon rather than t-test.\n\nFor the model, please discuss why you included the confounders that you did and also would not use (or justify) CT/RT since I have concerns about the reliability of that variable (mentioned above). Please make sure you outline which comorbidities were chosen - I am considering about collinearity for some of these variables.\n\nDiscussion:\nThe first paragraph simply describes the findings - what is the significance of the findings?\n\nNeed to relate second paragraph to the manuscript findings.\n\nAs mentioned above - would reconsider the CT/RT classification.\n\nNeed to mention cardiovascular mortality literature in BC in general and mention the existing literature on racial disparities - examples are below but there is quite a bit of literature on this topic already that was largely not discussed.\n\nI would make sure that lack of cancer staging data and information on timing of diagnosis is also a limitation.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? 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?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-891
https://f1000research.com/articles/12-403/v1	14 Apr 23	{ "type": "Data Note", "title": "The identification of high-performing antibodies for Coiled-coil-helix-coiled-coil-helix domain containing protein 10 (CHCHD10) for use in Western Blot, immunoprecipitation and immunofluorescence", "authors": [ "Riham Ayoubi", "Walaa Alshafie", "Kathleen Southern", "Peter S. McPherson", "Carl Laflamme", "NeuroSGC/YCharOS/EDDU collaborative group", "Riham Ayoubi", "Walaa Alshafie", "Kathleen Southern", "Peter S. McPherson" ], "abstract": "CHCHD10 is a mitochondrial protein, implicated in the regulation of mitochondrial morphology and cristae structure, as well as the maintenance of mitochondrial DNA integrity. Recently discovered to be associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) in its mutant form, the scientific community would benefit from the availability of validated anti-CHCHD10 antibodies. In this study, we characterized four CHCHD10 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. As this study highlights high-performing antibodies for CHCHD10, we encourage readers to use it as a guide to select the most appropriate antibody for their specific needs.", "keywords": [ "Uniprot ID Q8WYQ3", "CHCHD10", "Coiled-coil-helix-coiled-coil-helix domain-containing protein 10", "antibody characterization", "antibody validation", "Western Blot", "immunoprecipitation", "immunofluorescence" ], "content": "Introduction\n\nCoiled-coil-helix-coiled-coil-helix domain containing protein 10 (CHCHD10) is a protein localized to the mitochondrial intermembrane space, and is postulated to be involved in the maintenance of mitochondrial organization and cristae structure.1 With two coiled-coil-helix-coiled-coil-helix domains, which are involved in various protein-protein interactions and cellular processes.2\n\nRecent studies have demonstrated that CHCHD10 is important for the survival of neurons.1 As such, CHCHD10 gene variants have been reported in patients with ALS, FTD, Parkinson’s disease, motor neuron disease, and mitochondrial myopathy, suggesting that they contribute to neurodegenerative disease progression.1,3,4 Additional work is needed to understand the underlying function and regulation of CHCHD10, in its native and mutant conformation, to advance the development of therapeutic strategies for targeting these deteriorating diseases. Mechanistic studies would be greatly facilitated with the availability of high-quality CHCHD10 antibodies.\n\nHere, we compared the performance of a range of commercially available CHCHD10 antibodies for Western Blot, immunoprecipitation and immunofluorescence, enabling biochemical and cellular assessment of CHCHD10 properties and function.\n\n\nResults and discussion\n\nOur standard protocol involves comparing readouts from wild-type and knockout cells.5–9 The first step was to identify a cell line(s) that expresses sufficient levels of CHCHD10 to generate a measurable signal to noise. To this end, we examined the DepMap transcriptomics databases to identify all cell lines that express the target at levels greater than 2.5 log2 (transcripts per million “TPM” +1), which we have found to be a suitable cut-off (Cancer Dependency Map Portal, RRID:SCR_017655). Commercially available HAP1 cells expressed the CHCHD10 transcript at RNA levels above the average range of cancer cells analyzed. Parental and CHCHD10 knockout HAP1 cells were obtained from Horizon Discovery. Parental HCT116 cells were obtained from Abcam for immunoprecipitation experiments (Table 1).\n\nFor Western Blot experiments, we resolved proteins from WT and CHCHD10 KO cell extracts and probed them side-by-side with all antibodies in parallel (Figure 1).6–12\n\nA) Lysates of HAP1 (WT and CHCHD10 KO) were prepared, and 50 μg of protein were processed for Western Blot with the indicated CHCHD10 antibodies. The Ponceau stained transfers of each blot are presented to show equal loading of WT and KO lysates and protein transfer efficiency from the polyacrylamide gels to the nitrocellulose membrane. Antibody dilutions were chosen according to the recommendations of the antibody supplier. Antibody dilution used: 25671-1-AP at 1/1000, MA5-27532* at 1/500, MA5-27535* at 1/500, MA5-27531* at 1/500. Predicted band size: 14 kDa. = monoclonal antibody.\n\nB) Lysates of HAP1 (WT and CHCHD10 KO) and HCT116 were prepared as in A). MA5-27531 was used at 1/500. = monoclonal antibody.\n\nFor immunoprecipitation experiments, we used the antibodies to immunopurify CHCHD10 from cell extracts. The performance of each antibody was evaluated using Western Blot by detecting the CHCHD10 protein in extracts, in the immunodepleted extracts and in the immunoprecipitates (Figure 2).6–12\n\nHCT116 lysates were prepared, and IP was performed using 1.0 μg of the indicated CHCHD10 antibodies pre-coupled to protein A or protein G Sepharose beads. Samples were washed and processed for Western Blot with the indicated CHCHD10 antibody. For Western Blot, 25671-1-AP and MA5-27531 were used at 1/1000. 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=immunoprecipitate, = monoclonal antibody.\n\nFor immunofluorescence, as described previously, antibodies were screened using a mosaic strategy.13 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\nHAP1 WT and CHCHD10 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 CHCHD10 antibodies and with the corresponding Alexa-fluor 555 coupled secondary antibody including DAPI. Acquisition of the blue (nucleus-DAPI), green (WT), red (antibody staining) and far-red (KO) channels was performed. Representative images of the merged blue and 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. When the concentration was not indicated by the supplier, which was the case for antibodies MA5-27532 and MA5-27535, we tested antibodies at 1/100 and 1/1000, respectively. At this concentration, the signal from each antibody was in the range of detection of the microscope used. Antibody dilution used: 25671-1-AP at 1/300, MA5-27532 at 1/100, MA5-27535* at 1/1000, MA5-27531* at 1/100. Bars = 10 μm. = monoclonal antibody.\n\nIn conclusion, we have screened CHCHD10 commercial antibodies by Western Blot, immunoprecipitation and immunofluorescence and identified high-quality antibodies under our standardized experimental conditions. The underlying data can be found on Zenodo.14,15\n\n\nMethods\n\nAll CHCHD10 antibodies are listed in Table 2, together with their corresponding Research Resource Identifiers (RRID), to ensure the antibodies are cited properly.16 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\nBoth HAP1 WT and CHCHD10 KO cell lines used are listed in Table 1, together with their corresponding RRID, to ensure the cell lines are cited properly.17 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.18 HAP1 WT and CHCHD10 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 1x protease inhibitor cocktail mix (MilliporeSigma, cat. number 78429). Lysates were sonicated briefly and incubated for 30 min on ice. Lysates were spun at ~110,000 x 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 8-16% gradient 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 from Thermo Fisher Scientific (cat. number 32106) prior to detection with the HyBlot CL autoradiography films from Denville (cat. number 1159T41).\n\nImmunoprecipitation was performed as described in our standard operating procedure.19 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\nHCT116 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 for 30 min at 4°C and spun at 110,000 x 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 hrs 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 8-16% polyacrylamide gels. As secondary detections systems, the Veriblot for immunoprecipitation detection reagent and the anti-mouse IgG for immunoprecipitation (HRP) from Abcam (cat. number ab131366 and ab131368, respectively) were used.\n\nImmunofluorescence was performed as described in our standard operating procedure.6–13 HAP1 WT and CHCHD10 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). The nuclei were labelled with DAPI (Thermo Fisher Scientific, cat. Number D3571) fluorescent stain. 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 CHCHD10 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 40x 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 CHCHD10, https://doi.org/10.5281/zenodo.5259992. 14\n\nZenodo: Dataset for the CHCHD10 antibody screening study, https://doi.org/10.5281/zenodo.7779321. 15\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgment\n\nWe would like to thank the NeuroSGC/YCharOS/EDDU collaborative group for their important contribution to the creation of an open scientific ecosystem of antibody manufacturers and knockout cell line suppliers, for the development of community-agreed protocols, and for their shared ideas, resources and collaboration. Members of the group can be found below.\n\nNeuroSGC/YCharOS/EDDU collaborative group: Riham Ayoubi, Aled M. Edwards, Carl Laflamme, Peter S. McPherson, Chetan Raina, and Kathleen Southern\n\nAn earlier version of this of this article can be found on Zenodo (doi: 10.5281/zenodo.5259992)\n\n\nReferences\n\nBannwarth S, Ait-El-Mkadem S, Chaussenot A, et al.: A mitochondrial origin for frontotemporal dementia and amyotrophic lateral sclerosis through CHCHD10 involvement. Brain. 2014; 137(Pt 8): 2329–2345. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCraven L, Tuppen HA, Greggains GD, et al.: Pronuclear transfer in human embryos to prevent transmission of mitochondrial DNA disease. Nature. 2010; 465(7294): 82–85. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIkeda A, Imai Y, Hattori N: Neurodegeneration-associated mitochondrial proteins, CHCHD2 and CHCHD10-what distinguishes the two? Front. Cell Dev. Biol. 2022; 10: 996061. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarjuhaahto S, Rasila TS, Molchanova SM, et al.: ALS and Parkinson's disease genes CHCHD10 and CHCHD2 modify synaptic transcriptomes in human iPSC-derived motor neurons. Neurobiol. Dis. 2020; 141: 104940. PubMed Abstract \| Publisher Full Text\n\nLaflamme C, McKeever PM, Kumar R, et al.: Implementation of an antibody characterization procedure and application to the major ALS/FTD disease gene C9ORF72. elife. 2019; 8: 8. Publisher Full Text\n\nAlshafie W, Fotouhi M, Shlaifer I, et al.: Identification of highly specific antibodies for Serine/threonine-protein kinase TBK1 for use in immunoblot, immunoprecipitation and immunofluorescence. F1000Res. 2022; 11: 977. Publisher Full Text\n\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; 2023(12): 172.\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\nAyoubi R, Alshafie W, Shlaifer I, et al.: The identification of high-performing antibodies for Sequestosome-1 for use in Western blot, immunoprecipitation and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 324. Publisher Full Text\n\nMcDowell I, Ayoubi R, Fotouhi M, et al.: The identification of high-preforming antibodies for Ubiquilin-2 for use in Western Blot, immunoprecipitation, and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 355. Publisher Full Text\n\nAyoubi R, McDowell I, Fotouhi M, et al.: The identification of high-performing antibodies for Profilin-1 for use in Western blot, immunoprecipitation and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 348. Publisher Full Text\n\nAlshafie W, McPherson P, Laflamme C: Antibody screening by Immunofluorescence.2021.\n\nAyoubi R, Alshafie W, Straub I, et al.: Antibody Characterization Report for Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial (CHCHD10).2021.\n\nLaflamme C: Dataset for the CHCHD10 antibody screening study. [Data set]. Zenodo. 2023.\n\nBandrowski A, Pairish M, Eckmann P, et al.: The Antibody Registry: ten years of registering antibodies. Nucleic Acids Res. 2023; 51(D1): D358–D367. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBairoch A: The Cellosaurus, a Cell-Line Knowledge Resource. J. Biomol. Tech. 2018; 29(2): 25–38. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAyoubi R, McPherson PS, Laflamme C: Antibody Screening by Immunoblot.2021.\n\nAyoubi R, Fotouhi M, McPherson P, et al.: Antibody screening by Immunoprecitation.2021." }	[ { "id": "176514", "date": "26 Jun 2023", "name": "Yang Liu", "expertise": [ "Reviewer Expertise Molecular mechanisms for infrared sensing in snakes and function & potential medical applications of snake venom." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review the manuscript entitled \"The identification of high-performing antibodies for Coiled-coil-helix-coiled-coil-helix domain containing protein 10 (CHCHD10) for use in Western Blot, immunoprecipitation and immunofluorescence .\"\nFour commercial antibodies for CHCHD10, a mitochondrial protein that affects mitochondrial morphology and DNA integrity, are profiled in the study. Mutations in CHCHD10 have been associated to ALS and FTD. Using a consistent experimental procedure based on comparing read-outs in knockout cell lines and isogenic parental controls, the researchers characterized four CHCHD10 commercial antibodies for Western Blot, immunoprecipitation, and immunofluorescence. The study discovered high-performing antibodies for CHCHD10 and recommends that readers use it as a guide to select the appropriate antibody for their specific needs.\nOverall, I find the paper to be well-written and informative. However, I recommend providing more discussion and interpretation of the results. It is best to evaluate the advantages and disadvantages of the following types of antibodies. Thank you for considering my feedback.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] }, { "id": "184169", "date": "19 Jul 2023", "name": "Derek P. Narendra", "expertise": [ "Reviewer Expertise neurogenetics", "mitochondrial 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\nIn general, the paper was well-written, and the data included are of high quality.\nA major concern is that the choice of antibodies excludes certain well validated commercial antibodies, which may skew the findings to favor those of the author’s commercial partners.\nThere are few suggestions that would make the manuscript stronger.\nThe rationale for choosing the commercial antibodies tested is not clear. The four come from only two suppliers. A notable omission is the the HPA003440 Atlas Antibodies / Sigma-Aldrich antibody, which has been used in several publications, including those that validated in KO cell lines and mouse models. It is not clear why this was not chosen in the head-to-head comparisons. How the antibodies tested were chosen should be discussed as well as the omission of several that have appeared in prior publications.\n\nIn the second sentence of the introduction, the authors should clarify that CHCHD10 has a single CHCH domain, which is composed of two CX9C motifs.\n\nIn the first sentence of the second paragraph, stating that CHCHD10 is important for neuronal survival implies that loss of its function results in neuronal death. This is not clear from the literature. CHCHD10 KO appears to be well-tolerated in mammals, and the mutations are thought to cause disease by a toxic gain-of-function (GoF) mechanism. This is perhaps best demonstrated in studies that have compared CHCHD10 KO mice to those with patient mutations knocked in (PMID: 30877432 and 35700042)1,2. This is also discussed in a recent review (PMID: 37021679). The introduction could be modified to clarify this point.\n\nFigure 1. It would be helpful to state the concentration of antibody used. A more informative head-to-head comparison might be to keep the concentration of antibody constant rather or in addition to using the supplier's recommended concentration.\n\nIn Figure 2 the authors should comment on whether it is possible the antibodies would also co-immunoprecipitate CHCHD2. Ideally this would also be assessed experimentally on CHCHD10 KO cells. We have observed cross-reactivity of antibodies for CHCHD2 and CHCHD10 in immunoprecipitation experiments. This affects the interpretation of results as a binding partner attributed to CHCHD10 may actually be binding CHCHD2.\n\nFor Figure 3, in addition to the shown images it would be helpful to see those windowed for the low intensity signal in the KO cells. This would allow better assessment of what appears to be a mitochondrial signal with some of the antibodies (e.g., MA5-27535 but maybe others). We have observed some cross-reactivity with its paralog CHCHD2. Whether this could be an explanation for the residual mitochondrial signal should be discussed and perhaps evaluated by assessment of double knockout cells.\n\nIs the rationale for creating the dataset(s) clearly described? Partly\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [ { "c_id": "9950", "date": "29 Nov 2023", "name": "Kathleen Southern", "role": "Author Response", "response": "Thank you to Derek Narenda for your report and feedback on this article. We appreciate your suggestions and will be submitting a new version of the manuscript to implement some of your suggested changes. To your first point, antibodies to be tested are donated by YCharOS partners (ycharos.com). Our consortium has the capacity to supply ~28% of all antibodies listed on the Antibody Registry (antibodyregistry.org). For this specific target, these were the antibodies the partners could donate to us at the time the study was taken place. If we found that many of the antibodies received by the partners were not successful under any of the applications, we would have searched elsewhere for antibodies and continued with further with the analysis. This was not the case for CHCHD10, and we were able to deliver results which demonstrated high-quality antibodies for each application. To your second and third point, we have made edits to the introduction to clarify that CHCHD10 contains a single CHCH domain with CX9C motifs and its importance to neuronal health. As for your suggestion regarding the concentration of the antibodies, in Table 2 you can find the concentration for each antibody. The commercial antibodies are received with a detailed data sheet that provides the concentration of the mixture. The antibodies are then diluted accordingly to provide the best signal to noise ratio. To respond to your fifth point, determining whether the antibodies co-immunoprecipiated CHCHD2 is outside the scope of this study. In this study, we sought to investigate whether antibodies were able to successfully target and pull-down CHCHD10 in an immunoprecipitation experiment. To further analyze whether CHCHD2 was immunoprecipitated along with CHCHD10 would be an interesting follow-up study for the experts that have determined which antibodies successfully immunoprecipitated CHCHD10 in this study. In Figure 2, we show antibody signal intensities with a similar dynamic range between the antibodies tested, enabling direct comparison of antibody performance for immunofluorescence. The signal coming from KO cells should be considered as a non-specific signal. We hope this response addresses all concerns and questions you had regarding the article. Thank you again, your response and feedback is well appreciated and important to the success of the YCharOS initiative to reduce the use of poor performing antibody resources in research." } ] } ]	1	https://f1000research.com/articles/12-403
https://f1000research.com/articles/12-889/v1	26 Jul 23	{ "type": "Study Protocol", "title": "Evaluation of premetastatic changes in lymph nodes(pN0) of oral tongue tumour: A prospective observational Study", "authors": [ "Rajalakshmi Geetha", "Subramania Iyer", "Pavithran Keechilat", "Gopalakrishna Iyer N", "Krishna Kumar Thankappan", "Smitha N V", "Pavithran Keechilat", "Gopalakrishna Iyer N", "Krishna Kumar Thankappan", "Smitha N V" ], "abstract": "Background: Tongue tumors show intra and inter-tumoral heterogenicity with high incidence, relapse and mortality rates necessitating further research. Recurrence/metastasis that occurs after surgical resection of primary cancer is often the reason for poor survival in these patients. Lymph nodes are the most common site of metastasis in tongue tumors. Therefore, premetastatic molecular changes can be best evaluated in lymph nodes which may epitomize the earliest events in the metastasis cascades. The presence of circulating tumor cells(CTCs) in the absence of nodal disease (N0) may represent tumor aggressiveness, suggesting an immune escape which may have high metastatic potential. This trial was developed to investigate the earliest pre-metastatic changes which may regulate tumor dormancy and predict metastasis. A better understanding of organotropism or pre-metastatic changes can help in theragnostic, thereby preventing the outbreak of overt metastasis. Methods: A single-institutional prospective observational cohort study. This trial will be conducted at a tertiary care Centre (Amrita Institute of Medical Sciences Kochi). Eligible patients will be enrolled after obtaining informed consent. The dissected lymph nodes will be subjected to histopathological and immunohistochemical analyses for premetastatic niche (PMN) formation. In addition, circulating tumor cells will be evaluated before treatment and 6 months after treatment. The patients will be followed up for a period of two years to correlate the findings with the recurrence-free survival. Expected results: The pre-metastatic changes, if detected will be a predictive biomarker. It may help to define future drug targets for metastasis chemoprevention\n\n. CTCs may define the tumor aggressiveness ,there by prognostication and helps in better disease management. Ethics and dissemination: The study has received the following approval: Ethics Committee of Amrita School of Medicine (ECASM-AIMS-2022-048).Trial Registered Prospectively( CTRI/2022/03/041256 ) on 22/03/2022 under Clinical Trial Registry of India", "keywords": [ "Oral Tongue Squamous Cell Carcinoma", "Premetastatic Niche", "Circulating Tumor Cells", "Circulating Tumor Emboli", "Disease free survival." ], "content": "Introduction\n\nTumor metastasis is a major factor that leads to treatment failure and mortality. The cure for cancer metastasis is still challenging, so treating cancer effectively depend on our ability in arresting or preventing metastasis. Tumor mortality is a result of late diagnosis, so research into early detection is of greater importance in improving patient outcomes.\n\nThe WHO anticipates that by 2040, the global cancer burden will reach 27.5 million with approximately 16.3 million deaths.1,2 In the WHO 2022 updates, oral squamous cell carcinoma is the 16th most common cancer globally, and the incidence of tongue cancer in persons younger than 45 years has increased worldwide.3 One-third global burden of oral cancer is from India, tongue and floor of mouth comprise more than 50% of oral cancers.4 The high tongue tumor prevalence in India demands scaling up relevant research in this area to deliver an optimal outcome. Recent data projecting a distressing trend in the recurrence and mortality rates of tongue cancers with increasing incidence in the non-habit associated tongue tumor.5\n\nDespite of advances in treatment modalities, the inability to control the metastatic process is one of the common reasons for treatment failures and high morbidity rates. Tumor metastasis is still not fully understood. Research may be of great importance to understand the tumor biology, heterogenicity, disease presentation and progression for tailoring accurate, affordable early detection tools and disease monitoring to interdict metastasis, thus survival outcomes.\n\nOur primary objective of this study is the molecular profiling of tumor-free lymph nodes (N0) to assess the PMN changes and correlate them with recurrence -free survival in oral tongue squamous cell carcinoma patients.\n\nThe secondary objective is to evaluate the efficacy of CTC (circulating tumor cells) and CTM (circulating tumor micro emboli) in terms of relapse, and disease-free survival in N0 patients.\n\nTongue tumors are a matter of concern for oncologists, researchers and public health policymakers. Patients with tongue tumors have a higher proportion of treatment failures, even after standard treatment protocols. Treatment and clinical decisions on N0 neck in the early stages are still challenging. The primary goal is to investigate the early pre metastatic alterations even before a detectable metastasis and its association in initiating metastasis.\n\nThis study may help in\n\n• Elucidating molecular metastatic driving events before or during early stages of metastatic colonization.\n\n• Identifying definite lymph node architecture parameters in predicting metastasis before tumor cells arrive.\n\n• Studying the significance of CTC/CTM occurring at early nodal-free tumors.\n\n\nMethods\n\nThe PMN study is designed as a prospective cohort observational study.\n\nThis study will take place at the Tertiary Care Advanced Centre (Department of Head & Neck Oncology & Pathology), Amrita Institute of Medical Sciences, Kochi (India).\n\nPMN CTC trial protocol registration has been done under the Clinical Trial Registry of India with registration number CTRI/2022/03/041256 dated 22/03/2022. Patient accruals began in July 2022 and are projected to be concluded by July 2024. This protocol has been designed following the SPIRIT 2013 Statement.\n\nThe cohort will be adults aged 18-80 years, reporting to the Head and Neck Surgery department of Amrita Institute of Medical Sciences Kochi (tertiary care centre) with histopathological confirmed oral tongue squamous cell carcinoma who has not undergone any other treatment other than diagnostic biopsy, planned for curative intent surgery with neck dissection.\n\nEligibility criteria are summarised in Table 1.\n\nOral carcinoma commonly known as oral squamous carcinoma (OSCC) occurs as an ulcero proliferative lesion affecting any site starting from the lips to the oropharynx. OTSCC is the most common OSCC and often initiates at the flat thin squamous cells that line the surface of the tongue.9 The aggressive biological behaviour and clinically unpredictable prognosis of tongue cancer with close affinity to the vascular lymphatic network necessitate the need for further research in this area.\n\nPatient inclusion is done based on the inclusion criteria. The trial will enroll 97 eligible patients. After obtaining written informed consent, blood samples and tissue biopsy blocks will be collected from them.\n\nFor CTC/CTM evaluation – Blood samples with minimum trauma will be collected before and 6 months after surgery. 5 mL of peripheral whole blood samples will be collected in 10-mL vacutainer tubes (Becton Dickinson, New Jersey). The blood samples will be stored in the refrigerator at 2 to 80 C. CTCs will be isolated by using Drugs Controller General of India (DCGI) approved OncoDiscover liquid biopsy technology. The OncoDiscover CTC isolation technique uses multifunctional, iron oxide-based, magneto-polymeric, and anti-epithelial cell adhesion molecule (EpCAM) targeting superparamagnetic nanoparticles.10 Enumeration of CTC is based on CD45-, EpCAM+ and CK8,CK18 &CK19+ expression. CTM clusters are a group of two or more aggregated CTCs. The number of CTCs positive for PD-L1 expression is also evaluated.\n\nLymph nodes from these patients will be fixed and sectioned for routine histopathological evaluation. Formalin-fixed paraffin-embedded (FFPE) samples of the study may include T 1 to T4 with and without nodal metastasis. The lymph node samples will be grouped as Group A & B (Figure 1) based on histopathological findings.\n\nThe lymph nodes collected for analysis will include nodes without disease both in groups, where there is no nodal disease (-ve LN in NO) and those with nodal disease (-ve LN in N+). Also, will include lymph nodes with disease (LN+) and those with ECS (LN++). The molecular markers studied in the lymph nodes will be STAT 3, LOX 2, and VEGF A. IHC technique to be employed with primary and secondary antibody standardization protocol.\n\nGroup A: First echelon lymph nodes will be sampled in pathologic N0 (-ve node in NO).\n\nGroup B: In node-positive cases, - a normal uninvolved lymph node is taken just distal to the level of lowest positivity ie. if level 2 is involved, an uninvolved node from level 3 is taken (B1). The lymph nodes with positive disease (B2) and those with extracapsular spread (B3) will be included in the analysis when present.\n\nTo investigate the molecular characteristic features in the formation of premetastatic lymph nodes, selecting nonmetastatic LNs in the vicinity of metastatic LNs seems to be most suitable. Being taken from the same patient most of the other variables can be avoided.\n\nThe preparation of slides will be done in accordance with standard IHC techniques. Manual IHC with antigen retrieval in pressure cooker will be done. All antibody standardization will be done according to the company protocol manual. All stained slides shall be photomicrographed within 48 hours. Interpretation will be performed independently by two pathologists who were blinded to the other parameters of the subject. In cases of disparity, a third pathologist will be consulted and the best concordant result will be accepted for analysis. IHC slides will be graded according to staining intensity. The patients will be followed up as per the standard of care ie 2 monthly for the first year and 3 monthly in the second year. Clinical evaluation supplemented by imaging if needed will be used during follow-up. The overall survival, recurrence-free survival, locoregional, and systemic failure rates will be determined at the end of two years follow-ups.\n\n\n\n• The correlation of molecular expression of STAT 3, LOX 2, and VEGF in the premetastatic nodes (-ve N) with recurrence -free survival. These markers will be correlated individually. This will allow us to analyse the significance of premetastatic niche formation and the pathways leading to it.\n\n• To correlate the presence of CTC/CTM at two different time points to recurrence-free survival. This will allow us to establish the role of liquid biopsy in prognostication ie. the presence of CTC as a predictor/indicator of tumor spread via blood or lymphatic channels.\n\n• The evaluation of Stat3 expression in tissue and PD- L1 in CTC will reveal on the local and systemic immune status of patients respectively. Those PD-L -1positive CTCs may be a strong indicator of those exceptional CTCs that escape the immune surveillance mechanism.\n\n\n\n• The molecular markers for PMN will be compared in N0 and N+/N++ patients. This may allow a better understanding of the pathways of PMN formation. We expect to see the PMN changes be more prominent in the -ve N samples of N+/N++ patients.\n\n• Any architectural histopathologic feature which correlates with the PMN changes if identified will also help as a predictive marker.\n\n• To identify the role of CTC to predict PMN formation.\n\nAll subjects will be part of the trial for two years post initiation of the treatment or till the time when they show progressive incurable disease.\n\nSample size calculation\n\nThe sample size is determined by the formula, n=(Z1−α22)pqd2, z = Co-efficient of significance (1.96), α = Level of significance (5.0%), p= Prevalence of oral tongue tumour (50.0%) q = 1-p (50.0%), d = Desired precision (10.0%).\n\nThe minimum sample size for the study is computed and found to be 97 patients.\n\nStatistical method\n\nChi-square Test to test the statistical significance of the association of the molecular expression (severity) of antibodies in lymph nodes and circulating tumor cells as numbers in oral tongue squamous cell carcinoma patients. To find the survival probability of disease-free survival, Kaplan Meier analysis and the comparison will be done using a log-rank test.\n\n\n\n• The study investigates the molecular characteristics of the premetastatic, metastatic lymph nodes in OTSCC related to the most suitable and real control group.\n\n• The CTC PMN association if present may help to correlate two triggering factors in overt metastasis formation.\n\n• The primary limitation of this study is the limited number of antibodies used to identify the molecular PMN characteristics. The study is aiming to co-relate the molecular markers of different possible events in organ remodelling and immature pre-metastatic niche formation. However, to get a wholesome picture of PMN features a greater number of antibodies to be included for evaluation. Due to budgetary constraints, we have limited our molecular markers by choosing the best which describe the maximum possible molecular events. Also, the lack of sequential blood evaluation for CTC in more frequent intervals will not allow us to comment on its time of appearance and its effect on metastasis accurately.\n\nCTC evaluation is based only on EpCAM and cytokeratin without considering the Epithelial-Mesenchymal Transition (EMT) mechanism, stemness characteristics or its subpopulations.\n\nSite investigators will take up the responsibility for the conduct of the study. Project investigators are responsible for ensuring International Conference on Harmonisation Good Clinical Practice guidelines. Periodic review and data monitoring will be done by the University research team.\n\nThe study is still in the recruiting phase. 27 patients have been recruited. In all these subjects the CTC sample has been evaluated at the pre-treatment time. The lymph node specimens after fixation have been collected as per protocol. The standardization of the IHC markers is ongoing after which the evaluation of the nodes will ensue. The patient follow-up is also progressing at the specified dates.\n\n\nDiscussion\n\nMetastasis can even occur many years after surgical resection of primary cancer due to tumor dormancy. Subramaniam N et al5 on a study of OTSCC show 20-30% recurrence within 12 months and 40-50% mortality within 5year even after guideline-based treatment. This study showed younger patients had a higher incidence of tongue tumours with increased adverse pathological features.5\n\nIn the study by Mizrachi et al. 15% of cN0 oral cancer patients developed neck recurrence.6 Blatt et al. in their study on tumor recurrence among OSCC, which is one of the largest retrospective studies on oral squamous cell carcinoma described that recurrence is very frequent especially in the first six months after primary tumor diagnosis, they reported approximately 64% with local recurrences.7\n\nThe new paradigms of metastatic biology research signify that metastasis is not a late onset event in tumor development nor related to tumor volume. Although progress has been made in understanding the mechanism of cancer spread, the complexity of the metastatic process remains a stumbling block.8 Cancer cells are dynamic, with greater plasticity and can build their own niches.8,9 Each cancer cell must be viewed as an organism capable of developing an entire tumour.8 Metastasis is a process in which genetic instability of the primary tumor fuels cell heterogeneity, permitting cloning of a few metastatic cells that ultimately emerge and spread the tumour.9–11\n\nTumor metastasis is now believed to be closely pursued by prometastatic milieu, premetastatic niche and metastatic niche formation.12 Premetastatic niche is an area devoid of tumour cells, but it can nurture cancer cells. It provides a favourable microenvironment for tumour invasion, endurance and/or proliferation of malignant cells later to develop into metastasis.13\n\nThese are noncancerous changes in a tumor-free organ and may be the most primitive suggestion of metastasis. Lymph nodes have been suggested to offer fertile soil for cancer cell seeding, proliferation, and metastasis.14 These act as crucial metastatic spots and are a decisive prognostic parameter in diverse tumor types.15,16\n\nPrimary tumor initiates the sentinel lymph node remodelling by releasing extracellular vesicles, soluble factors, a variety of cytokines, and growth factors before metastasis spread.11,17\n\nRecent studies have provided evidence on the critical role of primary tumour in tumor progression and metastatic spread.16,18 Extra Cellular Matrix (ECM) remodelling is the key defining feature of PMN development. Fibronectin (FN), lysyl oxidase (LOX), bone marrow-derived cells (VEGFR-1), and matrix metalloproteinase (MMP)-9are key factors responsible for PMN initiation. The lysyl oxidase (LOX) family plays pivotal roles in PMN collagen remodelling, and thus in immune cell recruitment by ECM pre-conditioning.19,20 Wakisaka N et al., in their study of OSCC clarified that tumour-draining sentinel lymph nodes showed greater lymphangiogenesis even much before cancer metastasis. It can function as a permissive \"lymphatic niche\" for tumour cell survival.21\n\nThe primary tumor-derived secretory factors result in lymphangiogenesis and high endothelial venule (HEV) remodelling which are critical vascular events in PMN formation12,19 (Figure 2). Lymphangiogenesis in the premetastatic niche is a dynamic phase in tumor metastasis and lymphatic vessels may serve as a starting site for lymphatic dissemination of tumours.\n\nTumor-derived factors (VEGF, LOX, Tumour Growth Factors, extracellular vesicles) initiates immunosuppression by recruiting macrophages, MDSCs and regulatory T cells.18–20 Though it has been widely accepted that far-reaching effects of cancer progression are achieved through immunosuppression, preliminary studies12,18,20of PMN were focused on extracellular matrix modifications and stromal reprogramming.\n\nRecruited myeloid cells are critical drivers of PMN formation and inflammation. PMN inflammation is shaped by the production of damage-associated molecular pattern (DAMP) molecules. DAMP recognition receptors induce potent STAT3- and NF-kB-mediated inflammatory signaling which regulates PMN myeloid cell composition and function.19,22\n\nSTAT3 is a cytoplasmic transcription factor that regulates cell angiogenesis, inflammation, proliferation, differentiation, apoptosis, and immune response.22 Recent studies have suggested that activated STAT 3 upregulates VEGF expression, thereby inducing tumour angiogenesis. STAT3 activation also increases immunosuppression activities.23‐25\n\nWu LJ et al., on immunohistochemical analyses demonstrated that overexpression of STAT3 in tumor cell-free lymph nodes of gastric tumors was significantly associated with tumor recurrence.26 They also revealed that persistent STAT3 activation in tumor-free lymph nodes was positively related to poor overall survival.26 Several pre-clinical studies have suggested STAT3 inhibition may be a promising target for improving targeted cancer treatment.27,28\n\nLOXL2 has found in promoting lung pre-metastatic niche formation, there by lung metastasis and its pathological role in metastasis has been established.29\n\nLOX is a tumor-secreted protein increased in hypoxia and is found to be critically involved in premetastatic niche formation. LOX expression is associated with metastasis and poor survival in patients with breast or head and neck cancer.30\n\nClinical data show that tumor-derived VEGF-A and VEGF-D generate lymphatic vessels before lymph node-induced metastasis, and are associated with lymph node metastasis.31\n\nA newly published literature showed that the tumor cells manage to infiltrate the lymph nodes by tricking the immune system to accept them as the body’s own cells. This gives tumor cells an easy entry for enabling metastasis.32\n\nSTAT3 activation plays a major role in protecting the tumour cells from the body’s immune surveillance during their transit through circulation.33 STAT3 is found to induce immunosuppression by upregulating PD-L1 in head and neck squamous cell carcinoma. STAT3 signalling activation was found to increase the probability of tumour cell survival, thus increasing the chances of invading distant organs potentially to form secondary tumour.33‐35\n\nEvolving evidence establishes a time-series event—the premetastatic niche has a reflective impact on cancer metastasis.19–20,36 Tumor-promoting pre-metastatic changes in secondary organs may bring an unrecognized degree of complexity in curing metastatic disease. The critical machinery in PMN establishment is primary tumor-derived factors, exosomes, cell-free DNA (cfDNA), and circulating tumor cells.37,38\n\nCTC characterizes microscopically disseminated disease which may have clinical implications. So, CTCs detection in node-negative patients may imply evidence of tumor cells that have escaped from lymphatic filtering and immunosurveillance mechanism.39,40 Even though CTCs decrease during cascades of metastatic events but their self-seeding potential41 is dangerous and can invade the primary tumour or progresses to clinically noticeable metastases. Blood vessels in tumors are abnormal, defective, and possess leaky endothelium.42 This may influence the internal environment of tumors and perhaps the rate of angiogenesis. The loose vasculature and close anatomical access of the tongue may ease the re-entry of CTC to the primary site other than the potential risk of distant metastasis.43,44 CTC detection in mouse models demonstrated that metastatic dissemination is not necessarily a unidirectional process.45 Recent study demonstrated that lymphatic and haematogenous route can even occur together. The study demonstrated that tumour cells invade blood vessels within lymphnode and leaves the lymph node and enter circulation.45,46\n\nMetastatic progression is now presumed to be of linear and parallel models.47–49 The genetic and epigenetic alterations within the primary tumor waves metastases in the linear progression model whereas in the parallel model, the preclinical distribution of less advanced disseminated tumor cells with self-regulating selection expands at the ectopic sites.47–49 The presence of CTC can characterize both tumor progression models or even indicate lymph node skip metastasis.\n\nHristozova T et al.50 suggested a strong correlation of CTC with regional metastasis in inoperable head and neck squamous cell carcinoma. Qayyumi et al.51 found CTC as a poor prognostic factor in the overall survival of naïve OSCC patients in the Indian population. In their study, they found that pre-surgical CTC level has strong adversity on clinicopathological factors. They reported a positive correlation between CTC number and nodal metastasis. They concluded that 20.5% of clinically node-negative patients were pathological harboring metastasis.\n\nCTCs may represent cells that are predisposed to the evolution of metastasis with friable intercellular connections. CTCs symbolize a biologically aggressive tumor with higher versatility to evade the immune surveillance mechanism.52 These characteristics of CTCs may provide a valuable tool to detect this clinical subgroup and guide systemic therapies in a more individualized manner.52\n\nThe survival of CTCs is subjected to their ability to withstand various nonspecific forces, the turbulence of circulation etc.52,53 So, a very low percentage of tumor cells survive which further establishes micro metastasis in distant organs.54\n\nCirculating tumor microemboli not always a mere tumor cell cluster but it may exhibit varying phenotypic and molecular characteristics than single CTCs. These may provide intuitions into the heterogeneity and biological behaviour of tumour.55 CTM metastases by cell jamming that produces homotypic monoclonal or polyclonal tumor clusters. These cells can interact with stromal or immune cells in the inflammatory peri-tumoral infiltrate forming heterotypic clusters. Clustering of CTC can withstand shear stress resistance and enhances their stemness with increased metastatic potential.56\n\nAlthough studies on the clinical significance of PD-L1-positive (PD-L1+) CTCs in head and neck cancers are in their infancy, PD-L 1 positive CTC has clinical relevance in many other solid cancers. PD L 1 may be upregulated in CTCs undergoing EMT and its expression is correlated with poor survival and therapy resistance.57 Some recent works have shown that it could be a prognostic biomarker in renal, epithelial ovarian and lung, advanced urothelial and metastatic breast malignancies.57–59\n\nTissue biopsy fails to reveal on the spatiotemporal heterogenicity and its expression is tissue may not be always adequate, thus it could also help to predict the anti PD L 1 or targeted therapy responses.58 The expression of PD-L1 on circulating tumor cells may also be a reliable predictive biomarker.60\n\nPD -L 1 expression in conventional immunohistochemistry assays lacks accuracy and reliability as the staining of cytoplasmic proteins interferes with cell membrane protein estimation.61\n\nAs discussed earlier, STAT3 activation increases immunosuppression and found to induce immunosuppression by upregulating PD-L1 in head and neck squamous cell carcinoma. Concordance in local immunosuppression by STAT 3 tissue molecular profiling and PD L 1 on CTC/liquid biopsy for systemic immunosuppression will be interesting to look at, which is also being done in this study.\n\nThe utility of CTCs in the diagnosis of early-stage cancers are least explored because CTCs were initially believed to be a feature of advanced-stage disease.62,63 More clinical trials to look at the pre- and postsurgical CTC counts in the same patient may be necessary for therapeutic implications.63 Evolving evidences specifies that CTCs detecting at early stages are indicating the development of aggressive cancers.64 Therefore, this study may have great potential to be used for early cancer detection as well as avoiding overdiagnosis of indolent disease. This study also opens windows to the budding concept of cancer metastasis chemoprevention.\n\nEthics &dissemination\n\nThe trial will be conducted by the principles of the Declaration of Helsinki and guidelines of the Indian Council of Medical Research. The protocol has been approved by the Ethics Committee Amrita School of Medicine (AIMS), Kochi India (ECASM-AIMS-2022-048). The principal investigator will submit an Annual Progress report throughout the clinical trial or as on request. The final report along with trial end notification will also be submitted. No unauthorized persons will have access to any data about this trail. Patients will be educated about the trial which will detail the exact nature of the trial, implications, and constraints, followed by which printed information sheets will be given. Informed consent will be taken and documented.\n\n\nConclusion\n\nPremetastatic niche formation has been found to have a role in defining tumor progression. The present study will help to elucidate their significance in oral cancers,which is less studied. It may be difficult to histologically assess the PMN changes in other metastatic prone organs like liver or lung, but changes in the lymph nodes can be easily evaluated. So, these changes in lymph node and the correlation with circulating tumor cells may act as an indicator of both regional as well as distant metastasis, thus delineate better targets for therapy.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgments\n\nThe authors would like to thank Onco Discover (Actorius Innovations and Research Pvt Ltd) for their CTC isolation technological and research support. We would also like to thank Amrita Vishwa Vidyapeetham – Amrita Institute of Medical Sciences, Kochi.\n\n\nReferences\n\nSung H, Ferlay J, Siegel RL, et al.: Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. 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Oncoimmunology. 2020; 9(1): 1738798. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPage R, Patil D, Akolkar D, et al.: Circulating tumor cell assay to non-invasively evaluate PD-L1 and other therapeutic targets in multiple cancers. PLoS One. 2022; 17(6): e0270139. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXuan Z, Yulin B, Bi M, et al.: From rough to precise: PD-L1 evaluation for predicting the efficacy of PD-1/PD-L1 blockades. Fronitiers in Immunology. 2022; 13: 1–17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLawrence R, Watters M, Davies CR, et al.: Circulating tumour cells for early detection of clinically relevant cancer. Nat. Rev. Clin. Oncol. 2023; 20: 487–500. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRajalakshmi G, Pavithran K, Smitha NV, et al.: Circulating tumor cells in oral squamous cell carcinoma – Current status of its usefulness in clinical practice. J. Head Neck Physicians Surg. 2023; 11: 13–19.\n\nRied K, Eng P, Sali A: Screening for circulating tumour cells allows early detection of cancer and monitoring of treatment effectiveness: an observational study. Asian Pac. J. Cancer Prev. 2017; 18: 2275–2285. PubMed Abstract \| Publisher Full Text" }	[ { "id": "190856", "date": "14 Aug 2023", "name": "Maya Ramesh", "expertise": [ "Reviewer Expertise Immunohistochemical study in Oral Cancer", "dental fluorosis" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study goal is to find the premetastatic changes in oral tongue carcinoma which are very common in India. So, the study is relevant in the Indian scenario which can provide unsurpassed outcomes. The study methodology is good as it uses liquid as well as tissue biopsy. The schematic representation is fully describing the methodology but more narrative on lymph node sampling is better appreciated. Only very few studies have been done in oral cancers with liquid biopsy.\nCirculating tumor cells have been implicated in loco-regional and distant metastasis and their role is head and neck region1 is found but lack of evidence in tongue tumor. PDL-1 can represent the immune status of the patients and it is found to be a good biomarker2. So, how far premetastatic changes can be addressed with liquid biopsy in tongue tumors has to be proved and at present lacks high scientific representation.\nImmunohistochemistry – More number of antibodies might have been considered as clearly mentioned in methodological issues.\nThe authors have well illustrated the rationale with supporting literature, so if the rationale can be achieved it is a good protocol that can be replicated by the scientific community.\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": [] }, { "id": "204183", "date": "29 Sep 2023", "name": "Pankaj Chaturvedi", "expertise": [ "Reviewer Expertise Head & Neck Oncology", "Circulating tumour cells", "molecular markers" ], "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\nTongue cancers have high risk of regional failure even after receiving standard treatment protocols. There is unmet need for detecting the premetastatic changes which can predict regional or distant failures. However, the major caveat in detecting these premetastatic markers is the heterogeneity of tumor, the impact of heterogeneity in the development of LN metastasis, and multiple mechanisms involved1.\nLymph node lymphangiogenesis (LNL) is one of the most distinctive aspects of premetastatic changes and thus a strong predictor of lymph node metastasis. However, LNL is a complex process modulated by various growth factors and pathways2. VEGF-C, VEGF-D, and VEGF-A are some of the most researched components for lymphangiogenesis3. Their elevated levels are associated with LN and distant metastasis4,5. Several tyrosine kinase receptors are targeted by receptor tyrosine kinase inhibitors, however, the exact pathway is unknown6. The S1PR1-STAT3 pathway enables myeloid cells to intravasate, turning the organ microenvironment conducive for proliferation, survival, and initiation of metastasis7. LOX expression is mainly in the tumor cells which are exposed to relevant levels of hypoxia. LOX is an important component of pre-metastatic niche formation and metastasis8. Even though there are no standard treatment available, there is promising preliminary data regarding therapeutic targeting of STAT3 and LOX9,10.\nCirculating tumor cells (CTCs) are rare cells that escape from the primary tumor and enter into the bloodstream to form metastatic deposits. Elevated CTC levels have a strong correlation with adverse survival outcomes11. Even though, it is a difficult task to establish a permanent in vitro cell line to conduct experiments12. The CTCs have the potential for personalized treatment due to the possibility of individualized drug susceptibility testing13.\nSeveral growth hormones, RNA, cytoplasmic proteins, and growth factors like Periostin, VEGF, Angiopoietins, Laminin γ2, and Insulin-like growth factor (IGF)-1/2 which are involved in the induction of lymphangiogenesis. Moreover the activation of mTOR, podoplanin, and lymphatic vessel endothelial hyaluronan receptor 1(LYVE-1), extracellular vesicle, and HPV +ve tumors may affect the lymphangiogenesis6.\nThe objectives of the present protocol which are to evaluate the correlation of molecular expression of STAT 3, LOX 2, and VEGF in the tumor-free lymph nodes (N0) to assess the premetastatic niche changes and recurrence-free survival and to evaluate the efficacy of CTC (circulating tumor cells) and CTM (circulating tumor microemboli) in terms of relapse, and disease-free survival in oral tongue squamous cell carcinoma patients is quite relevant . Moreover, the study design and methodology is described in detail and seems appropriate to achieve the above mentioned objectives.\nThe admirable part of the present study is that it aims to include the various mechanisms of LN pre-metastatic niche creation in HNSCC, which are dependent on lymphangiogenesis, activation of the S1PR1-STAT3 pathway, LOX pathway, and CTCs. However, paying attention to other molecular pathways of lymphangiogenesis is suggested as a single molecular pathway is likely to lead to failure in terms of therapeutic development. Further research is needed to elucidate the optimal therapeutic molecular target(s) and explore newer HNSCC treatments, which can support new strategies for the patients.\nThe absence of any previous study or information regarding the architectural histopathologic features to correlate with PMN changes makes it ambiguous. However, an appropriate description of these changes and photographic documentation might provide important 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? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-889
https://f1000research.com/articles/12-887/v1	26 Jul 23	{ "type": "Research Article", "title": "Critical thinking about treatment effects in Eastern Africa: development and Rasch analysis of an assessment tool", "authors": [ "Astrid Dahlgren", "Daniel Semakula", "Faith Chesire", "Michael Mugisha", "Esther Nakyejwe", "Allen Nsangi", "Laetitia Nyirazinyoye", "Marlyn A. Ochieng", "Andrew David Oxman", "Ronald Ssenyonga", "Clarisse Marie Claudine Simbi", "Daniel Semakula", "Faith Chesire", "Michael Mugisha", "Esther Nakyejwe", "Allen Nsangi", "Laetitia Nyirazinyoye", "Marlyn A. Ochieng", "Andrew David Oxman", "Ronald Ssenyonga", "Clarisse Marie Claudine Simbi" ], "abstract": "Background: Every day we are faced with different treatment claims, in the news, in social media, and by our family and friends. Some of these claims are true, but many are unsubstantiated. Without being supported by reliable evidence such guidance can lead to waste and harmful health choices. The Informed Health Choices (IHC) Network facilitates development of interventions for teaching children and adults the ability to assess treatment claims (informedhealthchoices.org). Our objective was to develop and evaluate a new assessment tool developed from the item bank for use in an upcoming trial of lower secondary school resources in Uganda, Kenya, and Rwanda. Methods: A cross-sectional study evaluating a questionnaire including two item-sets was used. The first evaluated ability using multiple-choice questions (scored dichotomously) and the other evaluated intended behaviour and self-efficacy (measured using Likert scales). This study was conducted in Uganda, Kenya, and Rwanda in 2021. We recruited children (over 12 years old) and adults through schools and our networks. We entered 1,671 responses into our analysis. Summary and individual fit to the Rasch model (including Cronbach’s Alpha) were assessed using the RUMM2030 software. Results: Both item-sets were found to have good fit to the Rasch model and were acceptable to our target audience. The reliability was good (Cronbach’s alpha >0.7). Observations of the individual item and person fit provided us with guidance on how we could improve the design, scoring, and administration of the two item-sets. There was no local dependency in either of the item-sets, and both item-sets were found to have acceptable unidimensionality. Conclusion: To our knowledge, this is the first instrument validated for measuring ability to assess treatment claims in Uganda, Kenya and Rwanda. Overall, the two item-sets were found to have satisfactory measurement properties.", "keywords": [ "health literacy", "Rasch analysis", "critical thinking", "informed choice", "evidence-based practice" ], "content": "Introduction\n\nEvery day we are faced with different treatment claims, in the news, in social media, and by our family and friends. Some of these claims are true, but many are unsubstantiated.1,2 Without being supported by reliable evidence such guidance can lead to waste and harmful health choices.3,4 Thus, improving people’s ability to assess whether treatment claims are based on reliable evidence may lead to better health outcomes. The spread of misinformation during the Covid-19 pandemic has further emphasized the importance of promoting critical thinking and science literacy as a public health initiative.5,6\n\nThe Informed Health Choices (IHC) Network facilitates development of interventions for teaching children and adults the ability to assess treatment claims (informedhealthchoices.org). We have developed a list of Key Concepts that people need to know to be able to assess claims about treatment effects.7 By ‘treatment’ we refer to any intervention (action) intended to improve health, including preventive, therapeutic, and rehabilitative interventions, and public health or health system interventions. In two recent randomized trials in Uganda, we found that primary school children and their parents could be taught to apply these concepts.8,9 Currently we are preparing for a new trial in Kenya, Rwanda, and Uganda to evaluate a set of educational resources for lower secondary schools (the IHC secondary school resources).\n\nThe Claim Evaluation Tools item bank was first developed for use in the abovementioned trials in Uganda, evaluating learning outcomes in primary school children and their parents.8,9 We also developed the item bank so that it could be used as a flexible resource for teachers and researchers, enabling them to design their own instrument for their own purposes.10,11 The item bank can be used for creating tests in schools (including higher education) and for research purposes in, for example, surveys and randomized trials.\n\nSince it was first developed, the item bank has been periodically revised to reflect changes we have made to the Key Concepts list. Since our first trials in Uganda, researchers have developed instruments using items from the item bank in other contexts, including China, Mexico, and Norway.12–14 Other studies are underway in Croatia and the USA. Currently, the item bank includes more than 200 items, with three to four multiple-choice questions (MCQs) available for assessing knowledge and the ability to apply each concept in the list. The item bank also includes a sample of literacy questions for use in contexts where reading ability may be a barrier for responding to the MCQs. It also includes items for assessing people’s intended behaviours and self-efficacy (scored on 5-point Likert scales). All items are written in plain language and are suitable for both children and adults.\n\nIn the present study, our objective was to develop and evaluate the psychometric properties of a new assessment tool developed from the item bank for use in Uganda, Kenya, and Rwanda. This outcome measure will be used in randomised trials of the IHC lower secondary school resources.\n\n\nMethods\n\nBelow we describe how we designed the questionnaire, how it was administered, and how we analysed and report the data. The protocol and underlying data for this study has been published.34,35\n\nFor this study we included both ability items and the items measuring intended behaviour and self-efficacy.\n\nWe planned on removing MCQs with sub-optimal measurement properties based on the results of this study. Therefore, we included more MCQs than we plan to use in the trial (two MCQs per Key Concept). The educational intervention we will evaluate in the randomised trials addresses nine Key Concepts (Table 1). For each of those concepts, we included three MCQs in the questionnaire, a total of 27 MCQs assessing ability. All MCQs included 3 response options.\n\n\n\n1. Do not assume that treatments are safe.\n\n\n\n2. Do not assume that treatments have large, dramatic effects.\n\n\n\n3. Do not assume that comparisons are not needed.\n\n\n\n4. Do not assume that personal experiences alone are sufficient.\n\n\n\n5. Do not assume that a treatment is better based on how new or technologically impressive it is.\n\n\n\n6. Do not assume that a treatment is helpful or safe based on how widely used it is or has been.\n\n\n\n7. Consider whether the people being compared were similar.\n\n\n\n8. Be cautious of small studies.\n\n\n\n9. Weigh the benefits and savings against the harms and costs of acting or not.\n\nWe included three items that assess intended behaviour and four items that assess self-efficacy. The Likert scales include four response options ranging from very likely to very unlikely (intended behaviour) or very difficult to very easy (self-efficacy), and a fifth option: ‘I don’t know’.\n\nIn addition, we included demographic questions asking about gender, age, educational level, country of residence, training in research methods, and experience with participation in randomised trials. Gender, age, and country of residence were important for the psychometric analysis (testing for differential item functioning). The other background factors were used to ascertain that we were able to recruit people with a spread in ability level (ability to assess treatment claims). Level of education and familiarity with research methods have been shown to be associated with more correct answers.14\n\nIn preparation for this study, we conducted cognitive interviews and piloted the questionnaire with individuals from our potential target groups in Uganda, Kenya, and Rwanda.11,15 The objective was to get feedback from members of our target groups in the three contexts on the acceptability and relevance of the terminology and formats used in the questionnaire. Even though the items included in the Claim Evaluation Tools item bank have previously gone through an extensive development process in Uganda, we considered it important to get feedback from people in our target groups in Rwanda and Kenya, where the items had not been tested before.\n\nWe recruited schools in May- August 2021 through the project’s teacher networks. In the interviews the students were encouraged to think aloud about how they understood the scenarios and response options, and to identify any issues they had regarding comprehension of terminology or format. The researcher noted down all identified issues. All feedback was summarised by the lead investigators and the findings was discussed in the project group including the research teams in all three contexts.\n\nPiloting took place in a classroom setting. The purpose and instructions of the test was introduced to the students by a member of the research team in collaboration with the teacher, observations were made regarding time taken to complete the questionnaire and comprehension of the format (incorrectly filled in response options).\n\nFindings coming out of the interviews and pilots led to only minor changes, such as changing some of the names and other terminology used in the MCQs to improve familiarity in the two new contexts. We also changed the format of the intended behaviour and self-efficacy items from a traditional Likert-scale to resemble a multiple-choice format, keeping the same response options (Figure 1).\n\nWe made that change because the Likert-scale format was unfamiliar to some of the students in the three contexts, and the MCQ format was more familiar and acceptable to the students. The pilot studies also provided us with information about the time needed to complete the questionnaire (between 30 and 60 minutes) and what we could expect in terms of missing responses in the upcoming trial.\n\nPreviously, several tests have been developed from the claim evaluation tools item bank. The test developed for this study was named the Critical Thinking about Health test. A copy of the test evaluated in this study is available us extended data.36\n\nThere is no gold standard for the number of respondents needed for Rasch analysis. This is a pragmatic judgement considering the number of items evaluated and the statistical power needed to identify item bias resulting from background variables.16–18 Rasch analysis does not require a representative sample. However, the sample should include enough people to allow for evaluating differential functioning and a spread in ability. Studies have found that a sample of 200-250 people per group is suitable for detecting differential item functioning (DIF).19,20 We expected both item-sets to work in the same way for children and adults and to have no differential functioning by gender.11 For this evaluation, we also needed a sample of people with different ability to assess treatment claims. There are few background variables that may predict ability to assess treatment claims, but higher education involving training in statistics or research methods may be a factor.14 Consequently, we estimated that recruiting approximately 500 people in each country, with an equal distribution of men and women, and lower secondary school students and adults would be adequate (Table 2). We also made sure to recruit people from higher education contexts, through the university networks in each context, as well as people in our local communities, social media, and students from schools participating in piloting of the educational intervention. We commenced data collection in July 2021 and was completed December in the same year.\n\nAll recruitment and data collection were done during lock down due to COVID-19, leading us to use varied strategies for recruiting our respondents.\n\nIn Uganda we recruited participants using our networks there including teachers, students, and National advisory panel networks. For students, we used three strategies, including visiting students at their homes, reaching out through the student network, and also requested teachers who were conducting online revision classes to introduce us to their students via the platforms to introduce the project and share the questionnaire link via WhatsApp or Telegram (both media apps for communication) after obtaining consent. For adults, we recruited people with higher education qualifications through university platforms i.e., the University faculty platforms, a PhD forum which has over 40 PhD fellows, students studying medicine WhatsApp groups, and a teachers’ network WhatsApp group. However, for the local communities, we visited food and clothes markets and asked them to complete the questionnaires. All data collection was done in the central region (Kampala and Wakiso) and the northern region (in Gulu district) of Uganda.\n\nIn Kenya we recruited students from three schools that participated in piloting the IHC secondary school resources. In those schools, we purposively included all the participants from one stream except those that had been selected for the pilot. Each school had about three-four classes and each class had about 40 students. For adults, we included the student’s institution of tertiary education and members of the community with low education levels (secondary and below), and those that could read and owned a Smartphone. For the students, we purposively included students from two faculties (Health and Arts and Sciences). Through the Dean of students, we invited them to a meeting where we introduced the project, outcome measure and sought their verbal consent. We then shared the link to the test and asked them to log in and participate. For community members, we used our database to recruit members that were actively involved in the institute’s previous and ongoing community-based projects in rural settings in Butere sub-County. Although we reached out to many members, only a few members responded thus we resorted to recruit more from the student’s fraternity (pursuing diploma and certificate courses). We used a similar recruitment and consenting process described for the students above.\n\nIn Rwanda, for adults, we used WhatsApp and recruited using the snowballing method through our networks, including the projects teachers’ network and students’ network in Rwanda. The teachers network included lower secondary school teachers who were from different schools, and they varied in terms of work experience, age, subject area and schools they teach from. Similarly, the students’ network included students from similar schools as members of teacher’s network. They also varied in their age, sex, and history of school performance (high or low performing students). We also used emails and reached out to adults who work or previously worked with the school of public health researchers in Rwanda. We also engaged a teacher’s network who also responded to the test. We recruited students through schools that participated in the development and pilot of the intervention in Kigali city and surrounding neighborhoods.\n\nMost of the data collection was done online, using a service hosted by the University of Oslo (Nettskjema). One small sample (students in Kenya) used paper questionnaires in a classroom setting and administrated as an exam as part of pilot testing of the IHC secondary school resources. The test was administrated by a teacher under the instructions of the research team. The paper questionnaires were scanned and added to the data collected online.\n\nEthical approval was obtained from the relevant authorities in each country; Masinde Muliro University of Science and Technology, Institutional Ethics Review Committee (MMUST/IERC/75/19, License No: NACOSTI/P/21/8103) the Rwanda National Ethics Committee 916/RNEC/2019, School of Medicine Research Ethics Committee (REC REF 2020-139)/Uganda National Council of Science and Technology (HS916ES).\n\nAll participants were given written information about the purpose of the study and that participation was voluntary, and how the findings would be used to improve the validity and reliability of the Critical Thinking about Health test. Children participating through their schools were also given oral information. We obtained written consent from all adult participants, the minor’s guardians, and written assent from the minors.\n\nSince this was a knowledge test, just as a regular school exam, this study did not collect any personal or other sensitive information that could lead to identification of the respondents. None of the members of this project group had access to information that could identify individual participants during or after data collection.\n\nRasch analysis is a dynamic way of developing measurement tools with construct validity.14 The approach is used to address important measurement issues required for validating an outcome measure, including internal construct validity (by testing for unidimensionality), invariance of the items (item-person-interaction), and item bias (differential item function).21,22\n\nWe imported the data from Excel (version 2208) into RUMM2030 (https://www.rummlab.com.au/) and followed the basic steps of Rasch analysis as recommended in the literature.21,23 R is a freely accessible software environment for statistical computing and graphics including Rasch analysis that can be used to run a similar analysis (https://www.r-project.org/). We analysed the two item-sets separately based on the assumption that these measure different underling traits. The MCQs were scored dichotomously as correct or incorrect. We applied the polytomous model to the intended behaviour and self-efficacy items.22 When entered into RUMM2030, missing data was coded as “0”.\n\nThe first step in the analysis involved exploring the class interval structure (number and size of ability groups) and the summary statistics (person-Item distribution). In Rasch analysis, the ratio between any two items should be constant across different ‘ability’ groups. The response patterns to an item-set is tested against what is expected by the model which is a probabilistic form of Guttman scaling.21 In other words, the easier the item is, the more likely it will be ‘passed’, and the more able the person is the more likely he or she will pass.21 We explored this relationship using the summary statistics function in RUMM2030.23 In RUMM2030, the item-person interaction is presented on a logit scale, where the mean item location is ‘0’. If the instrument is a well-targeted measure (not too easy or too difficult), the mean location for individuals would be around the value of zero.22 If the person location is higher than zero, this indicates that the test is easy, if the person location is lower than zero this indicates that the test is difficult. The item and person fit residual statistics assess the degree of divergence (or residual) between the expected and observed data for each person item when summed for all items and all individuals respectively for each test set.22 In RUMM2030 this is reported as an approximate z-score, representing a standardized normal distribution.22 Ideally, item and person fit should have a mean of zero and a standard deviation of one.22\n\nWe calculated Cronbach’s alpha to assess the reliability of both item-sets by removing missing data. A Cronbach’s alpha above 0.7 was considered acceptable.22\n\nThe principal component analysis/t-test protocol is used to test the hypothesis of unidimensionality. This is done by identifying the two most divergent item subsets (using the residual principal component function in RUMM2030), and then calculating t-tests.22 If ≤5% of tests are significant, strict unidimensionality can be inferred.24 However, the concept of ‘unidimensionality’ is not ‘definite’ but relative and should be supplemented with quantitative or qualitative interpretation of the explicit variable definition and considering the context and purpose of the measurement.24,25\n\nWe tested for local dependency by using the residual correlations function in RUMM2030. Data from this output was copied into Excel (version 2208) and any residual correlations greater than 0.2 above the average was considered as potential problematic dependency.22\n\nWe identified individuals and items with ‘misfit’ to the Rasch model by chi-square statistics and by exploring the fit residuals. Items with statistically significant chi-square probabilities do not fit the model at 0.01 significance level, items within a ±2.5 fit residual range are considered to be potentially problematic.22 Similarly, individuals with a fit residual of ±2.5 were considered as not fitting the model. Such extreme values can be an indication of, for example, guessing or copying, and that the item-set is not appropriate.\n\nWe examined differential item functioning (DIF) by age, gender, and country of residence. It was our objective to include only items that could be applied fairly across these demographic variables. Ideally, all items in the Claim Evaluation Tools item bank are expected to work in the same way for men and women, and across age groups. There are two types of DIF. Uniform DIF is when the difference between groups for an item is systematic - for example adults having systematically higher ability compared to lower secondary school students. This is less problematic (when it is known) than non-uniform DIF, where the difference between groups on an item is inconsistent across ability groups.21 For this study, we considered non-uniform DIF as unacceptable. We predicted that we would find uniform DIF by country, as we know from other studies that there are differences in ability-by-concept across countries.14 Uniform DIF by gender and age was unwanted but would be considered in relation to the other findings from the Rasch analysis. The reason for this was that the questionnaire will be used for measuring differences between an intervention and a comparison group, and systematic DIF would therefore not be a problem in our study.\n\nIn the item characteristic curve plot the expected scores and the observed scores for the class intervals of the different ability levels are displayed. We observed the item characteristic curve for each item and made note of items that showed under-discrimination, over-discrimination, or had several deviating ability groups.22 We considered items with under-discrimination and classic over-discrimination for removal. Marginal over-discrimination was not considered to be a problem for our purposes.\n\nFor the polytomous items we explored the threshold ordering (fit to the expected logical order of the response options) to check for disordered thresholds. Disordered thresholds suggest that the scoring categories are not progressing as expected, and that the item is not working properly.22\n\nThis study follows the STROBE-reporting standards.38\n\n\nResults\n\nA total of 1,671 responses were entered into the analysis distributed across 10 ability groups identified by the RUMM2030 software of which 49% were women and 40% were young people (under 18). Of these, 35% were from Kenya, 34% from Uganda, and 31% from Rwanda. Missing data was minimal only 0.004%, and thus had no impact on the analysis.\n\nThe person-item distribution shows that both item sets are well targeted (mean person location was -0.218 for the ability item set and 0.084 for the Likert item-set.\n\nFor the ability items, the person fit residual was -0.204 (SD 0.741) and thus showed satisfactory fit to the model. The items’ fit residual was 0.712 (SD 2.235) and warranted further investigation in subsequent analyses.\n\nFor the Likert items, the item fit residual was 0.543 (SD 0.938), indicating reasonable fit. However, the high standard deviation for the person fit residual (-0.546, SD 1.783) suggested some misfit to the model.\n\nBoth item-sets were found to be reliable, with a Cronbach’s alpha of 0.72 and 0.79 for the ability and Likert item-sets respectively.\n\nIn the analysis of the ability item-set, we identified one person with a highly negative fit residual (adult, female, Rwanda) and two with highly positive fit residuals (male, young person, Rwanda and adult, female, Rwanda). Of the 27 MCQs, three items had extreme negative values, and four items had extreme positive values.\n\nThere were no items with extreme values in the Likert item-set. However, several misfitting persons were identified (296 individuals) with high negative residuals and two individuals with high positive residuals.\n\nThe majority of the ability items had a good fit to the item characteristics curve (Figure 2). Four items showed evidence of classic overdiscrimination, of which two of these also had very high negative fit residuals (Figure 3). Four items showed sign of classic underdiscrimination and were considered candidates for removal (Figure 4). Most Likert-items showed a good fit, although two items were slightly overdiscriminating, this was considered acceptable.\n\nIn the DIF analysis of the 27 ability items, two items showed uniform DIF by gender (one item where males did systematically better and one where females had higher ability). Three items showed DIF by age, of which two were uniform (one item where young people performed better and one item where adults had higher ability). One item had non-uniform DIF by age. Uniform DIF by country was found for 10 items, the ranking of the three countries differing across these items.\n\nThere was no DIF by gender, age, or country in the analysis of the Likert item-set.\n\nIn the Likert item-set, two items were found to be slightly over-discriminating and were therefore considered acceptable. The remaining items showed very good fit.\n\nWhen exploring the ordering of the thresholds, we found that the three Likert items evaluating intended behaviour were disorganized. A reanalysis of these suggest that these could be improved by dichotomising the response options. The four items evaluating self-efficacy showed a good fit.\n\nIn the analysis of the ability item-set, 8% of the T-tests were significant.\n\nThe magnitude of multidimensionality in Likert-items were found satisfactory at 5% and considered to be unidimensional.\n\nThere were no item-pairs correlations above 0.2 of the average value in any of the item-sets, suggesting no important redundancy.\n\nThe outcome measure to be used in the final trial was reduced to include only two MCQs for each Key Concept to be assessed. We removed the ability-items with suboptimal fit. Since the Likert-items were all found to have good fit, these remained unchanged.\n\nThe revised outcome measure has been published as extended data.37\n\n\nDiscussion\n\nOverall, both item-sets were found to have good fit to the Rasch model and suitable for our target audience. The reliability of both item-sets was also good. Observations of the individual item and person fit provided us with guidance on how to improve the design and administration of the two item-sets.\n\nWhen observing each individual item’s fit to the Rasch model in the ability item-set, we identified some items that could be removed to improve the questionnaire. Of 27 ability items, three had differential item functioning by age or gender of which only one of these were highly problematic (non-uniform). As expected, some items also showed differential item functioning by country. Possible explanations for this may be that there are differences in cultural beliefs or because there are differences in the curricula taught in schools. Considering that the differential item functioning by country was uniform and that we are planning to use the outcome measure in randomised trials comparing effects between comparison groups in each specific context, this was not considered to be a concern for our purposes. We also identified some items with poor measurement properties by observing the item characters curves. Taken together with the item showing non-uniform DIF, these were considered for removal from the final outcome measure to be used in our upcoming trial.\n\nIn the analysis of the Likert item-set, two issues were identified that we needed to address. Three items measuring intended behaviour showed disordered response categories, furthermore we identified a high number of people with extreme values. This can be an indication that some of the respondents had difficulty answering these questions. As noted in the methods, we observed that some people in the studied contexts were unfamiliar with intended behaviour and self-efficacy questions. The results from this study suggested that we need to plan carefully for how this item-set is administered and ensure that people are adequately instructed about the format and purpose of these questions. The results also suggested that we should either redesign the attitude items so that the response options are dichotomized (with three response options instead of five) or dichotomise the answers by collapsing the response options in the analysis following the trial. We did the latter in the trial of the IHC primary school resources by combining likely (or difficult) and very likely, and combining unlikely, very unlikely, and ‘don’t know’).26\n\nWe found no important redundancy in the item-sets (dependency between item pairs), and both item-sets appear to measure only one underlying trait (unidimensionality). The ability item-set had a somewhat higher percentage of T-tests above the statistical threshold of 5%.24 Considering that this is the first time we have observed this in one of the many Rasch analyses we have done on instruments developed from the Claim Evaluation Tools item bank, we considered the magnitude of unidimensionality observed in the ability item-set acceptable.12–14\n\nThe overabundance of unreliable treatment claims that accompanied the COVID-19 pandemic has highlighted the need for facilitating critical thinking as an important public health initiative.5 This is essential to protect people against unreliable treatment claims and enable them to make informed treatment choices.\n\nHealth literacy is defined in many ways, but typically includes the ability to think critically (sometimes referred to as critical health literacy).27,28 A conceptual framework is helpful when developing assessment tools.29 Health literacy is often measured using self-report.30 Furthermore, many of the health literacy instruments available aim to capture other domains of health literacy such as functional and social literacy.30,31 In addition to measuring perceptions of one’s own abilities (self-report or self-efficacy), it is important to measure abilities objectively (performance). The association between self-report and performance is not straightforward.32 The Health Literacy Tool shed, a database of health literacy measures has indexed 16 instruments evaluating an aspect of health literacy intended for adolescents using an objective measurement of performance, of which eight are available in English.30 The Claim Evaluation Tools have a narrower scope than most of these and focusses on one critical skill, the ability to assess treatment claims and make informed treatment choices. Although these instruments can provide information about people’s general health literacy skills, applying a more specific assessment tool in, for example, mapping studies, makes it easier to design interventions targeting the specific gaps identified.\n\nOne limitation of this study is that the adult population included more people with higher education than the general population in each of these three settings. Thus, the test might be more difficult for people with less education. However, although participants with higher education are somewhat more likely to answering the ability questions correctly, there does not seem to be a strong association.14,33 Another limitation is that the findings of this study are exclusive to the three Eastern African countries, and the validity and reliability in other contexts are uncertain. The item-sets validated in this study should therefore undergo further psychometric testing if used elsewhere.\n\nThe strategy of using pilot testing and a Rasch analysis have been found to be a robust method for developing measurement tools in several contexts.10–13 An important strength of this study is that we used explicit and transparent methods, following the principal steps recommended for Rasch analysis.21–23 Another strength is that we were able to recruit enough people despite the fact all three countries were burdened by the pandemic during the data collection. The results of this study and subsequent design of the questionnaire based on these results ensures that both the ability and Likert item-sets are a valid and reliable outcome measure for the randomised trials of the IHC lower secondary school intervention in all three countries.\n\n\nConclusion\n\nTo our knowledge, this is the first measurement tool developed for measuring ability, intended behaviours, and self-efficacy for critical thinking about treatments in Kenya and Rwanda, as well as in Uganda. The two item-sets we evaluated in this study were found to be reliable and to have satisfactory measurement properties.\n\nThe findings from our analysis were used to redesign and improve the ability item-set. The results also informed guidance for how the Likert item-set should be administered and analysed.", "appendix": "Data availability\n\nZenodo: Critical thinking about treatment effects in Eastern Africa. Data set uncoded. [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7680780. 34\n\nThe project contains the following underlying data:\n\n• data-209546-2021-12-22-1147-utf_final_eclaim_rasch_2021.xlsx. (Raw data electronically collected - adults and students).\n\n• data-237440-2021-12-22-1155-utf_pilot Rwanda_Rasch_2021.xlsx. (Raw data collected from paper-based questionnaires used in the pilot survey - students).\n\nZenodo: Study protocol: Assessment of validity and reliability of a questionnaire based on the Claim Evaluation Tools Item bank in Uganda, Kenya and Rwanda. https://doi.org/10.5281/zenodo.7680616. 35\n\nThe project contains the following extended data:\n\n• Protocol_Claim_Choice 2021 23 03.docx.(2)pdf. (Study protocol)\n\nZenodo: Critical thinking about treatment effects in Eastern Africa. The Critical Thinking about Health test (before Rasch analysis). Zenodo. https://doi.org/10.5281/zenodo.7756037. 36\n\nThe project contains the following extended data:\n\n• Critical thinking about treatments test – Vis - Nettskjema.pdf. (Original test validated as part of this study).\n\nZenodo: Critical thinking about treatment effects in Eastern Africa. The Critical Thinking about Health test. https://doi.org/10.5281/zenodo.7680606. 37\n\nThe project contains the following extended data:\n\n• Test_CHOICE_final_with literacy and userexperience_march_2022_FORMATD.pdf. (Final revised test).\n\nZenodo: STROBE checklist for ‘Critical thinking about treatment effects in Eastern Africa: development and Rasch analysis of an assessment tool’. https://doi.org/10.5281/zenodo.7680586. 38\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe would like to thank Sarah Rosenbaum for providing her expertise in designing the questionnaire. Furthermore, we would like to thank the rest of Informed Health Choices team for their valuable feedback and discussion in planning and conducting this study. We are also very grateful for all the secondary school students and adults who took time to contribute to this study and to the ministry of education and school administration for allowing students participation.\n\n\nReferences\n\nMian A, Khan S: Coronavirus: the spread of misinformation. BMC Med. 2020; 18(1): 89. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOxman M, Larun L, Pérez Gaxiola G, et al.: Quality of information in news media reports about the effects of health interventions: Systematic review and meta-analyses. F1000Res. 2022; 10(433): 433. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrownlee S, Chalkidou K, Doust J, et al.: Evidence for overuse of medical services around the world. Lancet. 2017; 390(10090): 156–168. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGlasziou P, Straus S, Brownlee S, et al.: Evidence for underuse of effective medical services around the world. Lancet. 2017; 390(10090): 169–177. PubMed Abstract \| Publisher Full Text\n\nThe Lancet Infectious D: The COVID-19 infodemic. Lancet Infect. Dis. 2020; 20(8): 875. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThe Lancet R: Going viral: misinformation in the time of COVID-19. Lancet Rheumatol. 2021; 3(6): e393. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOxman A, Chalmers I, Austvoll-Dahlgren A, et al.: Key Concepts for assessing claims about treatment effects and making well-informed treatment choices. F1000Res. 2019; 7(1784): 1784. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNsangi A, Semakula D, Oxman AD, et al.: Effects of the Informed Health Choices primary school intervention on the ability of children in Uganda to assess the reliability of claims about treatment effects, 1-year follow-up: a cluster-randomised trial. Trials. 2020; 21(1): 27. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSemakula D, Nsangi A, Oxman AD, et al.: Effects of the Informed Health Choices podcast on the ability of parents of primary school children in Uganda to assess the trustworthiness of claims about treatment effects: one-year follow up of a randomised trial. Trials. 2020; 21(1): 187. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAustvoll-Dahlgren A, Guttersrud O, Nsangi A, et al.: Measuring ability to assess claims about treatment effects: a latent trait analysis of items from the ‘Claim Evaluation Tools’ database using Rasch modelling. BMJ Open. 2017; 7(5): e013185. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAustvoll-Dahlgren A, Semakula D, Nsangi A, et al.: Measuring ability to assess claims about treatment effects: the development of the ‘Claim Evaluation Tools’. BMJ Open. 2017; 7(5): e013184. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPerez-Gaxiola G, Austvoll-Dahlgren A: Validacion de un cuestionario para medir la habilidad de la poblacion general para evaluar afirmaciones acerca de tratamientos medicos. Gac. Med. Mex. 2018; 154(4): 480–495. PubMed Abstract \| Publisher Full Text\n\nWang Q, Austvoll-Dahlgren A, Zhang J, et al.: Evaluating people’s ability to assess treatment claims: Validating a test in Mandarin from Claim Evaluation Tools database. J. Evid. Based Med. 2019; 12(2): 140–146. PubMed Abstract \| Publisher Full Text\n\nDahlgren A, Furuseth-Olsen K, Rose C, et al.: The Norwegian public?s ability to assess treatment claims: results of a cross-sectional study of critical health literacy [version 2; peer review: 1 approved, 1 approved with reservations]. F1000Res. 2021; 9(179). Publisher Full Text\n\nBloem EF, van Zuuren FJ , Koeneman MA, et al.: Clarifying quality of life assessment: do theoretical models capture the underlying cognitive processes? Qual. Life Res. 2008; 17(8): 1093–1102. PubMed Abstract \| Publisher Full Text\n\nChoi SW, Cook KF, Dodd BG: Parameter recovery for the partial credit model using MULTILOG. J. Outcome Meas. 1997; 1(2): 114–142. PubMed Abstract\n\nLinacre JM: Sample size and item calibration stability. Rasch Measurement Transactions. 1994; 328.\n\nClauser BE, Mazor KM: Using Statistical Procedures to Identify Differentially Functioning Test Items. Educ. Meas. Issues Pract. 1998; 17(1): 31–44.\n\nRogers HJ, Swaminathan H: A Comparison of Logistic Regression and Mantel-Haenszel Procedures for Detecting Differential Item Functioning. Appl. Psychol. Meas. 1993; 17(2): 105–116. Publisher Full Text\n\nNarayanan P, Swaminathan H: Performance of the Mantel-Haenszel and Simultaneous Item Bias Procedures for Detecting Differential Item Functioning. Appl. Psychol. Meas. 1994; 18(4): 315–328. Publisher Full Text\n\nTennant A, Conaghan PG: The Rasch measurement model in rheumatology: what is it and why use it? When should it be applied, and what should one look for in a Rasch paper? Arthritis Rheum. 2007; 57(8): 1358–1362. PubMed Abstract \| Publisher Full Text\n\nPsylab Group: Introductory Rasch Analysis Using RUMM2030. Psychometric Labaratory for Health Sciences: The Section of Rehabilitation Medicine University of Leeds; 2016.\n\nRumm Laboratory Pty Ltd: Displaying the RUMM2030 analysis. Rasch unidimensional measurement model; 2015.\n\nHagell P: Testing Rating Scale Unidimensionality Using the Principal Component Analysis (PCA)/t-Test Protocol with the Rasch Model: The Primacy of Theory over Statistics. Open J. Stat. 2014; 04: 456–465. Publisher Full Text\n\nAndrich D: Rasch Models for Measurement. Beverly Hills: Sage Publications I; 1988.\n\nNsangi A, Semakula D, Oxman AD, et al.: Effects of the Informed Health Choices primary school intervention on the ability of children in Uganda to assess the reliability of claims about treatment effects: a cluster-randomised controlled trial. Lancet. 2017; 390(10092): 374–388. PubMed Abstract \| Publisher Full Text\n\nChinn D: Critical health literacy: A review and critical analysis. Soc. Sci. Med. 2011; 73(1): 60–67. Publisher Full Text\n\nGuo S, Armstrong R, Waters E, et al.: Quality of health literacy instruments used in children and adolescents: a systematic review. BMJ Open. 2018; 8(6): e020080. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCOSMIN Taxonomy of Measurement Properties. http\n\nHealth Literacy Tool Shed: A database of health literacy measures. http\n\nNguyen TH, Paasche-Orlow MK, McCormack LA: The State of the Science of Health Literacy Measurement. Stud. Health Technol. Inform. 2017; 240: 17–33. PubMed Abstract\n\nKiechle ES, Bailey SC, Hedlund LA, et al.: Different Measures, Different Outcomes? A Systematic Review of Performance-Based versus Self-Reported Measures of Health Literacy and Numeracy. J. Gen. Intern. Med. 2015; 30(10): 1538–1546. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSørensen K, Pelikan JM, Röthlin F, et al.: Health literacy in Europe: comparative results of the European health literacy survey (HLS-EU). Eur. J. Pub. Health. 2015; 25(6): 1053–1058. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDahlgren A: Critical thinking about treatment effects in Eastern Africa. Data set uncoded. Data set. Zenodo. 2023. Publisher Full Text\n\nDahlgren A, Semakula D, Oxman A, et al.: Study protocol: Assessment of validity and reliability of a questionnaire based on the Claim Evaluation Tools Item bank in Uganda, Kenya and Rwanda. Dataset. Zenodo. 2023. Publisher Full Text\n\nDahlgren A: Critical thinking about treatment effects in Eastern Africa. The Critical Thinking about Health test (before Rasch analysis). Zenodo. 2023. Publisher Full Text\n\nDahlgren A: Critical thinking about treatment effects in Eastern Africa. The Critical Thinking about Health test. Zenodo. 2023. Publisher Full Text\n\nDahlgren A: Critical thinking about treatment effects in Eastern Africa: development and Rasch analysis of an assessment tool. STROBE checklist. Zenodo. 2023. Publisher Full Text" }	[ { "id": "244064", "date": "25 Mar 2024", "name": "Ngozika Esther Ezinne", "expertise": [ "Reviewer Expertise Eye", "Ocular surface diseases", "optometry", "ophthalmology and eye health" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Editor, Thanks for the opportunity to review the study. The study was interesting to read and had relevant information that can add to literature. Below are my comments. Introduction There was no clear justification for the need for the study. The aim of the study was not clearly stated.\n\nMethod The study failed to use method that is reproducible. Variations in the method used in recruiting participants and the population studied could create a bias that will make the findings from the study unreliable.\n\nMethod used in checking for fitness of the tool assessed was not well specified. Measures taken to ensure reliability of the tool was not clear. The study failed to provide information on how response dependency was checked and controlled. How dimensionality was measured was not clear. Scale of difficulty ranking was not provided. It is not clear if the findings from the study can be generalized since only three Eastern African countries were included in the study.\nOverall, the study findings are relevant and can add to the existing literature. However, it is not suitable in its current form. I therefore recommend major revision.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-887
https://f1000research.com/articles/12-886/v1	26 Jul 23	{ "type": "Case Report", "title": "Case Report: Ayurvedic Vamana and Virechana treatment in hypothyroidism and conception in a woman seeking infertility treatment at an ART clinic", "authors": [ "Vaishnavi Dhote", "Akash More", "Namrata Chaudhari", "Shilpa Dutta", "Nancy Nair", "Vaishnavi Dhote", "Namrata Chaudhari", "Shilpa Dutta", "Nancy Nair" ], "abstract": "The most common condition impacting patients who present with ovulatory failure leading to infertility is hypothyroidism. Normal thyroxin levels and its milder counterpart, subclinical hypothyroidism, which is characterised by raised thyroid stimulating hormone (TSH) levels, may also be a factor in altered reproductive function. Conventional and persistent Panchkarma procedures, which include Vamana and Virechana Karma, foster wellness. Vamana and Virechana Karma symbolise the development of emesis and purification, resulting in improvements in the body’s capacity to eradicate toxins, especially through the intestine. Sroto shodhaka, Agnivardhaka, and dosha pratyanika chikitsa are the best therapies for hypothyroidism, assuming the prevalence of the Kapha and Pitta doshas. We found that Vamana and Virechana helped in the treatment of hypothyroidism. We report a case highlighting the beneficial effects of ayurvedic treatment of Vamana and Virechana in a woman with hypothyroidism seeking infertility treatment at our centre.", "keywords": [ "Hypothyroidism", "infertility", "Vamana", "ovulatory dysfunction", "Thyroxine" ], "content": "Introduction\n\nInfertility is defined as a failure to get pregnant after twelve months for women over the age of 30-40 or after one year of regular, unprotected sexual intercourse.1 Over the past several decades, the thyroid-stimulating hormone (TSH) was diagnosed to have a role in reproductive issues such as ovulatory dysfunction, infertility, miscarriage, and harmful maternal problems (gestational hypertension, preeclampsia, anaemia).2 Numerous studies have connected the physiology of reproduction, ovarian function, and thyroid function.3 The menstrual cycle, oestrogen and androgen metabolism, folliculogenesis, and endometrial receptivity may all be affected by TSH.4 The mainstream Indian medical practice referred to as Ayurveda continues to be among the oldest remaining common with an extensive intellectual and experimental foundation.5 The three fundamental ideas, known as doshas (vata, pitta, and kapha), are drawn from the five components of studies. Vata and its sub-doshas regulate input/output processes and motion. Pitta and its sub-doshas regulate throughtout, turnover, and thus energy, and Kapha and its sub-doshas regulate storage, structure, and lubrication. These fundamental physiological processes in living systems maintain their identity throughout their life history.6 Several instances of lifestyle disorders include diabetes insipidus, hypertension, and thyroid dysfunction. Thyroid disease is becoming more prevalent in society on a daily basis. In general population, hypothyroidism affects 3.8–6% of people.7 There are two types of thyroid dysfunction: overactivity (hyperthyroidism) and underactivity (hypothyroidism). The thyroid gland produces insufficient thyroid hormone in hyperthyroidism.8 An underactive thyroid is a common description of hypothyroidism. A common problem in women is hypothyroidism, who tend to demonstrate ovulatory disorders leading to infertility. Subclinical hypothyroidism (SH), a modestly raised level of TSH, is a milder form of hypothyroidism. The most frequent side effects of hypothyroidism include infertility, weight issues, depression, and chronic fatigue.8 The guru (heaviness) attribute of the kapha dosha is present in SH. It also possesses the manda, or dullness, attribute. Reducing manda guna of the Kapha dosha should be the primary goal of ayurvedic treatment for thyroid problems like hypothyroidism.\n\nIn this case report, a 29-year-old woman with hypothyroidism who had been married for the previous seven years is featured. The patient TSH level returned to within tentative normal range after receiving Vamana Virechhana treatment to diagnosed her doshas, which contributed to deal with patient’s infertility difficulties and thus, resulted in a positive clinical pregnancy.\n\n\nCase presentation\n\nA 29-year-old South Asian woman who was a housewife by profession, with irregular menstrual cycles and infertility came to consult for her condition at our infertility centre. Thyroxine (T4) and triiodothyronine (T3) are the two main thyroid hormones that are inadequately produced by the thyroid gland in hypothyroidism. These hormones are crucial for controlling metabolism and maintaining the normal functioning of several organs and bodily systems.\n\nPatient husband worked as a businessman. They were married for five years with no earlier conception. They were diagnosed with primary infertility. The family medical record reveals that there were no history of smoking, alcoholism or any other substance use. However, the female patient had undergone cholecystectomy two years prior to seeking treatment for infertility. Treatment, although the thyroxin medication was continued.\n\nThere was no family history of thyroid disease or any other affliction or disorder in the patient. Additionally, there was no history of infertility in the family.\n\nFemale examination\n\nAccording to laboratory tests, patient TSH level was 7.91 mU/L, which was over the average limit that was applicable to TSH. This could indicate hypothyroidism. The research of the patient’s husband’s semen analysis discovered a 79 million/mL count and 85% motility. It demonstrates that her male partner was not a factor in the couple’s infertility. Further research on haemoglobin showed 14 g/dL in females. Both a urine test and fasting plasma glucose results were within normal range. The results obtained from the pelvic uterine ultrasound were normal, and the ovaries seemed to be in good health. The other parts of the clinical examination seen to be in normal condition. The thyroid hormone, also known as profile (T3, T4, anti-thyroid peroxidase (Anti-TPO), and TSH was tested using an access immunoassay equipment. In addition, a urine test and fasting plasma glucose results were within normal range. The results of the pelvic uterine ultrasound were normal, and the ovaries appeared in optimal condition. The rest of the clinical examination average appeared to be in normal condition. The thyroid hormone profile (T3, T4, anti-thyroid peroxidase (Anti-TPO)) was tested using an access immunoassay instrument. T3 reported hormonal profile was 0.50 ng/mL, while T4 was four g/dL. T3 reported hormonal profile was 0.50 ng/mL, whereas T4 was 4 g/dL.\n\nAn important biomarker for determining a woman’s ovarian reserve is AMH (anti-Mullerian hormone).9 A normal ovarian reserve is often predicted by serum AMH levels between 2 to 6.8 ng/mL. The patient’s serum AMH value in our case study was 2.6 ng/mL. TSH levels of 15.91 mIU/L, FSH (follicle stimulating hormone) levels of 4.86 mIU/mL, oestrogen levels of 515.525 pg/mL, and LH (luteinizing hormone) levels of 8.85 IU/mL were identified in the patient’s hormonal level.\n\nPerformance quality of TSH hormones was determined using a quality control serum (Lyphocheck - Immunoassay Additionally from Bio-Rad, Hercules, CA). Anti-TPO antibody levels were greater than 30 nmol/L, and the T4 level was 0.8 ng/dL; T3 levels were below 100 ng/dL.\n\nSupplying of thyroid supplement however, didn’t result in considerable improvement in our patient. Hence, we opted for ayurvedic medications. We advised the patient to start with Go Ghrita 25 mL once a day on an empty stomach at around 7 am every day. The dosage was recommended to be gradually increased to 20 mL till the seventh day of the treatment. She was also advised medications for Vamana in the combination of Madan-Phal Pippali Churna 5 g along with Saindhava Lavana 1 g and honey 10 g once a day around 7 am on an empty stomach. For virechana medication, a combination of Kwath made from Draksha Churna 18 g, Aragwadha Churna 18 g, Haritiki Churna 20 g, Kutaki Churna 10 g in 500 mL of water, reducing it to 55 mL with Erand Tailam 40 mL, was advised to be taken in the evening. This treatment was advised to be followed for 30 days. After 30 days of treatment, we conducted a laboratory investigation of her thyroid profile again. Her TSH value was found to be 1.05 mIU/mL. This value indicated a normal thyroid parameter. We then planned to do further IVF treatment on the patient. ATSH was reduced to 3.73 mIU/L with the administration of 125 mcg of thyroid supplement tablets over a year in previous treatments.\n\nShe was started with a short antagonist protocol where in we started GnRH, clomiphene citrate and letrozole on the first day of her menstrual cycle. On day 13 of her menstrual cycle, we triggered the patient with HCG for the final preparation of ovum pickup (OPU). The maturation of follicles was observed via ultrasonography. Then, 36 hours after the trigger, we performed the OPU procedure on the patient. Four MII oocytes were retrieved during the procedure, and we then performed ICSI (intra-cytoplasmic sperm injection) on the oocytes. We conducted a fresh embryo transfer for the patient.\n\nThe patient was discharged after the embryo transfer went smoothly, with the recommendation to follow up. She was also instructed on the administration of intralipid injection, 500 mg of hydroxyprogesterone, and injectable human chorionic gonadotrophin (HCG). After two weeks had passed since the embryo transfer, we took a blood sample from the patient and sent it to our lab centre in Wardha for an HCG test. The final report was favourable, positive for pregnancy. The quantity of -HCG was 1150 mlU/mL, which indicates a positive clinical pregnancy outcome.\n\n\nDiscussion\n\nExcessive hypothyroidism often results in infertility and delayed implantation. The direct effects that thyroid hormones have on oocytes indicate that they directly interfere with the normal function of the ovaries. They have an impact on how LH and FSH, which are used for the treatment of granulosa cell function, are controlled. Trophoblast differentiation function assists to maintain the foetal placenta’s integrity and protects against conceptus loss before birth.8\n\nHypothyroidism can be recognised according to the Ayurvedic perspective as a broad spectrum of afflication encompassing Kapha dusti (Kapha, one of Ayurveda’s three doshas, is associated with the elements of earth and water. The body’s lubrication, structure, and stability are all under its control, and an imbalance in Kapha can make one feel heavy and exhausted). Rasa Dhatu dusti (imbalance of plasma tissue), Udanavruta Samana (the Sanskrit word “Udanavruta Samana” can be found in the medication system known as Ayurveda. It represents a specific type of pranayama, or breath control method, used to balance and integrate the body’s energies. The breath is directed upward and outward in Udanavruta Samana, releasing the “udana” energy and nurturing balance), Kaphavruta Samana, Agnimandya (slowness of digestion, loss of appetite), Kaphaja galaganda (Dysentry phlegm mumps), among others. The clinical presentation resembles the Kapha-associated Pitta dusti with vitiation of Vata spurred on by Margavarana and predominantly Rasavaha and Medovaha srotodusti lakshans, which are frequently categorised as Bahudoshavastha.10 If hypothyroidism gets treated early, it can have a significant impact on the speed at which women with thyroid antibodies become pregnant (on average, three to four years later), as well as the probability the pregnancy will be miscarried.11 Considering its high prevalence in infertile women, hypothyroidism should be ruled out during general examination as often as possible. After a few attempts, we treated the patient with an Ayurvedic treatment named Kapha dosha. Guru, which means heaviness, is a characteristic of the Kapha dosha. Additionally, it had the manda, or dullness, attribute. Reducing manda guna of the Kapha dosha should be the main goal of ayurvedic treatment for thyroid disorders, including hypothyroidism. By getting TSH levels in the normal range, our patient’s SH was cured.6 It is important that TSH levels are in the normal range (0.5 to 5.0 mLU/L) for successful conception.\n\nConventionally and persistent Panchkarma procedures, which include Vamana and Virechana Karma, foster wellness.12 Vamana and Virechana Karma symbolise the development of emesis and purgation, resulting in improvements in the body’s capacity to eradicate toxins, especially through the intestine. This Karma tends to be classified into three categories: Mridu (mild), Madhya (middle), and Tikshna (strong), depending on the level of severity of the process. These Karma are additionally taken out in three steps: Poorva Karma, Pradhan Karma, and Pashchat Karma, much like other Karma. Before conducting this Karma, Sneha Pana, fomentation, and oil massage are recommended to liquefy Dosha and toxins. Sroto shodhaka, Agnivardhaka, and dosha pratyanika chikitsa are the best therapies for hypothyroidism, assuming the prevalence of the Kapha and Pitta doshas.13\n\nThis formed the preliminary basis of our application of Vamana and Virechana medication in our patient. It was observed that patient thyroid profile was significantly improved upon the administration of ayurvedic medication, which resulted in a positive clinical pregnancy outcome.\n\n\nConclusions\n\nThis case report examined the impact of ayurvedic Vamana and Virechana medication for the treatment of hypothyroidism, which resulted in infertility in our patient. Our result indicated that there was considerable significant improvement in the levels of TSH, which is a prerequisite factor for the determination of thyroid profile. Performing IVF treatment in our patient resulted in positive clinical pregnancy outcome.\n\nThe study highlights the beneficial effects of Ayurveda an antiquated technique. We should carefully consider this particular concept.\n\n\nConsent\n\nThe couple registered in our infertility clinic gave their written informed consent for the publication of this case report.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article, and no additional data sources are required.\n\n\nReferences\n\nVander Borght M, Wyns C: Fertility and infertility: Definition and epidemiology. Clin. Biochem. 2018; 62: 2–10. Publisher Full Text\n\nSwathi Nayak C, Sandyashree PK: Clinical study of thyroid dysfunction in pregnant women and its effect on maternal and fetal outcome.\n\nKrassas GE, Poppe K, Glinoer D: Thyroid function and human reproductive health. Endocr. Rev. 2010; 31: 702–755. Publisher Full Text\n\nZhou D, Deng H, Xia M, et al.: The relationship between TSH levels and clinical pregnancy outcomes for patients who undergo in vitro fertilization/intracytoplasmic sperm injection: a retrospective study. Transl. Pediatr. 2022; 11(8): 1301–1310. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChauhan A, Semwal D, Mishra S, et al.: Ayurvedic research and methodology: Present status and future strategies. AYU (An International Quarterly Journal of Research in Ayurveda). 2015; 36(4): 364. Publisher Full Text\n\nKumar S, Dobos GJ, Rampp T: The Significance of Ayurvedic Medicinal Plants. J. Evid. Based Complementary Altern. Med. 2017; 22: 494–501. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShilpa S, Venkatesha MC: Understanding personality from Ayurvedic perspective for psychological assessment: A case. AYU (An International Quarterly Journal of Research in Ayurveda). 2011; 32(1): 12–19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKoyyada A, Orsu P: Role of hypothyroidism and associated pathways in pregnancy and infertility: Clinical insights. Tzu Chi Med. J. 2020; 32: 312. Publisher Full Text\n\nIwase A, Nakamura T, Osuka S, et al.: Anti-Müllerian hormone as a marker of ovarian reserve: What have we learned, and what should we know? Reprod. Med. Biol. 2016; 15(3): 127–136. Publisher Full Text\n\nMisriya KH, Bhagyashree, Desai AS, et al.: Effect of Vasanthika Vamana Karma on TSH levels - A Successful Case Series. AYUSHDHARA. 2022; 9(Suppl2): 19–23. Publisher Full Text\n\nAlexander EK, Pearce EN, Brent GA, et al.: 2017 Guidelines of the American Thyroid Association for the Diagnosis and Management of Thyroid Disease during Pregnancy and the Postpartum. Thyroid. 2017; 27(3): 315–389. PubMed Abstract \| Publisher Full Text\n\nBhatted S, Thakar A, Shukla V, et al.: A study on Vasantika Vamana (therapeutic emesis in spring season) - A preventive measure for diseases of Kapha origin. AYU (An International Quarterly Journal of Research in Ayurveda). 2011; 32(2): 181–186. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMehta A, Parwe S: Evaluation of Vamana and Virechana Karma in the Treatment of Hypothyroidism – A Study Protocol. J. Pharm. Res. Int. 2021; 161–169. Publisher Full Text" }	[ { "id": "200039", "date": "11 Sep 2023", "name": "Soni Kapil", "expertise": [ "Reviewer Expertise Ayurvedic obstetrics and gynaecology 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 congratulate the authors for doing good work in the case of infertility associated with hypothyroidism, but a few essential details are missing from the research paper:\nHow did the authors determine that cycles of female were anovulatory without describing the report of follicular study?\n\nTreatment protocol followed for Vaman and Virechan is not in relevance with textual description.\n\nDiscussion part is inadequate to describe rationality of selection of treatment protocol and its relevance in present case.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] }, { "id": "336431", "date": "06 Nov 2024", "name": "S Prashanth", "expertise": [ "Reviewer Expertise AYUSH", "Yoga and Naturopathy", "Complimentary system of medicine", "Acupuncture", "Massage" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIntroduction: The age of women facing infertility is mentioned as 30-40 years; your patient is 29 years old and has been having issues for the past 5 years, which means she has been infertile for the last 4 years, Kindly clarify this with proper references. mention clearly on the prevalence and clear background only related to \"women-hypothyroidism-primary infertility-Ayurveda\". General comments: 1. it would be better if the possible mechanisms of the interventions used were included. 2. Could you explain why the patient suggested IVF directly once the thyroid profile normalizes? 3. If the patient takes clomiphene citrate and letrozole tablets, what is the role of ayurvedic management? 4. Is the IVF procedure carried out by an expert? mention it. 5. The conclusion and background of the study did not match; the background says about thyroid and infertility, whereas the conclusion mentioned performing IVF treatment. - clarify the difference and change accordingly. 6. clarify - whether the ART clinic is an integrated clinic or the ayurvedic and IVF management given in different setups. 7. kindly mention the data - date of pre-assessment, duration of intervention, post-assessment, follow-up, and successful delivery of the baby.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-886
https://f1000research.com/articles/12-884/v1	25 Jul 23	{ "type": "Data Note", "title": "The identification of high-performing antibodies for Charged multivesicular body protein 2b for use in Western Blot, immunoprecipitation and immunofluorescence", "authors": [ "Walaa Alshafie", "Maryam Fotouhi", "Riham Ayoubi", "Irina Shlaifer", "Kathleen Southern", "Peter S. McPherson", "Carl Laflamme", "NeuroSGC/YCharOS/EDDU collaborative group", "Walaa Alshafie", "Maryam Fotouhi", "Riham Ayoubi", "Irina Shlaifer", "Kathleen Southern", "Peter S. McPherson" ], "abstract": "Charged multivesicular body protein 2B is a subunit of the endosomal sorting complex required for transport III (ESRCT-III), a complex implicated in the lysosomal degradation pathway and formation of multivesicular bodies. Mutations to the CHMP2B gene can result in abnormal protein aggregates in neurons and is therefore predicted to be associated in neurodegenerative diseases, including across the ALS-FTD spectrum. Through our standardized experimental protocol which compares read-outs in knockout cell lines and isogenic parental controls, this study aims to enhance the reproducibility of research on this target by characterizing eight commercial antibodies against charged multivesicular body protein 2b using Western Blot, immunoprecipitation, and immunofluorescence. 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 Q9UQN3", "CHMP2B", "Charged multivesicular body protein 2b", "antibody characterization", "antibody validation", "Western Blot", "immunoprecipitation", "immunofluorescence" ], "content": "Introduction\n\nCharged multivesicular body protein 2B, encoded by the CHMP2B gene, is a core component of the endosomal sorting complex required for transport III (ESCTR-III) which plays a pivotal role in the biogenesis of multivesicular bodies (MVB) and is thus involved in endocytic trafficking of proteins.1 MVB’s are late endosomes formed by scission of intraluminal vesicles from the limiting membrane of the endosome to then deliver cargo proteins to the lysosome, enabling degradation of membrane proteins.2,3 As a subunit of the ESCRT-III complex, Charged multivesicular body protein 2 is essential to the pathway of lysosomal degradation.\n\nMutations to the CHMP2B gene have been predicted to be associated with amyotrophic lateral sclerosis (ALS)4 and frontotemporal dementia (FTD).5 Affected neurons having abnormal ubiquitin-positive protein deposits which can be attributed to dysfunctional lysosomal degradation.1\n\nCHMP2B mutations related to the ALS-FTD spectrum have advanced the understanding of the role endosomal-lysosomal and autophagic dysregulation play in neurodegeneration.1 As the exact mechanisms remain unknown, the availability of high-quality Charged multivesicular body protein 2 antibodies would greatly facilitate mechanistic studies.\n\nHere, we compared the performance of a range of commercially available antibodies for Charged multivesicular body protein 2b and identified high-performing antibodies for Western Blot, immunoprecipitation and immunofluorescence, enabling biochemical and cellular assessment of Charged multivesicular body protein 2 properties and function.\n\n\nResults and discussion\n\nOur standard protocol involves comparing readouts from wild-type (WT) and knockout (KO) cells.6,7 To identify a cell line that expresses adequate levels of Charged multivesicular body protein 2b protein to provide sufficient signal to noise, we examined public proteomics databases, namely PaxDB8 and DepMap.9 U2OS was identified as a suitable cell line and thus U2OS was modified with CRISPR/Cas9 to knockout the corresponding CHMP2B gene (Table 1).\n\nFor Western Blot experiments, we resolved proteins from WT and CHMP2B KO cell extracts and probed them side-by-side with all antibodies in parallel (Figure 1).7,10–19\n\nLysates of U2OS (WT and CHMP2B KO) were prepared and 50 μg of protein were processed for Western Blot with the indicated Charged multivesicular body protein 2b 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. When the concentration was not indicated by the supplier, which was the case for antibody MA5-21591, the antibody was tested at 1/1000. Antibody dilution used: MAB7509 at 1/400; MA5-21591* at 1/1000; MA5-36184 at 1/500; ab157208 at 1/1000; 76173** at 1/1000; GTX118181 at 1/1000; GTX109610 at 1/1000; A13410 at 1/500. Predicted band size: 24 kDa. Monoclonal antibody; Recombinant antibody.\n\nFor immunoprecipitation experiments, we used the antibodies to immunopurify Charged multivesicular body protein 2b from U2OS cell extracts. The performance of each antibody was evaluated by detecting the Charged multivesicular body protein 2b protein in extracts, in the immunodepleted extracts and in the immunoprecipitates (Figure 2).7,10–19\n\nU2OS lysates were prepared, and IP was performed using 1.0 μg of the indicated Charged multivesicular body protein 2b antibodies pre-coupled to Dynabeads protein G or protein A. Samples were washed and processed for Western Blot with the indicated Charged multivesicular body protein 2b antibody. For Western Blot, ab157208* was used at 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.20 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\nU2OS WT and CHMP2B 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 Charged multivesicular body protein 2b antibodies and with the corresponding Alexa-fluor 555 coupled secondary antibody including DAPI. Acquisition of the blue (nucleus-DAPI), green (WT), red (antibody staining) and far-red (KO) channels was performed. Representative images of the merged blue and 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 to antibodies ab157208* and A13410, which were titrated to 1/1000 and 1/800, respectively, as the signals were too weak when following the suppliers' recommendations. When the concentration was not indicated by the supplier, which was the case for antibodies MA5-21791* and 76173, we tested antibodies at 1/500. At this concentration, the signal from each antibody was in the range of detection of the microscope used. Antibody dilution used: MAB7509 at 1/500; MA5-21591* at 1/500; MA5-36184 at 1/1000; ab157208 at 1/100; 76173** at 1/500; GTX118181 at 1/500; GTX109610 at 1/1000; A13410 at 1/800. Bars=10 μm. Monoclonal antibody; Recombinant antibody.\n\nIn conclusion, we have screened Charged multivesicular body protein 2b 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.21,22\n\n\nMethods\n\nAll Charged multivesicular body protein 2b antibodies are listed in Table 2, together with their corresponding Research Resource Identifiers, or RRID, to ensure the antibodies are cited properly.23 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\nCell lines used are listed in Table 1. U2OS CHMP2B KO clone was generated with low passage cells using an open-access protocol available on Zenodo.org. The sequence of the guide RNA is the following: CCAAACAACUUGUGCAUCUA.\n\nBoth U2OS WT and CHMP2B KO cell lines used are listed in Table 1, together with their corresponding RRID, to ensure the cell lines are cited properly.24 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.25 U2OS WT and CHMP2B KO were collected in RIPA buffer (25 mM Tris-HCl pH 7.6, 150 mM NaCl, 1% NP-40, 1% sodium deoxycholate, 0.1% SDS) (Thermo Fisher Scientific, cat. number 89901) supplemented with 1× protease inhibitor cocktail mix (MilliporeSigma, cat. number P8340). Lysates were sonicated briefly and incubated for 30 min on ice. Lysates were spun at ~110,000 × g for 15 min at 4°C and equal protein aliquots of the supernatants were analyzed by SDS-PAGE and Western Blot. BLUelf prestained protein ladder (GeneDireX, cat. number PM008-0500) was used.\n\nWestern Blots were performed with large 4-20% 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 Signalling Technology, cat. number 9997). Following three washes with TBST, the peroxidase conjugated secondary antibody was incubated at a dilution of ~0.2 μg/mL in TBST with 5% milk for 1 hr at room temperature followed by three washes with TBST. Membranes were incubated with Pierce ECL (Thermo Fisher Scientific, cat. number 32106) prior to detection with the HyBlot CL autoradiography films (Denville, cat. number 1159T41).\n\nImmunoprecipitation was performed as described in our standard operating procedure.26 Antibody-bead conjugates were prepared by adding 1 μg or 2 μL of antibody at an unknown concentration to 500 μL of Pierce IP Lysis Buffer (Thermo Fisher Scientific, cat. number 87788) in a 1.5 mL microcentrifuge tube, together with 30 μL of Dynabeads protein A - (for rabbit antibodies) or protein G - (for mouse antibodies) (Thermo Fisher Scientific, cat. number 10002D and 10004D, respectively). Pierce IP Lysis Buffer was supplemented with the Halt Protease Inhibitor Cocktail 100X (Thermo Fisher Scientific, cat. number 78446) at a final concentration of 1×. Tubes were rocked for ~2 hrs at 4°C followed by several washes to remove unbound antibodies.\n\nU2OS WT were collected in Pierce IP buffer (25 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% NP-40 and 5% glycerol) supplemented with protease inhibitor. Lysates were rocked for 30 min at 4°C and spun at 110,000 × g for 15 min at 4°C. 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 IP lysis buffer and processed for SDS-PAGE and Western Blot on a 4-20% polyacrylamide gels. Prot-A:HRP (MilliporeSigma, cat. number P8651) was used as a secondary detection system at a dilution of 0.4 μg/mL for an experiment where a rabbit antibody was used for both immunoprecipitation and its corresponding immunoblot.\n\nImmunofluorescence was performed as described in our standard operating procedure.7,10–20 U2OS WT and CHMP2B KO were labelled with a green and a far-red fluorescence dye, respectively (Thermo Fisher Scientific, cat. number C2925 and C34565). The nuclei were labelled with DAPI (Thermo Fisher Scientific, cat. number D3571) fluorescent stain. WT and KO cells were plated on glass coverslips as a mosaic and incubated for 24 hrs in a cell culture incubator at 37oC, 5% CO. Cells were fixed in 4% paraformaldehyde (PFA) (Beantown chemical, cat. number 140770-10 ml) in phosphate buffered saline (PBS) (Wisent, cat. number 311-010-CL). Cells were permeabilized in PBS with 0.1% Triton X-100 (Thermo Fisher Scientific, cat. number BP151-500) for 10 min at room temperature and blocked with PBS containing 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 Charged multivesicular body protein 2b 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 63× 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 Charged multivesicular body protein 2b, https://doi.org/10.5281/zenodo.6370501. 21\n\nZenodo: Dataset for the Charged multivesicular body protein 2b antibody screening study, https://doi.org/10.5281/zenodo.8139356. 22\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 and Kathleen Southern.\n\nThank you to the Structural Genomics Consortium, a registered charity (no. 1097737), for your support on this project. The Structural Genomics Consortium receives funding from Bayer AG, Boehringer Ingelheim, Bristol-Myers Squibb, Genentech, Genome Canada through Ontario Genomics Institute (grant no. OGI-196), the EU and EFPIA through the Innovative Medicines Initiative 2 Joint Undertaking (EUbOPEN grant no. 875510), Janssen, Merck KGaA (also known as EMD in Canada and the United States), Pfizer and Takeda.\n\nAn earlier version of this of this article can be found on Zenodo (doi: 10.5281/zenodo.6370501).\n\n\nReferences\n\nUgbode C, West RJH: Lessons learned from CHMP2B, implications for frontotemporal dementia and amyotrophic lateral sclerosis. Neurobiol. Dis. 2021; 147: 105144. Publisher Full Text\n\nLi X, Bao H, Wang Z, et al.: Biogenesis and Function of Multivesicular Bodies in Plant Immunity. Front. Plant Sci. 2018; 9: 979. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPiper RC, Katzmann DJ: Biogenesis and function of multivesicular bodies. Annu. Rev. Cell Dev. Biol. 2007; 23: 519–547. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nParkinson N, Ince PG, Smith MO, et al.: ALS phenotypes with mutations in CHMP2B (charged multivesicular body protein 2B). Neurology. 2006; 67(6): 1074–1077. PubMed Abstract \| Publisher Full Text\n\nSkibinski G, Parkinson NJ, Brown JM, et al.: Mutations in the endosomal ESCRTIII-complex subunit CHMP2B in frontotemporal dementia. Nat. Genet. 2005; 37(8): 806–808. PubMed Abstract \| Publisher Full Text\n\nLaflamme C, McKeever PM, Kumar R, et al.: Implementation of an antibody characterization procedure and application to the major ALS/FTD disease gene C9ORF72. elife. 2019; 8: 8. Publisher Full Text\n\nAlshafie W, Fotouhi M, Shlaifer I, et al.: Identification of highly specific antibodies for Serine/threonine-protein kinase TBK1 for use in immunoblot, immunoprecipitation and immunofluorescence. F1000Res. 2022; 11: 977. Publisher Full Text\n\nWang M, Herrmann CJ, Simonovic M, et al.: Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics. 2015; 15(18): 3163–3168. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDepMap, Broad: DepMap 19Q3 Public ed.2019.\n\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\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\nAyoubi R, Alshafie W, Shlaifer I, et al.: The identification of high-performing antibodies for Sequestosome-1 for use in Western blot, immunoprecipitation and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 324. Publisher Full Text\n\nAyoubi R, McDowell I, Fotouhi M, et al.: The identification of high-performing antibodies for Profilin-1 for use in Western blot, immunoprecipitation and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 348. Publisher Full Text\n\nMcDowell I, Ayoubi R, Fotouhi M, et al.: The identification of high-preforming antibodies for Ubiquilin-2 for use in Western Blot, immunoprecipitation, and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 355. Publisher Full Text\n\nAlshafie W, Fotouhi M, Ayoubi R, et al.: The identification of high-performing antibodies for RNA-binding protein FUS for use in Western Blot, immunoprecipitation, and immunofluorescence [version 1; peer review: 1 approved with reservations]. F1000Res. 2023; 12: 376. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAyoubi R, Alshafie W, Southern K, et al.: The identification of high-performing antibodies for Coiled-coil-helix-coiled-coil-helix domain containing protein 10 (CHCHD10) for use in Western Blot, immunoprecipitation and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 403. 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: awaiting peer review]. F1000Res. 2023; 12: 277. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAyoubi R, Fotouhi M, Southern K, et al.: The identification of high-performing antibodies for Vacuolar protein sorting-associated protein 35 (hVPS35) for use in Western Blot, immunoprecipitation and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 452. Publisher Full Text\n\nAyoubi R, Alshafie W, You Z, et al.: The identification of high-performing antibodies for Superoxide dismutase [Cu-Zn] 1 (SOD1) for use in Western blot, immunoprecipitation, and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 391. Publisher Full Text\n\nAlshafie W, McPherson P, Laflamme C: Antibody screening by Immunofluorescence. Zenodo. 2021. Publisher Full Text\n\nFotouhi M, Alshafie W, Shlaifer I, et al.: Antibody Characterization Report for Charged multivesicular body protein 2b. [Dataset]. Zenodo. 2022. Publisher Full Text\n\nSouthern K: Dataset for the Charged multivesicular body protein 2b antibody screening study [Dataset]. 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. 2022; 51: D358–D367. Publisher 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. Zenodo. 2021. Publisher Full Text\n\nAyoubi R, Fotouhi M, McPherson P, et al.: Antibody screening by Immunoprecitation. Zenodo. 2021. Publisher Full Text" }	[ { "id": "190521", "date": "08 Aug 2023", "name": "Emma L. Clayton", "expertise": [ "Reviewer Expertise Neurodegeneration", "Membrane trafficking", "Synaptopathy" ], "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 line with the remit of the YCharOS (antibody characterisation through open science) initiative which seeks to characterise commercially available antibodies for every human protein, Alshafie et al. have compared the ability of a range of commercially available antibodies to detect CHMP2B by western blotting and immunofluorescence. The model used for these validation experiments (U2OS) was selected as a line known to express adequate levels of CHMP2B to provide sufficient signal to noise. Antibody validation was complemented through use of CRISPR/Cas9 knockout to generate CHMP2B deficient control lines.\nThis work is extremely helpful for researchers looking to source the best commercially available antibody to investigate their protein of interest, in particular the use of KO lines as a control to fully validate the specificity of the bands seen on the western blot images is powerful. The inclusion of the ponceau membranes to show protein transfer, and the inclusion of the whole length of the blot (to show non-specific bands) is a thorough and informative presentation of the antibody validation.\nFor the immunofluorescence data, the mosaic plating of the cells to allow the direct comparison of staining in adjacent cells allows for direct comparison and removes any variability due to differences in the staining protocol between conditions. This makes the comparisons between cells extremely powerful within images.\nI could suggest two additions to the paper that would be interesting for researchers looking at CHMP2B and would add to the general usefulness of this antibody insight for the research community.\nCHMP2B is generally cytosolic, and is temporarily recruited to the ESCRT-III complex to facilitate membrane invagination prior to VPS4 recruitment which then allows for membrane scission and ESCRT-III disassembly. When VPS4 is not fusion competent, CHMP2B is held in punctate structures in the cell1. In the immunofluorescence images in this article, the CHMP2B looks highly cytosolic as expected, however the adjacent KO cells don’t look particularly different to the WT cells. It is hard to see what is specific staining over background noise. To make this immunofluorescence antibody validation useful for the research community, inducing the punctate localisation of CHMP2B would be useful, in order to show true antibody specificity.\nI would also suggest adding the recognition sequences for the antibodies. This would be helpful in the case of mutations in CHMP2B which are associated with frontotemporal dementia and amyotrophic lateral sclerosis2. In particular, the mutation of CHMP2B associated with a familial form of frontotemporal dementia results in a C terminally truncated form of the protein3. If the antibody recognition sequence resides within the truncated portion of the protein (as we have unfortunately encountered in the past with CHMP2B antibodies), then the usefulness of an otherwise “good” CHMP2B antibody is compromised. Thus this information would be helpful for the research community interested in CHMP2B in neurodegenerative disease.\nIn summary however, this paper is a powerful resource for any researchers looking to work with wildtype CHMP2B. The detailed methods (with antibody dilutions and table of research resource identifiers) and in particular the powerful direct comparisons of WT and KO by western blotting provide high confidence in commercial antibody choice for a researcher looking to select an antibody for CHMP2B research.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] }, { "id": "196057", "date": "23 Aug 2023", "name": "Xiao-Xin Yan", "expertise": [ "Reviewer Expertise Neurodevelopment", "brain aging", "Alzheimer's 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\nThis manuscript reports the characterization of CHMP2B antibodies for the use in Western Blot, immunoprecipitation and immunofluorescence. Good CHMP2B antibodies would be very useful for study of not only ALS-FTD disorders as the authors indicated, but also for other neurodegenerative diseases or conditions, such as aging and AD-related formation of granulovacuolar degeneration (GVD) (Jiang et al., 20221). The utility of the antibodies in immunoprecipitation is particularly informative for research into potential interplay between CHMP2B and other molecular partners in the neuroscience field. I would appreciate if the authors could extend some more relavence either in the introduction or discussion on CHMP2B in relevance to GVD formation or protein sorting in neurodegeneratrive disorders.\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/12-884
https://f1000research.com/articles/12-882/v1	25 Jul 23	{ "type": "Research Article", "title": "The trend of oral cancer screening in Bangladesh, perceptions, and risk factors: a model comparison approach", "authors": [ "Irin Yasmin", "Md. Shahariar Rokon", "Elnaz Illias", "Md. Nafiul Alam Khan", "Md. Mahbub Alam", "Mohammad Delwer Hossain Hawlader", "Rajib Kumar Malakar", "Faroque Md. Mohsin", "Irin Yasmin", "Md. Shahariar Rokon", "Elnaz Illias", "Md. Nafiul Alam Khan", "Md. Mahbub Alam", "Mohammad Delwer Hossain Hawlader", "Rajib Kumar Malakar" ], "abstract": "Background: Oral cancer (OC) is a leading cause of death among cancer patients and a major public health concern in Bangladesh. Timely OC screening can help in the early detection of OC and could reduce the mortality rate in Bangladesh. We aimed to assess the tend of OC screening, perception and risk factors among dental patients. Methods: This was a facility-based cross-sectional study among 423 participants with dental problems using a convenience sampling technique. The collected data were analyzed by IBM SPSS 25 and various statistics, such as the chi-squared test, Poisson regression, logistic regression, etc., were used to attain the objectives. Results: Only 2.4% of the study participants underwent OC screening before the study period. The use of smokeless tobacco and smoking were significantly associated with the tend of OC screening. According to the Poisson model, previous smokeless tobacco users were 5 times (odds ratio (OR): 5.403, P<0.05) more likely than non-users to go for OC screening, which was 8 times (OR: 7.729, P=0.033) for the binary logistic regression. Having a family history of OC increased the odds of receiving an OC screening by nine times (OR: 9.544, P<0.002) compared to individuals without a family history of OC; it was 16 times (OR: 16.438, P=0.001) for the binary logistic regression. Conclusions: This study shows former smokeless tobacco users and past smokers are more likely to uptake OC screening than non-users. In addition, patients having a family history of OC increased the odds of receiving OC screening than subjects without a family history of OC. The lack of OC screening in Bangladesh highlights the need to implement a national-level screening program to help with the early diagnosis of OC and its prevention.", "keywords": [ "Oral cancer screening", "Risk factors", "Tobacco", "Model comparison approach", "Bangladesh" ], "content": "Introduction\n\nOral cancer (OC), comprising lip, tongue, and mouth cancers, collectively represents one of the most common cancers worldwide.1 As with other cancers, OC is a leading cause of death and a barrier to increasing life expectancy globally. A global estimate based on Global Statistics 2020 reports that nearly 377,713 new cases of OC were diagnosed in 185 countries, causing about 177,757 deaths and of which Asian countries accounted for almost two-thirds of all the new cases.2 Unfortunately, according to mouth and oral cancer statistics (2020), Bangladesh ranks second in terms of incidences of mouth and OC but first in deaths.3\n\nOC is a multifactorial disease associated with several risk factors including smoking,4–6 alcohol,1,4,6 human papillomavirus,1,6 smokeless tobacco,7,8 family history (first degree family members),9 and periodontal disease,1,10 while the smokeless tobacco practice and consumption of tobacco and alcohol are reasons that predispose the Asian population to OC.11 In fact, the prevalence of current tobacco use is 34.7% in Bangladesh,12 which is particularly worrying because tobacco use is one of the leading causes of OC.\n\nA number of studies suggest that a lack of early diagnosis and screening services, financial constraints, social and cultural factors, and lack of access to cancer services contribute to global disparities in OC outcomes.6,11,13–15 OC screening consists of a systematic clinical examination of the oral cavity, which includes examining the face, neck, lips, labial mucosa, buccal mucosa, gingiva, and the floor of the mouth, tongue, and palate.4 In order to prevent OC, early detection through screening is highly recommended by several studies,10,13,14 despite some controversy regarding the effectiveness of the assessment.6\n\nDetecting potential malignant lesions in the oral cavity can be done either by self-examination or clinical examination, making early detection more accessible and accurate. Subsequently, this can significantly reduce OC diagnostic delays quite often.6,13,16 Dental providers remain alert for signs of potentially malignant lesions or early-stage cancer in patients during routine oral examinations in practice. Cancer screening produces two special benefits which are “down-stage” and reduced mortality or morbidity. OC is particularly known for its premalignant phase, so the screening process is constructed to not only capture OC but also oral potentially malignant disorders, which are responsible for increasing the risk for OC.17\n\nA great deal of research on oral cancer screening has been conducted in many places like Europe,11 the USA,4 Africa,6 and India.13 At the same time, little work is being undertaken in Bangladesh despite the highest mortality and significant numbers of OC incidence. As a result, a remarkable improvement in screening rates for OC has not been achieved in Bangladesh. To our knowledge, there is a lack of literature that makes use of different statistical models to predict the variables influencing oral cancer screening.\n\nTo mitigate this concern, we can find ways to facilitate OC screening uptake in Bangladesh by exploring the status of OC screening and its potential associated variables. As a result, this study compares various regression models to find the odds of OC screening; those models were previously used in different studies for better understanding and outcomes.18–20\n\n\nMethods\n\nThis cross-sectional study was carried out among patients at National Healthcare Networks, Adabor Centre and Anan Specialised Dental Clinics, Uttara, Dhaka, Bangladesh. The inclusion criteria of the participants were (a) patient visited the center with dental problems, (b) age group > 18 years old, (c) willingly agreed to participate in the study.\n\nIn this study, we used convenience sampling method to collect our desired data. We used this method particularly for the lack of sampling frame, to reduce cost and time. By using formula, we obtained the minimum sample size required for the study.\n\nWhere is the sample size, z is the standard normal variate, p is the population’s percentage that possesses the attribute, and p + q = 1, and d is the largest error that can be made while predicting the population percentage. Considering the degrees of accuracy, d = 0.05, z = 1.96 and p = 0.34.12 Thus, we got the required sample size 342. However, for better understanding and analysis, we targeted more samples to be included. Thus, we gathered 423 unique samples.\n\nThe data collection was done by the research team. All of them are physicians and directly involved in study centers. Upon receiving written consent, data collectors were recorded patients’ sociodemographic data, clinical history and OC screening information upon inclusion criteria. Moreover, the supervisor randomly checked the collected data forms to avoid errors. For data collection, a semi-structured questionnaire was used that was developed based on previous studies.6,15 The questionnaire had three parts: the first part described the demographic characteristics of the respondents—the second part of the questionnaire, clinical information and healthcare utilisation and the last part-cancer screening data. Finally, we collected 423 data through face-to-face interviews (response rate: 98%) from the study hospitals between February to March 2022.\n\nThe dependent variable of this study was the presence of OC screening. We categorized the dependent variable into two categories. Which was defined as\n\nThe independent variables of the study were gender, age, marital status, education, occupation, living area, number of family members, monthly income, smokeless tobacco use (paansupari/jorda/tamak pata etc.), smoking status, dentist visit, last visit to the lentist, checkup routine, cost management for treatment, knowledge of OC, medium of getting information about OC, If the respondent had no idea about oral cancer (explain for the lack of knowledge), If OC screening test is free of cost, would the respondent examine or not, family history of OC. We used shortened names of the independent variables for analysis purposes and software restrictions (Table 1).\n\nAll statistical analysis was performed using R (R Core Team, 2020), RStudio (Rstudio Team, 2020), version 2021.9.1.372 and Statistical Packages for Social Science (SPSS) version 26. For background study or univariate analysis, we used frequency distribution. To measure the association between the response and the explanatory variable, we used the chi-square test.21 The expression is defined as10\n\nWhere, Aj observed and Bj expected cell frequencies. Furthermore, the test statistic follows chi-square distribution with (m-1) (n-1) degrees of freedom. Where m is the number of the categories of the covariate and n is the number of responses.\n\nIn order to find out the magnitude of the relationship between response and explanatory variable, we conducted three different regression models, namely Poisson regression, Binary logistic regression, Poisson regression with robust variance.\n\nThe binary logistic model is generally used for classification problems while utilizing maximum likelihood estimate.21 Let ai(i = 1, 2, …, n) be our outcome variable with categories 1, …, j, …, c and bi = (bi1, bi2, …, bin)’ as the column vector with k covariates. The expression is defined as22\n\nWhere ∇ represents probability of the event happening and 1−∇ represents probability of it not happening.\n\nPoisson regression20 is frequently used in epidemiology for longitudinal studies in which the outcome variable is the number of episodes of a disease that occur over time. The model formulation is23\n\nWhere n is the number of counts for given individual over time t. Xi is the model covariates and βi are the model parameters, also known as log relative risk. Previous studies showed significant improvement over general model using robust variance estimate and we used Poisson regression with robust variance.18,19 Finally, we compared these three models to using standard error and confidence interval of the estimates.\n\nThe written informed consent was obtained from each participant and the hospital authorities. Participants were assured that their personal information would remain confidential and be used only for academic purposes. In addition, participants were informed that they could withdraw at any time without negative consequences. The study protocol was approved by the Institutional Review Board of North South University in Bangladesh (Ref-2022/OR-NSU/IRB/1004).\n\n\nResults\n\nFor background study, we did frequency analysis to compare their frequencies and percentages, presented in Table 1. This table demonstrated that out of all respondents, 96.9% didn’t opt for OC screening, and only 2.4% had gone through the screening. Among our patients, 52% were females, and 48% were males. 83% of our patients were married, and we had only 16.1% of unmarried patients. Our responders were generally more educated (48.5%) than less educated (38%). Only 12.1% of the patients were self-employed, whereas 35.7% (151) were employed. Only 21.7% of respondents resided in rural areas, while 78.3% lived in cities. Only 17% of the respondents had ever used smokeless tobacco, while 23.6% were current users. More than half of the patients (53.7%) had a dental appointment the previous year compared to only 13.2% who had one within the last six months. Merely 12.3% of respondents reported seeing the dentist on a regular basis; the majority of respondents 73.8% only did so when they experienced dental problems. Most of the participants (96.2%) had no family history of oral cancer, and 68.3% of the patients were from lower-income groups. With a monthly income of more than BDT 400000, only 1.7% (7 of our respondents) were in the higher income group.\n\nInitially we performed chi-square test to determine whether our variables are associated with the dependent variable or not. In Table 2 we showed the results of the chi-square association test.\n\nWe were able to identify five significant variables that were related to our response variable using the chi-square test. We only selected these five variables to study further.\n\nTo determine the optimal result in this research, we applied three alternative regression models. In the first step, we used Poisson regression to find out the estimates as shown in the Table 3.\n\nWe discovered three statistically significant results in the Poisson regression model. Our model demonstrated that a person will be 98% (Odd Ratio (OR): 0.012, P < 0.000) less likely to opt for OC screening if all other variables remain constant. We also found that tobacco use significantly increased the odds of OC screening. According to the Poisson model, previous tobacco users were 5 (OR: 5.403, P < 0.05) times more likely than non-user to go for OC screening. Finally, having a family history of OC (FHO) increased the odds of OC screening by 9 (OR: 9.544, P < 0.002) times compared to people without a family history of OC.\n\nWe employed binary logistic regression to analyze the results in order to conduct further research. As indicated in Table 4 four statistically significant variables were discovered in our research based on the binary logistic regression. If all other variables remain constant, a person had almost no odds (OR: 0.009, P < 0.000) of OC screening. Additionally, binary logistic regression revealed that compared to non-users, previous tobacco use raised the odds of OC screening by a factor of up to 8 (OR: 7.729, P = 0.033). Also, family history of OC raised the odds of OC screening by 16 times (OR: 16.438, P = 0.001) than no family history of OC.\n\nThe findings were analyzed using Poisson regression with robust variance, as shown in Table 5. According to our model, the probabilities of going for OC screening were essentially zero if all other factors remained the same (OR: 0.012, P < 0.000). Four additional significant variables were also obtained by the Poisson model with robust variance. When compared to people who had never used tobacco, individuals who had a history of tobacco use had 5 (OR: 5.403, P = 0.05) times higher odds of OC screening. Additionally, former smokers had 2-fold higher likelihood of receiving an OC screening compared to non-users (OR: 2.342; P = 0.08 at the 10% significant level). Furthermore, our data showed that there were no odds of OC screening among those who occasionally visited the dentist for a checkup (Reason 2) (OR: 0.000, P = 0.000). Finally, having a family history of OC increased the odds of OC screening by 9 (OR: 9.544, P < 0.001) times that of those who had no family history of OC. It is evident that the findings of the Poisson regression and the Poisson regression with robust variance were the same, but they differed in the variance, standard error, and confidence interval of the estimates.\n\nFor better understanding and to find out the optimal model, we compared the odds and confidence interval of the odds ratio as represented in Table 6. The Poisson model produced significantly less standard error and provided narrower confidence intervals than the binary logistic regression, making it clear that it outperformed the latter by a wide margin. However, it becomes clear that the robust Poisson model performed significantly better than both the Poisson and the logistic regression models when compared to the Poisson model with robust variance.\n\nTable 6 shows that the confidence interval for the odds of past tobacco user is 0.934-31.266 for Poisson regression and 1.170-51.057 for logistic regression, but it becomes much narrower for robust Poisson regression at 0.988-29.552, indicating a better estimate interval. Additionally, the Poisson regression’s confidence interval for past “smoking” was 0.476-11.521, whilst the logistic regression’s range was 0.465-14.927. However, robust Poisson regression yielded a significantly narrower interval than those two, at 0.888-6.18. Likewise, the range of the logistic regression was 3.082-87.671, while the range of the Poisson regression’s confidence interval for FHO was 2.256-40.367. However, robust Poisson regression produced an interval that was 2.402-37.921, which was noticeably narrower than those two.\n\nRobust Poisson regression yielded a substantially lower standard error and a much smaller confidence interval for the estimate for each of the relevant examples.\n\n\nDiscussion\n\nFinding from this survey aimed at reporting the tend of OC screening and assessing risk factors associated with ever OC examination. Our findings indicate a lower rate of OC screening, with only 2.4% of respondents indicating that they had ever received OC screening. This finding is lower than the estimated 6.8% in Sudan,6 28% in India,24 and 30% in the USA.25 We found more than half of the patients visited the dentist twelve months ago, and seventy-three percent of patients reported that they visit the dentist when they have trouble with their teeth. These findings give a possible cause for concern as low levels of awareness of oral health may affect the chances of early presentation of OC. A greater emphasis should be placed on patient education regarding OC risk and detection, as there is no population screening program for this condition. A surprising result of this study was that 90% of patients had heard of OC screening. Even though this report indicates that participants are aware of screening for OC, it also exhibits a negative attitude or ignorance of its existence because only 2.4% of participants underwent OC screenings. This is the same situation that has been reported that only a few participants had ever received OC screenings despite hearing about OC screening before in different places.6,15 This gives cause for concern as low levels of OC screening will affect the chances of early detection of OC. It also highlights that extensive population-based surveys, awareness programs and establishing health literacy may need to be targeted more closely to encourage people to OC screening gradually.\n\nThere is a substantial body of evidence linking tobacco use as one of the leading causes of cancer and its death5; in that same way, using smokeless tobacco products, such as dipping and chewing tobacco, also leads to cancer mouth, esophagus, and throat cancers.8 According to data, compared to people who had never used smokeless tobacco, individuals with a history of smokeless tobacco use had five times higher odds of OC screening. The results of this study support previous studies suggesting that tobacco users had a significantly more positive attitude toward screening than non-tobacco users.14,15 The reason might be that continued anti-tobacco focus strategies such as advertising bans, higher taxes and prices, and restrictions contribute to behavioral changes in Bangladesh, although the country’s implementing smokeless tobacco control policies is insufficient.7 This study also observes that similar to the former smokeless tobacco users, former smokers had a 2-fold higher likelihood of receiving an OC screening than non-users which is in stark agreement with a prior study that reported that smoking was a significant determinant of receiving an OC screening.4,15 On the contrary, previous studies reported that former smokers were not a significant determinant of having a positive attitude or undergoing OC screening.4,14 A probable explanation for our finding might be that former smokers have a positive attitude toward OC screenings, and therefore, it is likely that opportunistic OC screening during dental checkups will yield positive results.\n\nA previous study indicated that regular visits to dentists or check-ups do not affect the uptake of OC screening.15 This result in line with our findings that there were no odds of OC screening among those who occasionally visited the dentist for a checkup. This result suggests that using the opportunity a dental appointment may provide to raise awareness may be increasingly vital to encouraging OC screening, and a previous study emphasised it.6 However, our study also suggests promoting public awareness concerning OC as a risk factor. The risk of many cancers is higher in subjects with a family history of cancer at a concordant site. It was also evident that OC had increased risks of family history at discordant sites.9 This present study demonstrated that having a family history of OC increased the odds of OC screening by nine times that of those with no family history of OC. This result is in line with a previous study conducted in India among women.13 The possible reason might be people with a family history of cancer/OC are better aware of cancer as a disease and hence participate more in OC screening.\n\nOf note, we observed a strong influence of the use of smokeless tobacco and smoking in the uptake of OC screening services. As shown in Table 5, the odds of having OC screening were higher among former smokeless tobacco users and former smokers. The findings in the present study concerning current smokeless tobacco users and smokers’ attitudes related to OC suggest strongly that awareness programs for OC screening are indispensable for them. Raising oral cancer awareness during dental appointments may be increasingly crucial to encouraging early detection. While anti-tobacco strategies such as advertising bans, higher taxes and prices, and restrictions continue to be implemented in Bangladesh, smokeless tobacco control policies remain inadequate.7 Therefore, policymakers must evolve and introduce new effective smokeless tobacco control policies. Additionally, this study revealed that visits to dentists or check-ups do not affect the uptake of OC screening. It concerns that low awareness among people and dentists is likely to hinder early presentation. To address this barrier, dental professionals and patients may need educational initiatives like training programs to improve health literacy surrounding OC risk factors. As well, general dentists’ confidence, expertise, and knowledge in conducting future OC screenings may need to be improved by implementing theory-based interventions.\n\nTo our knowledge, this study is the first to assess the tend and associated factors of OC screening among dental patients in Bangladesh. As well this is the first paper to compare OC screening ratios and confidence intervals from different strategies to a suitable reference. In this study, we particularly examined the odds ratio produced by several models. This research is among the first to compare different regression models while comparing their findings about OC screening in Bangladesh. Although qualitative studies are prevalent in OC screening, model comparison and model selection are less focused. So, we presented a different point of view when discussing OC screening. In order to initiate early treatment and avoid OC in its later stages, we used a variety of parameters in this study to determine the likelihood of OC screening. This research also emphasises already established factors (i.e., smoking and using tobacco) responsible for OC and further interpret the findings for the OC screening scenario in Bangladesh. Due to the nature of the study, we employed non-probability sampling for procuring and extracting the findings.\n\nWhile this research makes several contributions to understanding OC screening, there are some limitations. In this study, we used convenience sampling, which is a non-probability sampling method. So, the samples are not chosen by random selection. We collected samples that were readily available to us. So, it is only possible to generalise for some of the population. Due to the nature of the sampling method, the research may be subject to under-coverage bias and observer bias.\n\n\nConclusion\n\nThis study disclosed the tend and associated risk factors of OC screening among Bangladeshi dental patients using a model comparison approach. This study has found that only 2.4% of dental patients underwent OC screening before the study period. We also have found that former smokeless tobacco users and past smokers are more likely to uptake OC screening than non-users. In addition, patients having a family history of OC increased the odds of receiving OC screening than subjects without a family history of OC. The lack of OC screening in Bangladesh highlights the need to implement a national-level screening program to help with the early diagnosis of OC and its prevention.", "appendix": "Data availability\n\nOpen Science Framework. Association between Mediterranean diet adherence and dyslipidemia among diabetes mellitus patients. DOI: https://osf.io/2zh6y/.\n\nThis project contains the following underlying data:\n\n- data.xlsx (Complete survey responses)\n\n\nReferences\n\nOral health: World Health Organization (WHO). Accessed 17 Dec 2022. Reference Source\n\nSung H, Ferlay J, Siegel RL, et al.: Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J. Clin. 2021; 71: 209–249. PubMed Abstract \| Publisher Full Text\n\nMouth and oral cancer statistics\|WCRF International: Accessed 17 Dec 2022. Reference Source\n\nAkinkugbe AA, Garcia DT, Brickhouse TH, et al.: Lifestyle risk factor related disparities in oral cancer examination in the U.S: A population-based cross-sectional study. BMC Public Health. 2020; 20: 1–11. Publisher Full Text\n\nIslami F, Ann GS, Miller KD, et al.: Proportion and number of cancer cases and deaths attributable to potentially modifiable risk factors in the United States. CA Cancer J. Clin. 2018; 68: 31–54. PubMed Abstract \| Publisher Full Text\n\nBabiker TM, Osman KAA, Mohamed SA, et al.: Oral Cancer Awareness Among Dental Patients in Omdurman, Sudan: a cross-sectional Study. BMC Oral Health. 2017; 17: 69. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNaznin E, Wynne O, George J, et al.: Smokeless tobacco policy in Bangladesh: A stakeholder study of compatibility with the World Health Organization’s Framework Convention on Tobacco Control. Drug Alcohol Rev. 2021; 40: 856–863. PubMed Abstract \| Publisher Full Text\n\nMu G, Wang J, Liu Z, et al.: Association between smokeless tobacco use and oral cavity cancer risk in women compared with men: a systematic review and meta-analysis. BMC Cancer. 2021; 21: 960. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTurati F, Edefonti V, Bosetti C, et al.: Family history of cancer and the risk of cancer: A network of case-control studies. Ann. Oncol. 2013; 24: 2651–2656. PubMed Abstract \| Publisher Full Text\n\nLingen MW, Kalmar JR, Karrison T, et al.: Critical evaluation of diagnostic aids for the detection of oral cancer. Oral Oncol. 2008; 44: 10–22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSaraswat N, Pillay R, Everett B, et al.: Knowledge, attitudes and practices of South Asian immigrants in developed countries regarding oral cancer: An integrative review. BMC Cancer. 2020; 20: 1–16. Publisher Full Text\n\nPrevalence of current tobacco use (% of adults) - Bangladesh\|Data: Accessed 16 Dec 2022. Reference Source\n\nMishra GA, Shaikh HA, Pimple SA, et al.: Determinants of compliance to population-based oral cancer screening program among low socioeconomic women in Mumbai, India. Indian J. Community Med. 2021; 46: 210–215. PubMed Abstract \| Publisher Full Text\n\nNetuveli G, Sheiham A, Watt RG: Does the “inverse screening law” apply to oral cancer screening and regular dental check-ups? J. Med. Screen. 2016; 13: 47–50. PubMed Abstract \| Publisher Full Text\n\nAwojobi O, Scott SE, Newton T: Patients’ perceptions of oral cancer screening in dental practice: A cross-sectional study. BMC Oral Health. 2012; 12: 1–9. Publisher Full Text\n\nBouvard V, Nethan ST, Singh D, et al.: IARC Perspective on Oral Cancer Prevention. N. Engl. J. Med. 2022 Nov 24; 387(21): 1999–2005. PubMed Abstract \| Publisher Full Text\n\nWarnakulasuriya S, Kujan O, Aguirre-Urizar JM, et al.: Oral potentially malignant disorders: A consensus report from an international seminar on nomenclature and classification, convened by the WHO Collaborating Centre for Oral Cancer. Oral Dis. 2021; 27: 1862–1880. PubMed Abstract \| Publisher Full Text\n\nLin DY, Wei LJ: The robust inference for the cox proportional hazards model. J. Am. Stat. Assoc. 1989; 84: 1074–1078. Publisher Full Text\n\nBarros AJD, Hirakata VN: Alternatives for logistic regression in cross-sectional studies: An empirical comparison of models that directly estimate the prevalence ratio. BMC Med. Res. Methodol. 2003; 3: 1–13.\n\nRégression logistique vs autres modèles linéaires généralisés pour l’estimation de rapports de prévalences. Revue d’Epidémiologie et de Santé Publique. 1999; 47: 593–604. PubMed Abstract\n\nPearson K: Contributions to the mathematical theory of evolution. J. R. Stat. Soc. 1893 Dec 1; 56(4): 675–679.\n\nWHO: Pathology and Genetics of Head and Neck Tumours. IARC Press; 2005. Accessed 16 Dec 2022. Reference Source\n\nGhantous Y, Abu EI: GLOBAL INCIDENCE AND RISK FACTORS OF ORAL CANCER. Harefuah. 2017 Oct; 156(10): 645–649. PubMed Abstract\n\nMatos S, Boakye EA, Crosby D, et al.: Prevalence and Factors Associated with Oral Cavity and Pharyngeal Cancer Screening in a Rural Population. OTO Open. 2021; 5: 1–7. Publisher Full Text\n\nKravietz A, Angara P, Le M, et al.: Disparities in Screening for Head and Neck Cancer: Evidence from the NHANES, 2011-2014. Otolaryngol. Head Neck Surg. 2018; 159: 683–691. Publisher Full Text" }	[ { "id": "208803", "date": "30 Nov 2023", "name": "Daniel Cohen Goldemberg", "expertise": [ "Reviewer Expertise Oral cancer", "oral medicine", "oral pathology", "molecular pathology." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors presented a paper on the trend of oral cancer screening in Bangladesh, its perceptions, and risk factors, explored via different statistical tools. The paper is suitable for publication at F1000. It is clearly presented to the readers, introduction should also highlight the increase of oral cancer, particularly tongue cancer in younger patients, sometimes women, sometimes white, reported in several locations in the world. This should be brought again in the discussion, reinforcing the need for better training of oral medicine practitioners, not only in Bangladesh, but worldwide. Developing countries do not yet seem to be showing this increased tendency in younger women for tongue cancer, but it does not mean we have to be ready for this in the future and more importantly in the present. Our suggestions (me and both postdoctoral scientists that work for me) are all marked on the commented Word file of this paper for revision: Review from DCG and two coreviewers.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "192976", "date": "11 Sep 2024", "name": "Kamis Younis Gaballah", "expertise": [ "Reviewer Expertise oral cancer", "early detection", "prevention", "oral precancer" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript is Well-written and describes an essential aspect of early oral Cancer detection ie. oral Cancer screening. The paper focuses on public awareness of the importance of engaging in such a program. The value of opportunistic screening by oral health workers can not be over-emphasized. The data of the Current report shows that more than half of the participants have visited dentists either for oral health checks or for emergencies. In this regard, I expected the authors to comment on the lost golden opportunity by General Dental practitioners and cite some of the research that Showed The impact of educational Intervention on the ability of Oral healthcare workers to identify and suspect The malignancy of the oral cavity lesions. An example of a recent paper on this is Gaballah, K., Kujan, O. Ref 1\nOther key papers not cited isthe following S Warnakulasuriya, AR Kerr (Ref 2) Gustavo D Cruz,et.al 2002 (Ref 3) CC Uguru, et.al. 2023 (Ref 4)\nThe tables could be reduced to around four. Table one is not required as the data shown are already presented in the other tables.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-882
https://f1000research.com/articles/12-881/v1	25 Jul 23	{ "type": "Research Article", "title": "Synergistic effect of the combination of Chrysanthemum cinerariifolium (Trev.) and doxorubicin in inhibiting PI3K and Cyclin D in oral squamous cell carcinoma: in vitro study", "authors": [ "Anik Listiyana", "Yuanita Lely Rachmawati", "Hani Susianti", "Nurdiana Nurdiana", "Hidayat Sujuti", "Roihatul Mutiah", "Agustina Tri Endharti", "Anik Listiyana", "Yuanita Lely Rachmawati", "Hani Susianti", "Nurdiana Nurdiana", "Hidayat Sujuti", "Roihatul Mutiah" ], "abstract": "Background: The most common type of lips and oral cavity cancer is oral squamous cell carcinoma (OSCC). Doxorubicin (DX) is commonly used as a chemotherapy drug, but its use is limited due to risk factors and drug resistance. Chrysanthemum cinerariifolium (Trev.) (CC) has potential as an anticancer agent. Combining the plant extract and chemotherapy drug might prevent OSCC proliferation by inhibiting PI3K and cyclin D protein. Therefore, the present study aimed to determine the synergistic effect of the combination of C. cinerariifolium (Trev.) and doxorubicin in inhibiting PI3K and Cyclin D protein. Methods: Human oral squamous carcinoma cell lines SCC-9 were used in this study. A cytotoxicity assay was performed to obtain the IC50 value of CC ethanol extract and DX on the SCC-9 cell line. Synergism evaluation of the combination CC and DX was analyzed using CompuSyn software. ELISA and the immunofluorescent assay were performed to determine the level of PI3K and cyclin D in the SCC-9 cell line after being treated with IC50 value of CC, IC50 value of DX and three combinations of CC and DX [7/8 IC50 CC + 1/8 IC50 DX (dose 1), 6/8 IC50 CC + 2/8 IC50 DX (dose 2), and 4/8 IC50 CC + 4/8 IC50 DX (dose 3). Results: CC stem ethanol extract and DX inhibited the proliferation of SCC-9 cell lines with the IC50 value of 133.4 µg/mL and 288.3 nM, respectively. The combination of CC and DX at dose 2 (6/8 IC50 CC + 2/8 IC50 DX) exhibited a high decrease in PI3K and cyclin D expression. Conclusions: The combination of C. cinerariifolium and doxorubicin synergistically declined OSCC proliferation by inhibiting PI3K and cyclin D expression.", "keywords": [ "Chrysanthemum cinerariifolium (Trev.)", "Cyclin D", "doxorubicin", "IC50", "OSCC", "PI3K" ], "content": "Introduction\n\nCancer is a disease characterized by uncontrolled growth and abnormal cell spread, often resulting in death (American Cancer Society, 2020). According to Global Cancer Statistics, there were approximately 18.1 million new cases of cancer and 9.6 million deaths worldwide from cancer in 2018 (Ferlay et al., 2019). According to the World Cancer Research Fund (2018), lips and oral cavities cancer are the most common type of cancer. More than 90% of cancers in the oral cavity are oral squamous cell carcinoma (OSCC) (World Cancer Research Fund, 2018).\n\nThe genetic and epigenetic mutations in oncogenes or tumor suppressor genes lead to cell cycle dysregulation, inhibition of growth suppressor factors, and resistance to apoptosis (Lopez and Lopez, 2020). Mutations in the PI3K/Akt pathway contribute to the development of OSCC (Aali et al., 2020). The PI3K pathway involves cellular cell functions, including growth, angiogenesis and proliferation (Lakshminarayana et al., 2018). Alteration of this pathway leads to cell cycle dysregulation and contributes to the development of OSCC (Li et al., 2018). The activated PI3K pathway promotes cell proliferation and inhibits apoptosis. PI3K regulates the Akt protein, which then phosphorylates p21, causing the complex interaction of cyclins and cyclin-dependent kinases (CDK’s) and resulting in cell proliferation (Kidacki et al., 2015).\n\nCell proliferation also involves genes that play a role in cell cycle control (Saawarn et al., 2012). The cell cycle is a process of regulation of cell proliferation with several stages, including S, G2, M and G1 phases. This process requires cyclin/CDK interactions (Jain, 2019). Cyclin D1 is a protein that is overexpressed to more than 50% in the incidence of cancer (Qie and Diehl, 2016). Overexpression of cyclin D1 causes a shortening of the G1 phase, which results in abnormal cell proliferation and additional genetic lesions (Abid and Merza, 2014). Poor prognosis of OSSC is characterised by the low cell differentiation associated with overexpression of cyclin D (Ramos-García et al., 2019).\n\nThe rapid proliferation of OSCC causes most OSCC to be diagnosed at an advanced stage. Various treatments have been used to treat OSCC, but long-term survival is less than 50% (Kumar et al., 2015). Various treatments of OSCC that are frequently used are surgery, radiotherapy or a combination of radiotherapy and surgery, and chemotherapy. One chemotherapy drug commonly used for OSCC is doxorubicin (DX). DX works by inhibiting topoisomerase II, causing the termination of the cell cycle’s G2/M phase, which can subsequently induce apoptosis. However, chemotherapy drugs sometimes cause side effects, such as drug resistance (Mansoori et al., 2017). Due to these side effects, the treatment of OSCC requires combination therapy (Dasari and Tchounwou, 2014).\n\nReducing the dose of DX is required to minimize the side effect of doxorubicin (Fan et al., 2017). Combination chemotherapy can be applied in OSCC treatment to increase the therapeutic effect and reduce the side effects of chemotherapy drugs such as DX. The combined use of chemotherapy drugs and herbal plant compounds such as polyphenols have been shown to have low toxicity, which is particularly advantageous as it can reduce the dose of chemotherapy drugs (Mostafa et al., 2020). C. cinerariifolium (Trev.) (CC) extract can inhibit the growth of the T47D breast cancer cell line by inhibiting the cell cycle at G0-G1 and S phases (Mutiah et al., 2020). A previous study by Listiyana et al. (2019) revealed that the best cytotoxic activity against T47D cells was observed in CC stems. Therefore, the present study aimed to investigate the effect of the combination of ethanol extract of CC stems and DX) in inhibiting PI3K and cyclin D, which are proteins that play a role in increasing cell proliferation in OSCC.\n\n\nMethods\n\nCC was obtained from Punten Village, Batu City, East Java and identified at UPT Materia Medica Batu, East Java, Indonesia (no: 074/153/102.20-A/2-22). CC were harvested and the stems cut. The stems were cleaned, dried in the sun, and sorted. The dried stem samples were ground to a powder and then added with 96% ethanol in a ratio of 1:20. The mixture was extracted using UAE (Ultrasonication Assisted Extraction) for 2 min with three replications. Next, the filtrate was evaporated using a rotary evaporator at 50°C to produce a crude extract and concentrated using an oven at 40°C.\n\nThe in vitro study was conducted at the Biomedical Central Laboratory, Universitas Brawijaya. Human oral squamous carcinoma cell lines SCC-9 were purchased from American Type Culture Collection/ATCC, Virginia (catalog number: CRL-1629). Cells were cultured in a complete medium that consisting of 1:1 mixture of Dulbecco’s modified Eagle’s medium and Ham’s F12 medium (1.2 g/L sodium bicarbonate, 2.5 mM L-glutamine, 15 mM HEPES and 0.5 mM sodium pyruvate), supplemented with 90% of 400 ng/mL hydrocortisone and 10% fetal bovine serum.\n\nThis study used five concentration series of CC stem extract (700, 350, 175, 87.5, 43.5 and 21.875 μg/mL) and DX (800, 400, 200, 100, 50 and 25 nM). SCC-9 cell line was maintained with a complete medium in 96-well plates and then incubated for 24 h. After 24 h of incubation, the medium was removed and washed using Phosphate Buffered Saline (PBS). Then, each concentration of CC and DX was added into each well with three replications and incubated for 24 h. After 24 h, the medium was removed and washed using PBS, then added with Cell Counting Kit-8 (CCK-8) Reagent (Dojindo Laboratories, Japan). The absorbance of each sample was determined at 450 nm using a microplate reader. The IC50 value of CC and DX was determined using GraphPad Prism 8 (Graphpad Software, La Jolla, Canada, USA).\n\nA combination dose test was carried out based on the IC50 value of CC and DX with seven combinations including 7/8 IC50 CC + 1/8 IC50 DX, 6/8 IC50 CC + 2/8 IC50 DX, 5/8 IC50 CC + 3/8 IC50 DX, 4/8 IC50 CC + 4/8 IC50 DX, 3/8 IC50 CC + 5/8 IC50 DX, 2/8 IC50 CC + 6/8 IC50 DX, 1/8 IC50 CC + 7/8 IC50 DX.\n\nSCC-9 cells were grown in 96-well plates and then incubated for 24 h. After 24 h, the medium was removed and washed using PBS. Each combination of CC and DX was added into each well with three replications and incubated for 24 h. The medium was then removed and washed using PBS. Cell Counting Kit-8 (CCK-8) Reagent (Dojindo Laboratories, Japan) was added to each well. The absorbance of each sample was determined at 450 nm using a microplate reader. CompuSyn software was used to evaluate the synergistic combination of CC and DX. The results from this software were combination index (CI) values. The interpretation of the CI value is <0.1 = Strong synergist, 0.1–0.3 = Powerful synergist, 0.3–0.7 = Synergist, 0.7–0.9 = Light synergist, 0.9–1.1 = Additives, 1.1–1.45 = Light antagonist, 1.45–3.3 = Antagonist, >3.3 = Powerful antagonist.\n\nThe combination dose for this test was based on the synergism evaluation of the CC and DX combination, which showed synergistic results. This study used six treatment groups, including: control cells without treatment, IC50 value of CC, IC50 value of DX and three combinations of CC and DX [7/8 IC50 CC + 1/8 IC50 DX (dose 1), 6/8 IC50 CC + 2/8 IC50 DX (dose 2), and 4/8 IC50 CC + 4/8 IC50 DX (dose 3)].\n\nPI3K levels were measured using the enzyme-linked immunosorbent assay (ELISA). SCC-9 cells were grown in 24-well plates and then incubated for 24 h. After 24 h, the medium was removed and washed using PBS. Then, each treatment was treated to the cells with three replications and incubated for 24h. The medium was removed and washed using PBS. RIPA Lysis Buffer (RIPA Lysis Buffer-MB-030-0050, Rockland) was added and incubated at 2–8°C for 5 min. Cells were scraped rapidly and transferred to tubes on ice. Cells were centrifuged at 8,000 × g for 10 min at 4°C. The supernatant was then analyzed using the Human Phosphoinositide-3-kinase-interacting Protein 1, PIK3IP1 ELISA Kit (BT Lab, Cat No. E5870Hu, Shanghai Korain Biotech Co., Ltd, China) to measure PI3K levels in ng/mL.\n\nThe cyclin D expression was observed by the immunofluorescent assay. The medium was aspirated, incubated with 4% formaldehyde in PBS for 15 min at room temperature, and then rinsed three times with PBS. The first step for immunostaining was blocking the buffer for 60 min. During this step, cyclin D primary antibody (Cat No. bs-0623R, Bioss Antibodies Inc., USA) was prepared by diluting it with antibody dilution buffer, then aspirating the buffer solution. Cyclin D primary antibody was added and incubated for 24 h at 4°C. Then, the samples were rinsed three times with PBS for 5 min. Then, samples were added with fluorochrome-conjugated secondary antibody diluted in antibody dilution buffer and incubated for 1-2 h at room temperature in the dark. Samples were rinsed with PBS and then coated with Prolong Gold Antifade Reagent (#9071) or Prolong Gold Antifade Reagent with DAPI (#8961). Cyclin D expression was visualized using Olympus IX71 Fluorescent Microscope with 40x magnification, then photographed with Olympus Cell Sens software version 3.2. The pixel intensity in the cell nucleus reflecting the expression level was quantified using Image J software (Fiji) and presented as fluorescence (signal) intensity or integrated density (IntDen) value.\n\nData were reported as means ± standard deviation. Statistical significance was analyzed using one-way ANOVA (p < 0.05), then continued with the Post Hoc Tukey test.\n\n\nResults\n\nThe absorbance value of the SCC-9 cell line after being treated with CC and DX can be seen in Table 1. The higher concentration exhibited a lower absorbance value. It was indicated that the higher concentration of CC and DX decreased the cell viability of SCC-9 cell lines. The results also showed that IC50 values of CC and DX were 133.4 μg/mL and 288.3 nM, respectively (Figure 1).\n\nSynergism evaluation of the CC and DX combination, obtained from CompuSyn software, is presented in Table 2. From the seven combinations of doses analyzed, only three combinations showed synergistic effects, including 7/8 IC50 CC + 1/8 IC50 DX, 6/8 IC50 CC + 2/8 IC50 DX, and 4/8 IC50 CC + 4/8 IC50 DX with CI values respectively 0.694, 0.634 and 0.698. CompuSyn analysis also showed that the combination of CC and DX had a dose reduction index (DRI) > 1, indicating a mutual strengthening effect.\n\nThe results revealed that the SCC-9 cell line without treatment (control group) had the highest levels of PI3K (4.483 ± 0.59 ng/mL) (Figure 2). PI3K levels decreased significantly (p < 0.05) in all treatment groups. Interestingly, dose 2 showed the lowest levels of PI3K compared to all treatment groups, with PI3K levels of 0.715 ± 0.22 ng/mL. PI3K levels in the CC and DX combination group significantly decreased compared to the single CC and DX treatment group. Doses 1, 2 and 3 all were significantly different to the IC50 DX group (p = 0.001, 0.000 and 0.002, respectively), while when compared to the IC50 CC group, only doses 1 and 2 were significantly different (p = 0.001 and 0.000, respectively). From these results, CC and DX could reduce PI3k levels in single and combined treatments.\n\nPI3K levels (in ng/ml) were measured by ELISA. Control = medium + SCC-9 (without treatment), IC50 DX = medium + SCC-9 + IC50DX. IC50 CC = medium + SCC-9 + IC50 CC, Dose 1 = medium + SCC-9 + (7/8 IC50 CC + 1/8 IC50 DX), Dose 3 = medium + SCC-9 + (6/8 IC50 CC + 2/8 IC50 DX), Dose 3 = medium + SCC-9 + (4/8 IC50 CC + 4/8 IC50 DX). Data are expressed as mean ± SD, p < 0.05.\n\nCyclin D expression was observed from pixel intensity in the cell nuclei of the SCC-9 cells and presented as fluorescence (signal) intensity or integrated density (IntDen) value (Figure 3A). The results showed that CC and DX significantly decreased cyclin D expression in both single and combination treatments. The control group has the highest IntDen value, indicating that the control group expressed the highest Cyclin D. Cyclin D expression significantly declined (p < 0.05) in all treatment groups except the IC50 of DX. The lowest cyclin D expression was observed in dose 2 (Figure 3B).\n\nA) The fluorescence image was obtained from the fluorescent microscope. Cyclin D was expressed in the nucleus. Blue indicates cell nuclei with DAPI staining, and yellow indicates Cyclin D expression with FITC. The expression of Cyclin D is indicated by pixel intensity in the cell nucleus and fluorescence (signal) intensity or integrated density (IntDen) value. B) The graph shows the average Cyclin D expression. Control = medium + SCC-9 (without treatment), IC50 DX = medium + SCC-9 + IC50DX. IC50 CC = medium + SCC-9 + IC50 CC, Dose 1 = medium + SCC-9 + (7/8 IC50 CC + 1/8 IC50 DX), Dose 3 = medium + SCC-9 + (6/8 IC50 CC + 2/8 IC50 DX), Dose 3 = medium + SCC-9 + (4/8 IC50 CC + 4/8 IC50 DX). Data are expressed as mean±SD, p < 0.05.\n\n\nDiscussion\n\nDX is a chemotherapeutic agent that is widely used in cancer treatment, but this drug produces toxicity and drug resistance. In this study, DX, in combination with herbal plants, minimized the side effects and increased the therapeutic effect. Based on Table 1, the higher concentration of DX and CC caused a decrease in the cell viability of SCC-9 cells. El-Hamid et al. (2019) showed that DX could increase caspase-3 levels, thereby increasing cell apoptosis in the OSCC cell line. Several research studies also proved that CC could be used as an anticancer agent. C. cinerariifolium extract contained flavonoids and terpenoids (Mutiah et al., 2020). Flavonoids could suppress the proliferation of OSCC by stopping the cell cycle and inducing apoptosis (Listiyana et al., 2023a). Terpenoid compounds have anticancer activity in breast cancer (Bishayee et al., 2011). Listiyana et al. (2019) revealed that CC has a cytotoxic activity on T47D breast cancer cells.\n\nThe present study showed that the IC50 value of CC stem extract on the SCC-9 cell line was 133.4 μg/mL. Costa et al. (2017) stated that the strong anticancer activity of the extract is indicated by an IC50 value <500 μg/mL and weak anticancer activity is indicated by an IC50 value >500 μg/mL. The stem extract of CC and DX has strong anticancer activity on the SCC-9 cell line due to IC50 value <500 μg/mL. The IC50 value of DX is close to Abdolmohammadi et al. (2008) research, which stated that the IC50 value of doxorubicin on T47D cells was 250 nM.\n\nAn increase in PI3K and cyclin D can cause excessive cell proliferation of OSCC. Figure 2 showed that untreated SCC-9 cell lines had the highest PI3K levels. Excessive cell proliferation in OSCC may also be due to gene mutations that encode various components of signalling pathways in proliferation, such as PI3K and cyclin D. In OSCC, mutations and amplification of the PI3K gene occur, especially at advanced stages (Kozaki et al., 2006). Ferreira et al. (2017) found that PI3K expression was seen in >90% of OSCC patients, and there was an increase in the gingival tissue, hard palate, and alveolar ridge by immunohistochemistry methods. The untreated SCC-9 cell line expresses the highest cyclin D. Excessive expression of cyclin D1 causes a shortening of the G1 phase, resulting in abnormal cell proliferation (Saawarn et al., 2012). The poor prognosis in OSSC is markedly associated with low cell differentiation and overexpression of cyclin D (Ramos-García et al., 2019).\n\nPI3K levels decreased significantly in all treatment groups, indicating that the ethanol extract of CC stem and DX could inhibit PI3K expression. PI3K levels at the combined dose significantly decreased compared to the CC and DX single treatment group. CC significantly reduced cyclin D expression in a single treatment and combined with DX. Interestingly, the lowest PI3K and cyclin D expression levels were observed in dose 2. Furthermore, the combination in dose 2 had the best synergistic value (CI = 0.634) compared to doses 1 and 3, based on CompuSyn analysis (Table 2). Therefore, it can be concluded that dose 2 is the best combination dose for inhibiting the proliferation of the SCC-9 cells.\n\nCC and DX have the same mechanisms of action in inhibiting cell proliferation, especially in cell cycle inhibition. CC inhibits the G0-G1 and S phases of T47D cells (Mutiah et al., 2020), whereas DX cause G2/M phase termination in T47D cells (Abdolmohammadi et al., 2008). Dose 2 was a combination dose with a lower IC50 percentage of doxorubicin than CC. This study revealed that the combination of CC and DX could inhibit OSCC proliferation through the inhibition of PI3K and cyclin D. The use of the combination of CC and DX which have a synergistic mechanism of action, is expected to reduce the dose DX needed in OSCC therapy.\n\n\nConclusions\n\nC stem ethanol extract and DX inhibited SCC-9 cells with IC50 values of 133.4 μg/mL and 288.3 nM, respectively. The combination of CC and DX for dose 2 (6/8 IC50 CC + 2/8 IC50 DX) exhibited a high decrease in PI3K and cyclin D expression in SCC-9 cells. Therefore, the combination of CC and DX synergistically declined OSCC proliferation by inhibiting PI3K and cyclin D expression.\n\nThis research received ethical approval from the Health Research Ethics Commission (KEPK) of the Faculty of Medicine and Health Sciences, State University of Maulana Malik Ibrahim Islamic Malang, on April 21, 2022, with numbers 091/EC/KEPK-FKIK/2022.", "appendix": "Data availability\n\nFigshare: Synergistic effect of the combination of Chrysanthemum cinerariifolium (Trev.) and doxorubicin in inhibiting PI3K and Cyclin D in oral squamous cell carcinoma in vitro study, https://doi.org/10.6084/m9.figshare.22584580.v1 (Listiyana et al., 2023b).\n\nThis project contains the following underlying data:\n\n- Synergistic effect of the combination of Chrysanthemum cinerariifolium (Trev.) and doxorubicin in inhibiting PI3K and Cyclin D in oral squamous cell carcinoma in vitro study.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\nThank you to the Doctoral Study Program of Medical Science, Faculty of Medicine, Universitas Brawijaya, for their support. The author would like to thank the BOPTN Litabdimas LP2M UIN Maulana Malik Ibrahim Malang grant from the Ministry of Religion of the Republic of Indonesia.\n\n\nReferences\n\nAali M, Mesgarzadeh AH, Najjary S, et al.: Evaluating the role of microRNAs alterations in oral squamous cell carcinoma. Gene. 2020; 757: 144936. PubMed Abstract \| Publisher Full Text\n\nAbdolmohammadi MH, Fouladdel S, Shafiee A, et al.: Anticancer effect and cell cycle analysis on human breast cancer T47D cells treated extracts of Astrodaucus persicus (Boiss.) drude in comparison to doxorubicin. DARU. J. Pharm. Sci. 2008; 16(2): 112–118.\n\nAbid AM, Merza MS: Immunohistochemical Expression of Cyclin D1 and NF-kB p65 in Oral Lichen Planus and Oral Squamous Cell Carcinoma (Comparative Study). J. Baghdad Coll. Dent. 2014; 26(1): 80–87. Publisher Full Text\n\nAmerican Cancer Society: Cancer Facts and Figures 2020. 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World Cancer Research Fund International; 2018." }	[ { "id": "190705", "date": "11 May 2024", "name": "Laiping Zhong", "expertise": [ "Reviewer Expertise Oral cancer cell biology research", "chemotherapeutic therapy", "targeted therapy", "immunotherapy", "surgical therapy", "personalized precision therapy." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article aims to determine the synergistic effect of the combination of CC and doxorubicin in inhibiting PI3K and Cyclin D protein. A cytotoxicity assay was performed to obtain the IC50 value of CC and DX on the SCC-9 cell line. Synergism evaluation of the combination CC and DX was analyzed using CompuSyn software. ELISA and the immunofluorescent assay were used to determine the level of PI3K and cyclin D in the SCC-9 cell line after being treated with IC50 value of CC. They found that CC stem ethanol extract and DX inhibited the proliferation of SCC-9 cell lines with the IC50 value of 133.4 µg/mL and 288.3 nM, respectively. The combination of CC and DX at dose 2 (6/8 IC50 CC + 2/8 IC50 DX) exhibited a high decrease in PI3K and cyclin D expression. Although the results are interesting. Some issues require attention: 1. For the purity of the chemical composition of CC and the quality control of CC extracts, it might be helpful to present in the background or methods. 2. Only one OSCC cell line seems to be not enough, more OSCC cell lines will be better to avoid selection bias. 3. Besides the chemoagent of DX, some other chemoagents, such as cisplatine and taxel, are also be used in OSCC patients. 4. Western blot analysis might be appreciating for protein expression. Phosphorylated level of PI3K might also be detected. 5. Figures 2 and 3, it should be checked that the bar is almost same in the different groups 6. On the aspect of effects of the investigated agents, some cellular biological experiments might be helpful, such as cell proliferation, cell invasion, cell migration, cell cycle, clonal formation, or in vivo experiments.\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": [] } ]	1	https://f1000research.com/articles/12-881
https://f1000research.com/articles/12-879/v1	25 Jul 23	{ "type": "Research Article", "title": "Prevalence and predictors of virologic failure among HIV patients on antiretroviral therapy in Makueni County: a cross-sectional study", "authors": [ "Yvonne N. Kamau", "Marshal Mweu", "Martin Mulinge", "Marshal Mweu", "Martin Mulinge" ], "abstract": "Background: The growing number of people on antiretroviral therapy in Kenya has led to a decrease in HIV morbidity and mortality. However, virologic failure (VF) threatens to reverse these gains. In Makueni County, existing data indicate challenges in achieving viral load (VL) suppression among persons living with HIV (PLHIV). Few studies have been carried out investigating VF in the region despite its high incidence of HIV infections. Methods: An analytical cross-sectional study was conducted among PLHIV in Makueni County to investigate the determinants and estimate the prevalence of VF. The prevalence of VF and its associated 95% exact binomial confidence interval was estimated, and a mixed-effects logistic regression model used to evaluate the relationship between the predictors and VF. Results: The estimated period prevalence of VF between October 2018 and June 2019 was 13.2% (95% CI: 12.7%–13.8%). Being 15 years or older (aOR=0.53; 95% CI: 0.44 – 0.645) and having blood samples tested for reasons other than baseline VL measurement was associated with lower odds of VF: breastfeeding mothers (aOR=0.1; 95% CI: 0.01 – 0.97); clinical failure (aOR=0.08; 95% CI: 0.01 – 0.44); confirmation of VF (aOR=0.2; 95% CI: 0.07 – 0.62); no VL data (aOR=0.06; 95% CI: 0.01 – 0.31); routine VL (aOR=0.04; 95% CI: 0.01 – 0.12); drug substitution (aOR=0.03; 95% CI: 0.01 – 0.08). Taking ABC-based, AZT-based, or other non-TDF-Based regimens increased the odds of VF (aOR=1.61; 95% CI: 1.34 – 1.94), (aOR=1.75; 95% CI: 1.52 - 2.01), and (aOR=1.55; 95% CI: 0.99 - 2.44) respectively. Conclusion: This study showed that over 13% of HIV patients on ART in Makueni County had VF between October 2018 and June 2019. The significant risk factors associated with VF were found to be age lower than 15 years, taking a non-TDF-based ART regimen, and blood sampling for baseline VL measurements.", "keywords": [ "Virologic failure", "prevalence", "predictors", "HIV patients", "antiretroviral therapy", "Makueni County." ], "content": "Introduction\n\nOver the last decade, Kenya has made tremendous strides towards the control of the HIV epidemic; reporting a 68.5% reduction in HIV incidence between 2013 and 2021.1,2 This reduction has been attributed to the dramatic increase in antiretroviral therapy (ART) coverage from 5000 in 2003 to 1,199,101 in 2021 among people living with HIV (PLHIV).1,3,4 Emerging virologic failure could reverse these gains especially in areas where virologic monitoring has not been implemented in concert with ART scale-up.3,5,6 Virologic failure (VF) refers to a persistently detectable viral load (VL) exceeding 1000 copies/ml after at least six months of ART based on two successive measurements done within a three-month interval (with adherence support between measurements).7\n\nThe prevalence of VF is an important metric for the global control of HIV.8 In sub-Saharan Africa, the overall proportion of patients experiencing VF has been reported as 14% with a range from 0–43%.9–12 A study in Malawi reported VF in 32% of inpatients on ART between 2015 and 2017.13 A VF rate of 11.5% was reported in Northern Ethiopia after a median time on ART of 36 months.14 In Tanzania 25.4% of children on ART for four years experienced VF.15 In Kenya, 24% of adult patients on ART had VF between 2008 and 2011.3,5 A failure rate of 34% was reported among children 18 months to 12 years on first-line combination ART followed for a median 49 months.6\n\nThe predictors of VF have been largely grouped into patient and regimen-related factors.16,17 Among the patient-related factors, age, WHO stage, CD4 count, clinician skill level, suboptimal adherence, and treatment history have been highlighted as important predictors of VF.11,18–22 A meta-analytic study reported that about 70% of patients with VF would be virally suppressed following an adherence intervention.23 Additional factors including rural residency, gender, treatment interruption, opportunistic infections and tuberculosis (TB) co-infection were significantly associated with VF.24–26 Regimen-related factors including the potency and tolerability of the ART regimen have been reported as predictors of VF.17,27,28 Poor tolerability due to unpalatable formulations, toxicity and adverse drug events, large ART pill burden, high frequency dosing and complex handling of drugs increased the odds of VF.16,26,29–32 In Kenya, little has been published on VF. However, the few available studies identified predictors of VF among them poor drug adherence, young age, male gender, being married, low socio-economic status and clinical stage of disease.3,5,33 With VF being strongly predictive of higher risk of advanced disease and death,13,34 the economic burden associated with VF presents a challenge to the ART programs involved, and has potential serious public health implications for Kenya’s HIV response which is heavily dependent on external resources.1\n\nThe objectives of this study were to estimate the prevalence of virologic failure in HIV patients in Makueni County during the period of October 2018 and June 2019, and to identify the socio-demographic and regimen-related risk factors for virologic failure among the patients in Makueni County, Kenya.\n\n\nMethods\n\nThe study site was Makueni County, one of the 47 counties in Kenya located on the South-eastern part of the country. In 2020 the prevalence of HIV in Makueni County was 3.5%,35 with the county displaying a mixed epidemic pattern where HIV prevalence varied between 3%-10% among the general population and 23-30% among key populations.1 Data indicate that challenges faced with HIV epidemic control in Makueni County include moderate ART coverage with 21% unmet need, moderate testing inefficiencies, high mother to child transmission and low VL suppression among children.36 HIV services in Makueni County include HIV testing and treatment, prevention, and care services. These services are available for high risk populations, PLHIV and their partners, families and caregivers, according to the Kenya national guidelines.37 An analytical cross-sectional study design was employed to estimate the prevalence and identify the predictors of VF among PLHIV in Makueni County between October 2018 and June 2019, the period for which the data were available.\n\nData from this study were abstracted from the National Viral Load/early infant diagnosis (EID) monitoring system. This system is a repository of HIV VL and EID data and is managed by the National AIDS and STI Control Programme (NASCOP). Briefly, NASCOP spearheads the Ministry of Health’s interventions in tackling HIV/AIDS through policy formulation, coordination of procurement and supply chain management, training and monitoring and evaluation of the HIV response.38 The national VL/EID system is an electronic data management system for monitoring patients. It contains patient information on medication and ART history and demographic data. Health facilities feed data into the system which is available publicly via an interactive computer interface tool that graphically represents programme indicators.39,40\n\nData collected from all PLHIV across all ages, resident in Makueni County and who had VL tests done between October 2018 and June 2019 in point of care facilities under the national VL/EID monitoring system were included in the study. Additionally, those classified as receiving ART by either having detectable blood levels of selected ART or by reporting current ART use were also included. On the contrary, all PLHIV in Makueni County on ART for six months or less and those with missing information on key variables and/or invalid VL outcomes were excluded. An initial screening of the database showed that 23,067 entries were made between 2018 and 2019 from health facilities in Makueni County. A total of 16,340 eligible participants met the inclusion criteria and were selected for this study.\n\nA simple random sampling design was employed with a sampling frame that comprised all PLHIV with VL test results from point of care centers in Makueni County and who were enrolled in the national VL/EID monitoring framework between October 2018 and June 2019.\n\nFor this study, cases were defined as those with VF identified as detectable viral load ≥1,000 copies/ml after a minimum of six months on ART, as per the Kenya national treatment guidelines.37\n\nEthical approval for this study was granted by the Kenyatta National Hospital and University of Nairobi joint Ethics and Research Committee (KNH-ERC/A/508) on 14th December 2022. To safeguard participant confidentiality, any identifying information contained in the data was removed during the abstraction process.\n\nAll analyses were performed using R Statistical Software (v4.3.0; R Core Team 2023). Table 1 shows the predictor variables. Continuous variables were summarized using medians and ranges. For qualitative variables, frequencies and proportions were computed. The prevalence of VF and its associated 95% exact binomial confidence interval were estimated. This was followed by univariable mixed-effects logistic regression analysis to assess the effect of each predictor on VF. Code for the analysis is available as extended data.41 The inclusion of age as continuous predictor in the univariable models yielded insignificant results, age was grouped into two categories <15 years and ≥15years. The variables “sub-county” and “facility” were included as random effects to account for clustering. At this stage, a liberal P<0.20, was used to evaluate the significance of each of the predictors. Significant variables from the univariable analysis were included in a multivariable model where a backward stepwise approach was used to eliminate variables at P≥0.05. Notably, to minimise confounding, exclusion of these variables from the model was only considered if their removal resulted in a less than 30% change in the effects of the remaining variables.42 Two-way interactions were fitted between the remaining variables of the final model and assessed for significance.\n\n\nResults\n\nAll PLHIV in Makueni County and enrolled in the national VL/EID database were assessed for eligibility. An initial screening of the database showed that 23,067 entries were made between 2018 and 2019 from health facilities in Makueni County. A total of 16,340 eligible participants met the inclusion criteria and were selected for this study. Among those included, 15,014 were adolescents and adults aged ≥15 years, and 1,326 were children aged 0-14 years (Figure 1).\n\nTable 2 shows the descriptive statistics of the study. During the study period, the median age of the participants was 43 years (range: 0-93 years). Of the participants, 69.6% (n=11365) were female with 83.3% enrolled on a TDF-based ART regimen (n=13613) The estimated period prevalence of VF between October 2018 and June 2019 was 13.2% (95% CI: 12.7%-13.8%).\n\nFrom the results of the univariable analysis (Table 3), sex, age, partner, sample type, ART-regimen, and justification were found to be significantly associated with VF at a 20% significance level and were subsequently offered to the multivariable model.\n\nIn the multivariable analysis, only age, justification and ART-regimen were found to be significant predictors of VF at the 5% significance level (Table 4).\n\nBeing 15 years or older reduced the odds of VF by a factor of 0.53 (aOR=0.53; 95% CI: 0.44-0.645) controlling for the ART regimen and the justification for VL testing. Compared to patients taking a TDF-based ART-regimens, those taking ABC-based, AZT-based, or other regimens had about two times higher odds of VF (aOR=1.61; 95% CI: 1.34-1.94), (aOR=1.75; 95% CI: 1.52-2.01), and (aOR=1.55; 95% CI: 0.99-2.44) respectively, controlling for age and the justification for VL testing. Compared to patients whose blood samples were taken for baseline viral load measurement, those who gave samples for other reasons had lower odds of VF: breastfeeding mothers (aOR=0.1; 95% CI: 0.01-0.97); clinical failure (aOR=0.08; 95% CI: 0.01-0.44); confirmation of VF (aOR=0.2; 95% CI: 0.07-0.62); no VL data (aOR=0.06; 95% CI: 0.01-0.31); routine VL (aOR=0.04; 95% CI: 0.01-0.12); drug substitution (aOR=0.03; 95% CI: 0.01-0.08), controlling for their age and ART regimen.\n\n\nDiscussion\n\nIn this study the VF rate was estimated at 13.2% among HIV patients in Makueni County. This is an improvement in the VF rate compared to the national reports in 2015 when more than 60% of adults receiving ART in Makueni County had VF.43 This prevalence of VF is comparable with the findings from a national cross-sectional survey in Uganda that found a VF rate of 11%.10 A similar burden has been observed elsewhere in Sub-Saharan Africa.5,11,44–47 Nonetheless, the VF frequency was higher in Zimbabwe (30.6%)48 and Togo (51.6%),49 likely attributable to poor ART adherence.\n\nThis study revealed that younger age was associated with higher odds of VF. This is similar to the findings of a national-based household survey in Kenya where decreasing age was associated with higher risk of VF.2 A possible explanation for this finding could be that the youth face a myriad of challenges encompassing behavioral and psychosocial such as peer-related stigma, anxiety, lack of disclosure, sexual, reproductive and gender health concerns that may undermine adherence.47,50–53 Similarly, a study in South Africa showed that adolescents aged <15 years had higher risk of VF compared to older patients.54 High pill burden among adolescents could also explain the lack of adherence leading to VF.51 These findings have also been replicated elsewhere, with younger patients demonstrating poor adherence or higher levels of drug resistance mutations.11,15,50–52,55\n\nIn this study, patients taking Tenofovir (TDF) based ART regimens had lower odds of VF compared to those on zidovudine (AZT) or abacavir (ABC) based or other regimens. This corresponds to the research findings of a study in Uganda which showed that patients initiated on AZT-based regimens as compared with TDF-based ones were more likely to have VF.56 TDF-based regimens have been shown to be better tolerated with fewer side effects and hence better adherence.57 Nonetheless, one study reported that patients experiencing VF on a TDF-based regimen had higher rates of the NRTI-resistance mutation – K65R.52 Some studies have reported that ART-experienced patients have higher odds of VF compared to ART-naïve patients.58,59 Data suggests that drug resistance testing should be done for all patients with HIV RNA levels >1000 copies/ml.16 The absence of drug resistance in these patients indicates poor adherence. Drug-related reasons such as toxicity, frequency of dosing and pill burden should be investigated and strategies of optimizing ART adherence discussed.\n\nPatients tested for VF because of suspected clinical failure, repeat testers after suspected VF, breastfeeding mothers, those with no VL data, those undergoing routine viral loads and those with drug substitutions had overall reduced odds of VF compared to those tested at baseline. This is corroborated by the finding that patients on routine monitoring registered the lowest levels of VF10 due to enhanced adherence counselling and support. A Kenya nationwide analysis showed that the odds of VF were reduced as the frequency of VL monitoring increased.39 Contradictory findings were reported in Uganda where adolescents who had detectable VL at baseline testing were more likely to have VF upon a repeat viral load test regardless of their adherence level and change in ART regimen.53 Moreover, repeat testers who had active tuberculosis co-infection had higher odds of VF.10\n\nSex was not associated with VF in this study (Table 4). This agrees with the findings in other resource-limited settings which found no association between sex and VF.55,60,61 Other studies have however showed that being male was associated with higher risk of VF due to reluctance to access healthcare and poor adherence compared to women.25,46,51 In particular, a study in rural Cameroon found that men had higher odds of VF, independent of their adherence behaviours, ascribable to biological differences where men took longer to regenerate their CD4 count while on ART compared to women.62 Contrastingly, in Tanzania and UK, females were reported to be more likely to experience VF than males.15,27\n\nConsidering other study variables, the organizations partnering with the HIV care facilities did not emerge as significant predictors for VF. This was contrary to the findings of others studies where different levels of quality of care that the partners offer to the patients, program level differences or factors such as variations in policy and their implementation were attributed to higher odds of VF.11,52 Moreover, task shifting - comprising of the redistribution of tasks from highly qualified to less specialized healthcare workers where appropriate, to efficiently utilize the available human resources for health63,64 - was shown to be most successful in areas where the community health workers provided care under the supervision of experienced ART providers.63,65\n\nThe sample type collected was not independently associated with VF in this study. This is supported by findings from other studies that showed that using either DBS or plasma samples to quantify HIV viral loads resulted in findings that were reliable and comparable.59,66,67 In Malawi, one study reported that using plasma samples increased the precision of VL monitoring but was plagued by logistical and financial barriers thus unappealing in resource-limited settings.59 On the contrary, DBS samples were shown to be cost effective and easy to transport at ambient temperatures, but associated with reduced sensitivity with viral loads <5000 copies/ml.56,68\n\nThis study is not without limitations. The use of routine data that were not collected for research purposes handicapped the research since several exposure variables were not captured. The study did not analyze data on variables like income, education, or distance to the health facility that would have allowed for the control of more concealed sociodemographic confounders, because these are not routinely recorded in public health facilities. Additionally, some important factors leading to VF such as ART adherence, should be considered as potential factors in the study, but such information was not available. Failure to control for these factors may have led to residual confounding that could have biased the estimated odds ratios towards null. Furthermore, the study was based on outcome data collected at a single time point. Therefore, we might have overestimated the virologic failure rate due to individual temporal variability in biological markers. Nevertheless, the strength of this study rests on its sizeable statistical power afforded by the large sample size. Further investigations using cohort studies may be necessary to validate the study’s findings.\n\n\nConclusions\n\nThis study showed that around 13% of HIV patients on ART in Makueni County had VF during the period between October 2018 and June 2019. The factors associated with VF were lower age (≤15 years), the type of ART regimen and the justification for VL measurement.\n\nConsequently, (1) youth-friendly ART initiatives are warranted in this setting to reduce the VF prevalence among younger patients, (2) adherence support in patients taking regimens that are not TDF-based should also be prioritized, particularly in cases of suspected VF and before treatment switches, (3) routine viral load measurements should be conducted to ensure treatment success and prevent VF. However, if VF is confirmed, targeted HIV drug resistance testing to prevent unnecessary/premature switches should be considered.", "appendix": "Data availability\n\nThe viral load data for Makueni county used in this study is accessible upon placing a formal request to NASCOP, Kenya Dashboard (nascop.org).\n\nThe virologic failure analysis script for this manuscript is available from Figshare: Makueni_Data_Analysis_0123.R. https://doi.org/10.6084/m9.figshare.22633552.v2. 41\n\nThis project contains the following extended data:\n\n• Makueni_Data_Analysis_0123.R (virologic failure Rscript)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe express our sincere gratitude to NASCOP, Kenya for availing the data that have permitted this research.\n\n\nReferences\n\nMOH: Kenya World Aids Day: Progress Report 2013-2021. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGreig JE, du Cros PA , Mills C, et al.: Predictors of Raised Viral Load during Antiretroviral Therapy in Patients with and without Prior Antiretroviral Use: A Cross-Sectional Study. PLoS One. 2013; 8(8): 1–9. Publisher Full Text\n\nRutstein SE, Hosseinipour MC, Kamwendo D, et al.: Dried blood spots for viral load monitoring in malawi: Feasible and effective. PLoS One. 2015; 10(4): 1–17. Publisher Full Text\n\nIzudi J, Alioni S, Kerukadho E, et al.: Virological failure reduced with HIV-serostatus disclosure, extra baseline weight and rising CD4 cells among HIV-positive adults in Northwestern Uganda. BMC Infect. Dis. 2016; 16(1): 1–8.\n\nBadri M, Lawn SD, Wood R: Utility of CD4 cell counts for early prediction of virological failure during antiretroviral therapy in a resource-limited setting. BMC Infect. Dis. 2008; 8(December 2006): 1–8. Publisher Full Text\n\nBoullé C, Kouanfack C, Laborde-Balen G, et al.: Gender Differences in Adherence and Response to Antiretroviral Treatment in the Stratall Trial in Rural District Hospitals in Cameroon. J. Acquir. Immune Defic. Syndr. 2015; 69(3): 355–364. PubMed Abstract \| Publisher Full Text\n\nWHO: Task Shifting: Global Recommendations and Guidelines. World Heal Organ; 2008.\n\nGrimsrud A, Bygrave H, Doherty M, et al.: Reimagining HIV service delivery: The role of differentiated care from prevention to suppression. J. Int. AIDS Soc. 2016; 19(1): 10–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMa Y, Zhao D, Yu L, et al.: Predictors of virologic failure in HIV-1-infected adults receiving first-line antiretroviral therapy in 8 provinces in China. Clin. Infect. Dis. 2010; 50(2): 264–271. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGarrido C, Zahonero N, Corral A, et al.: Correlation between human immunodeficiency virus type 1 (HIV-1) RNA measurements obtained with dried blood spots and those obtained with plasma by use of Nuclisens EasyQ HIV-1 and Abbott RealTime HIV load tests. J. Clin. Microbiol. 2009; 47(4): 1031–1036. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJohannessen A, Garrido C, Zahonero N, et al.: Dried blood spots perform well in viral load monitoring of patients who receive antiretroviral treatment in rural Tanzania. Clin. Infect. Dis. 2009; 49(6): 976–981. PubMed Abstract \| Publisher Full Text\n\nPhillips A, Shroufi A, Vojnov L, et al.: Sustainable HIV treatment in Africa through viral-load-informed differentiated care. Nature. 2015; 528(7580): S68–S76. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "215895", "date": "02 Nov 2023", "name": "Siphamandla Bonga Gumede", "expertise": [ "Reviewer Expertise ART drug optimization", "adherence to ART or chronic medication", "Systematic reviews", "scoping reviews" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nKeywords\nthe idea here is to make it easy for anyone to use the keywords to search and find your article Online. But more than anything, keywords should help widen your search and retrieval of your article. These should not necessarily be the same words as in your title. Predictors, HIV patients are therefore not good keywords.\n\nInstead of 'Makueni County', i would put in 'Kenya'.\nIntroduction\nAuthors should include recent VF rates. 2008-2011 is over 10 years ago.\n\nAuthors are saying little has been published, but this is more than little. There is over 5 citations in this paragraph and part of it addresses the objectives of this current study? Unless authors rephrase this passage, there is no sufficient justification why this study is conducted since there are already findings from other studies reporting similar findings.\nMethods\nIt would be ideal to include some variables collected.\n\nTo avoid repetition with the first paragraph of the results, I would suggest that authors remove this.\n\nFor qualitative variables, frequencies and proportions were computed-How did authors achieve this in qualitative variables? Was this a mixed method study or quantitative study?\n\nIs figure 1 not supposed to be part of the results?\nResults\nThe results will need to be re-written detailing the available findings and linking with what is described in the methods. As is, the result section is not detailed enough.\n\nWhile this is probably important in other studies, what is the significant of analysing sample type in this case?\n\nTables 3-4: p values for other response options are missing in the univariate analysis unless this is chi squared tests.\nDiscussion\nAuthors should detail what could have led to such improvement?\n\nIt would have been best to compare current regimens based on the current Kenyan ART guidelines. Is the country not initiating DTG as their first line option?\n\nReference 57 is old and may not help in creating strong points for your argument? Beside, some of these regimens or drugs are probably not in the option list anymore.\n\nAuthors should revise this paragraph 3 (of discussion) based on the results or include lack of data for other regimens or drugs as limitations.\n\nWhat is the difference between a detectable VL and VF?\n\nDoes Kenyan MoH recommend VL testing at baseline?\n\nOn reasons why males are likely to experience VF than females. The discussion does not provide underlying reasons for VF among males. What is causing men's reluctance to access healthcare services?\n\nSupporting partners are most likely to provide high quality care and subsequently improving quality of care within public health settings. There is a need to elaborate on how and why this could be associated to VF?\n\nSample type: This study may not to be sufficient to report on this. I would remove anything to do with this from this study. This is also because authors do not provide possible reasons for such findings. If authors decide to keep this in the paper, they should provide more information on sample storage, sample preparation and RNA extraction? It might also be ideal to present some of the related findings in Pearson correlation analysis or related type of analysis.\nConclusion\nDrug resistance testing: This might be an expensive route than assessing and addressing adherence first. Please reconsider this statement\nData availability\nIt is better to say data not necessarily specify VL data. Being specific to VL may prompt questions on where do we obtain the other data, unless that is what you are referring to, then you may need to be specific on where data for the other variables is?\nSee annotated 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? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-879
https://f1000research.com/articles/11-1239/v1	01 Nov 22	{ "type": "Brief Report", "title": "Mastodon footprints found to be water erosion in the Quebrada de Chalán (Licto, Ecuador)", "authors": [ "Benito Mendoza", "Mauro Jiménez", "Pedro Pedro Carretero", "Jhonnatan Hernández", "Jennifer Loaiza", "Daniela Brito", "Geonatan Peñafiel", "Mauro Jiménez", "Pedro Pedro Carretero", "Jhonnatan Hernández", "Jennifer Loaiza", "Daniela Brito", "Geonatan Peñafiel" ], "abstract": "The Chalan ravine is a deep bed creek that runs through Licto (Ecuador). It has been known since the 19th century for the abundance of paleontological remains of Pleiostocene fauna and megafauna in its profiles, where entire remains of mastodons were recovered. The abundance of these remains made one of the high areas, where marmites exist in different forms, was traditionally considered as mastodon footprints. Archaeological prospecting, geographic information system (GIS) technology, unmanned aerial vehicle (UAV), photogrammetry, and the geological study of the place, allowed us to determine that the mythical traces of mastodon were marmites made by the water erosion produced in the same ravine over time.", "keywords": [ "Andean geology", "mastodon footprints", "water erosion", "Chalán" ], "content": "Introduction\n\nIn the late 19th century, foreign researchers began to arrive in the Quebrada de Chalán, attracted by the legend of the existence of bones of giant hominids. It was Juan Félix Proaño who, in 1884, after a great collapse in the Quebrada, proceeded to excavate the remains of a complete mastodon that had been exposed. These remains were sent to the Central University of Ecuador (Quito), where they disappeared after a large fire (Branco, 1938; Román, 2010).\n\nLater, other scholars such as Spillmann (1931) and Hoffstetter (1952) came, attracted by the wealth of remains of Pleistocene animals, with the desire to carry out their research.\n\nTherefore, the region is one of the main Pleistocene sites of Ecuador in terms of fossil remains from that period. From then on, new legends emerged with the arrival of these scholars in the first half of the 20th century, one of them being the object of our study, that the area of the marmites were actually mastodon footprints that had been fossilized as they fled before the eruption of the nearby Tulabug volcano. So much so that this legend has been taken as truth, since it was “endorsed by foreign scientists” and, although it had never been reported into a scientific study, it has been transmitted among the inhabitants of the place up to this day. Thus, even today all the living in the area think that the marmites correspond to the aforementioned fossilized traces of mastodons, so that information panels and a marketing campaign have been created in the area. Newspapers such as “La Prensa de Riobamba”, “Diario de Riobamba” or “El Telégrafo” (national) continue to consider these features as traces of mastodons and, from time to time, they take out in their pages reports on the aforementioned footprints, thus feeding the myth and confusing both locals and visitors (La Prensa, 2021; de Riobamba, 2019; El Telegrafo, 2016).\n\nThe objective of this research was to determine whether the existing marks in the study area were the product of (as tradition says) traces of mastodons that lived in the area during the Pleistocene, or were caused by water erosion (marmites) of the rock resulting from the passage of water.\n\n\nMethods\n\nVisual archaeological surface survey was carried out in the study area, in which it was determined that there are no archaeological or paleontological remains in the marmite area (Fernández, 1989). For this purpose, aerial photogrammetry was used using an unmanned aerial vehicle (drone) that includes a camera, obtaining qualitative and quantitative information from the earth’s surface, through a process of recording, measuring, and interpreting photographic images. The UAV used to obtain aerial digital cartography was a DJI Phantom 4 Pro V2.0 multirotor drone with a 20 MP aero-ported camera. The generation of photogrammetric products was carried out in three stages (Casella, Drechsel, Winter, Benninghoff, and Rovere, 2020; Gasparini, Moreno-Escribano, and Monterroso-Checa, 2020; Stott, Williams, & Hoey, 2020):\n\n‐ In the first stage, the flight path or flight plan was defined using Pix4DCapture software; parameters such as flight area in hectares, flight time in minutes, number of images to be captured, flight height in meters was configured, Pixel size in cm/px, horizontal and longitudinal overlap 75% recommended by the software, speed in m/s, a camera angle of 90°and number of batteries to be used.\n\n‐ The second stage consisted of preliminary survey of the terrain, location of control points (GCP) for correct orthophoto georeferencing and desired elevation models.\n\n‐ In the third stage the flight was carried out on 15 July 2021 at an altitude of 150 m, for 18 minutes, using two batteries, and recording 199 aerial images with a spatial resolution of 4.5 cm/px.\n\nThe captured photographs were stored in the drone’s internal memory and downloaded to the computer. The images were processed in the Pix4DMapper software, according to the methodology recommended by the manufacturer and described below:\n\n‐ When the software was started, the new project option was selected and the path where the postprocess files were created was defined.\n\n‐ Once the new project was generated, the photographs captured by the drone were added, the software automatically detects the camera used and the coordinate system; in this case they are geographical coordinates. These coordinates are then transformed into the same software to Mercator’s Universal Transversal UTM.\n\n‐ For 3D processing, 3D Maps processing was selected to obtain orthomosaic, point cloud and digital elevation models, in the initial processing the image scale and geometrically verified pairing were determined.\n\n‐ The processing of the dense point cloud was performed with a classification to improve the generation of the digital MDT terrain model, generate the digital surface model, orthomosaic. Additionally, a process of ortho rectification and contours was performed with a range of 5m.\n\nIn addition, at each processing stage the software generates a quality report that serves to evaluate whether the relative accuracy of the project is good or not, comparing coincidences between 2D key points, vertices, and lines, which indicate how many points of union two or more images share.\n\nThe results obtained were transformed into digital cartography using the measurement tools available in a GIS environment (ArcMap and Globalmapper). From this information, the digital elevation model determined the direction of the water flow of the Chalan Gorge and certain details that are not observed from the surface. In addition, geological areas of interest for the field visit were identified to recognize the Geological Formations, classifying them according to their lithology. Likewise, satellite images from Google Earth Pro were used to identify important flaws, key morphologies for subsequent field verification (Lanis & Razuvaev, 2018). From this preliminary information, the area of the Chalan Gorge and the area near the marmites were covered in 5 days to corroborate the information collected.\n\n\nResults and discussion\n\nThe Quebrada de Chalán (Figure 1) is located in the south-central area of the Ecuadorian Inter-Andean Valley, specifically on the border of the Licto and Punín parishes, in Riobamba, Chimborazo province. It was formed from the slopes of the Tulabug volcano (3336 meters above sea level [masl]). The average altitude of the Chalán gorge is 2953 masl. (coordinates: 17M 763279.11/9802664), it is located 15 km from the city of Riobamba by the Riobamba-Macas road (Román, 2010)\n\nIn the dry seasons (July to December) there are completely arid areas and other moistened spaces that provide a small but constant flow of water, that add up as it descends, thickening the flow of the stream. The land at the top of the ravine has little slope; in the middle part, this changes to a deep bed with slopes between rugged and steep, with steep flanks; in short sections the ravine slope decreases, causing the formation of sinks, holes and the water drainage by fractures in the rocks and the porosity of the soil. At the bottom, the ravine narrows to form a V, and the water current forms rapid and small jumps, until it flows into the Colorada ravine, named for its reddish strata (Reinoso, 1974).\n\nAs described by Sauer (1965), Wolf (1892), Clapperton and Vera (1986) and Buenaño (2019) (Buenaño, 2019), the Chalán ravine is located in the geological unit called the Cangahua Formation (Cangagua), this unit in the province of Chimborazo has a maximum power or thickness of 22 m. This Cangahua formation is the result of the volcanic activity of the Tulabug, which produced fine pyroclasts, easily transportable by the wind, that were deposited in the depressions of the inter-Andean valley, or in stagnant lakes; in certain areas they were consolidated, but without developing any stratification. Sauer (1965) determined that, according to the mineralogical composition of the andesites and dacites present in the formation, these originated after the second glaciation. In addition, what was described by Román (2010) determines that the Chalán ravine belongs to the Upper Pleistocene, specifically to the Third Interglacial Phase, since this is shown by the ichnofossil content (Coprinisphaera ecuadoriensis) present in the Cangahua geological unit (Sauer, 1965). The topsoil has variable thickness, composed of fine powder of whitish coloration with many cangagua balls; these fossil spheres serve as guide horizons to establish the relative age of the other strata, accumulated in thicknesses of several centimeters, as a result of the frequent volcanic eruptions in this area (Reinoso, 1974).\n\nThe Chalán gorge is recognized for its paleontological and archaeological richness, as it describes fauna from the late Pleistocene and the Prehistory of man in Ecuador (Román, 2010). In this context, as described by settlers, there are “bones of giants” in the surroundings of the ravine, being recorded for the first time by the chroniclers of the Indies in stories and legends, which alluded to ancient races of giants that would have populated these places in times immemorial. Juan de Velasco (1789) in his work “History of the Kingdom of Quito” describes the biological importance of the country and the presence of this type of gigantic bones buried in different strata of the soil and in several localities of the country. From these findings, those Ecuadorian legends of giants and strange beings that populated past times east were born (Reinoso, 1974).\n\nThere are several groups of fossil mammals present in the Pleistocene fauna of the Chalán quebrada and its surroundings (Wagner, 1883). Branco (1938) described in detail the ungulates of the area, especially equidae, camelids and cervids. As described by Román (2013) in 1894, the first mastodon discovered in the Pleistocene site of Quebrada Chalán was excavated. The remains of this specimen were preserved in good condition of fossilization at the Central University of Quito.\n\nIn this context, there are many notes from the national press that affirm the possibility that the marks on the rocks of the upper part of the ravine are traces of mastodons, the same that can be observed since a flood uncovered this area (Maggi, 2016; Moncayo, 2019; Yurak, 2020; La Prensa, 2021).\n\nOn 8, 9 and 10 September 2021, several surveys were carried out through the ravine in order to obtain a detailed geological description of the area. Most of the outcrops were in inaccessible places, however, observations that could be made from a long distance revealed that the strata are sandwiched between white and yellow layers. The white strata are made up of fine grain given to the popcorn structure that covers these strata; on the other hand, the yellow strata are made up of a somewhat coarser grain that does not allow the formation of said structure. According to the works presented by Sauer (1965), these strata correspond to poorly consolidated volcanic tuffs.\n\nThe area of greatest interest of the Chalán revine is located at the coordinates 17M 763287,78 East/9803423,94 North at an altitude of 2963 masl, and corresponds to an outcrop formed by three strata arranged in the form of terraces resulting from water erosion. The terraces are the result of the different degrees of resistance to erosion that each stratum presents, as shown in Figure 2.\n\nStratum 1 was the most superficial and of which the thickness was not possible to measure, since its roof of this was eroded. It is reddish (possibly the result of weathering by water), it did not present stratifications, was well consolidated; the clasts inside were sub-regulatory, their sizes varied between 1 to 5 mm, poorly ordered, supported matrix, made up of fine grains; the mineral content corresponded mostly to plagioclase quartz and hornblendas. Stratum 2 bordered 1, by means of a concordant contact, had a thickness of 2 m, was yellowish, had no stratifications, was well consolidated; the clasts inside were angular, its size varied from 2 to 15 mm, without order, supported matrix, made up of fine grains, without mineral content. On the roof of the stratum there were a series of marks ranging from 8 to 30 cm in diameter (Figure 3), due to their characteristics and according to Sauer (1965) this stratum was classified as a volcanic tova of chemical affinity towards an andesitic or dacite composition.\n\nStratum 3 limits with stratum 2 by a concordant contact; it is not possible to measure its thickness since the base of this is not seen; it was white, although in areas it was purple as a result of weathering by water; it did not present stratifications, was well consolidated, without clast content; it was made up of very fine grains without mineral content.\n\nThis type of erosion is known as giant marmites, the formation process of which is induced by defects in the bed producing flow alterations, generating turbulence or whirlpools. At this point the diaclases have an important role in the beginning and progress of the formation of the marmites (Ortega, Gómez, Perez & Wohl, 2014; Pelletier, Sweeney, Roering and Finnegan, 2015). The way in which the marmites are formed is described in Figure 4, in which the evolution of erosion with respect to time is evidenced (Lorenc, Muñoz, & Saavedra, 1995).\n\nFigure 5 shows in a general way the erosion that occurs in the upper part of the Chalán ravine. This is stuated just before a wall of approximately 10 m of altitude.\n\nThe geological evidence and the erosion that shows the soil from the geomorphological point of view the formations that are in the upper part of the Chalán ravine correspond to marmites (Figure 6). They had various diameters and depths. As it is necessary to categorise each of them, there were marmites of type A (erosion caused by natural abrasion less than 50 cm in diameter and depth), B, C, D (these three are deeper abrasions, where the particles cannot be lifted by vertical energy), E (in this type lateral erosion predominates, developing angular edges in the upper parts of the holes) and F (these are of the asymmetric type, favoring the tangential flow of the water, observing the formation of other marmites) as described by (Lorenc, Muñoz, & Saavedra, 1995).\n\n\nConclusions\n\nAlthough it is true that the Chalán ravine has a large number of paleontological remains of Pleistocene fauna and megafauna, perhaps one of the most important in Andean territory so that even today the remains are visible with the naked eye in several walls of the lower areas of the Quebrada, the study area has known a significant erosion over time.\n\nPrecisely this erosion, produced above all by the water that passed through the ravine, is what has led to the form of the marmites that have been confused first, and mythologized later, as a series of mastodons fleeing before one of the eruptions of the Tulabug volcano.\n\nThe photogrammetric study, the arrangement of the marmites, their shape, the study of runoff and the geological interpretation, have allowed to determine that these features were not fossilized mastodon footprints, but erosion of the indicated strata wwhich, with the passage of time and the conditions described above, have caused this type of hole in the form of footprints in the rock.", "appendix": "Data availability\n\nZenodo: Mastodon footprints or water erosion in the Quebrada de Chalán (Licto, Ecuador), https://zenodo.org/record/6959979 (Mendoza et al., 2022).\n\nThis project contains the following underlying data:\n\nCHALAN 2_dtm.prj (orthophoto obtained with the drone, the digital elevation model of the terrain)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nBranco W: About A Fossil Mammal Fauna of Punín. Quito, Ecuador:Annals of the Central University of Ecuador;1938.\n\nBuenaño P: Geological and geophysical analysis applied to hydrogeological prospecting between the towns of Riobamba and Pungalá. Quito:National Polytechnic School;2019.\n\nClapperton C, Vera R: The Quaternary glacial sequence in Ecuador: a reinterpretation of the work of Walter Sauer. Journal of Quaternary Science. 1986; 1(1): 45–56.\n\nCasella E, Drechsel J, Winter C, et al.: Accuracy of sand beach topography surveying by drones and photogrammetry. Geo-Marine Letters .2020; 40(2):255–268. Publisher Full Text\n\nde Riobamba D : Quebrada de Chalán. In the footsteps of megafauna. Diario de Riobamba. Recalled on 12 of 2021.05 of 12 of 2019.Reference Source\n\nFernández Díaz M: The Profession of Drone Pilot in the field of Cultural Heritage and Archaeology: science and dissemination from the air.2018.\n\nFernández V:Archaeological prospecting: approaches, aids and techniques. Theory and Method of Archaeology. 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Geophysical Research Letters. 2015; 42(3): 797–803.\n\nReinoso G: Punín and Chalán. Cuenca:Separata de la Revista N°4 de Antropología;1974.\n\nRomán J: Resumption of paleontological research at the Pleistocene site of Punín, Quebrada de Chalán, province of Chimborazo, Ecuador. In X Argentine Congress of Paleontology and Biostratigraphy and VII Latin American Congress of Paleontology (La Plata, 2010).2010.\n\nRomán J: Puesta en valor y propuesta de quebrada Chalán, provincia de Chimborazo, como el primer parque paleontológico del Ecuador (Tesis de Maestría) .Madrid:Universidad Complutense de Madrid;2013.\n\nSauer W: Geología del Ecuador .Quito:Editorial del Ministerio de Educación;1965.\n\nSpillmann F: Die Säugetiere Ecuadors im Wandel der Zeit .Ecuador:Universidad Central del Ecuador;1931.\n\nStott E, Williams RD, Hoey TB: Ground Control Point Distribution for Accurate Kilometre-Scale Topographic Mapping Using an RTK-GNSS Unmanned Aerial Vehicle and SfM Photogrammetry. Drones 2020 .2020; 4(3):55. Publisher Full Text\n\nEl Telégrafo:La Quebrada de Chalán, el lugar donde yacen las huellas de mastodontes. El Telégrafo.28 de 11 de 2016.Recuperado el 12 de 2021 de https://www.eltelegrafo.com.ec/noticias/regional/1/la-quebrada-chalan-el-lugar-donde-yacen-las-huellas-de-mastodontes\n\nThe Telegraph: The Quebrada de Chalán, the place where the mastodon footprints lie. The Telegraph;28 of 11 of 2016. Retrieved 12 of 2021.Reference Source\n\nVelasco JD:Historia del reino de Quito en la América meridional.1789.\n\nWagner A: Ueber fossile Säugetiernochen am Cimborasso. Sitzugsberichte der königlich bayerischen Akademie der Wissenschaften zu München. 1883; 3: 330–338.\n\nWolf T: Geografía y geología del Ecuador; publicada por órden del supremo gobierno de la república por Teodoro Wolf. Tipografía de FA Brockhaus;1892.\n\nYurak:Yurak.05 de 11 de 2020.Recuperado el 12 de 2021, de. https://yurakproducciones.wordpress.com/2020/11/05/de-que-son-las-huellas-halladas-en-la-quebrada-chalan/" }	[ { "id": "159655", "date": "12 Jan 2023", "name": "Valeria Lupiano", "expertise": [ "Reviewer Expertise Geology", "geomorphology", "landslides" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 paper that aims to show how the footprints, found in Quebrada de Chalán (Licto, Ecuador), attributed to Mastodon by local people, are instead a geomorphological phenomenon (river potholes) related to fluvial erosion and the lithology of the site. They did a field survey and used aerial photogrammetry to prove this.\nThe manuscript is well structured but needs a revision of English language.\nIt is necessary to explain the mechanism that leads to the formation of river potholes by commenting on Figure 5. Also mention the factors that predispose to the phenomenon. See for example:\nOrtega, J. A., Gómez-Heras, M., Perez-López, R., & Wohl, E. (2014). Multiscale structural and lithologic controls in the development of stream potholes on granite bedrock rivers. Geomorphology, 204, 588-598.\n\nKale, V. S., & Joshi, V. U. (2004). Evidence of formation of potholes in bedrock on human timescale: Indrayani river, Pune district, Maharashtra. Current Science, 723-726.\nThe conclusions are very meager, should be supplemented with some consideration.\nMinor revision:\nfigure 1: insert a small map with Ecuador location; In the legend change \"m.s.n.m.\" in \"m a.s.l.\";\n\nIn the text change \"masl\" in \"m a.s.l.\";\n\nArcMap and globalmapper cite as: ESRI year. ArcMap, Release xx. Redlands, CA: Environmental Systems Research Institute. Blue Marble year. Globalmapper Release....;\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Not applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "9914", "date": "25 Jul 2023", "name": "Benito Mendoza", "role": "Author Response", "response": "Dear reviewer, a thorough review of the English writing was conducted, taking into account minor corrections. Additionally, the study was analyzed with respect to new suggested literature, which led to further explanation on how the marmites could have originated." } ] }, { "id": "163369", "date": "14 Mar 2023", "name": "Matthew Bennett", "expertise": [ "Reviewer Expertise Footprints" ], "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 paper which documents erosional scours previously thought to be mastodon footprints. While I agree with their conclusions, they do not describe the traces in sufficient detail to ensure that others can benefit from their work. More detailed description of the traces is really needed, close up scans or photogrammetry models. Some morphometric comparison with known proscibean footprints would strengthen the work. The evolutionary model for the scours does not seem supported by any data I can see. It may well be accurate but it needs to be evidenced. Work in progress is my assessment and the authors should be encouraged to revise the article.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? 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? Partly", "responses": [ { "c_id": "9915", "date": "25 Jul 2023", "name": "Benito Mendoza", "role": "Author Response", "response": "Dear reviewer, while the presented work requires more data to determine whether the traces are mastodon footprints or erosional scours, a thorough revision has been conducted. Additional paragraphs have been added to reinforce the initial theory presented in the paper, supported by a literature review and macro and microscale analysis. It is important to note that there are limited indications of mastodon footprints in South America, and this topic is just beginning to be studied. Consequently, the conclusions leave open the possibility of furthering this research through geophysical methods and comparative analysis with similar features found in Argentina and Chile. This will be explored in future work to ascertain whether these are indeed mastodon footprints or erosional scours." } ] } ]	1	https://f1000research.com/articles/11-1239
https://f1000research.com/articles/12-360/v1	03 Apr 23	{ "type": "Research Article", "title": "Mortality due to traffic accidents in Colombia: Profiles of pedestrians and cyclists, 1998-2019", "authors": [ "Gino Montenegro-Martínez", "Maite-Catalina Agudelo-Cifuentes", "Diana-Isabel Muñoz-Rodriguez", "Gino Montenegro-Martínez", "Diana-Isabel Muñoz-Rodriguez" ], "abstract": "Background: Traffic accidents are an important issue for public health and a threat for sustainable development, with pedestrians and cyclists having been recognized as the most vulnerable actors on the streets. The objective of this study was to analyze the profiles of pedestrians and cyclists who died as a result of traffic accidents in Colombia during the 1998-2019 period. Methods: An observational and descriptive study, with the deaths due to traffic accidents in Colombia between 1998 and 2019 as data source. Secondary data were taken from the Vital statistics of Colombia (EEVV), published by Departamento Administrativo Nacional de Estadística (DANE). A trend analysis of the number of deaths during the period under study was performed, and such number was examined against sex to identify potential differences. Multiple correspondence analysis was employed to elaborate the profile of pedestrians and cyclists who die due to traffic accidents. Three profiles were prepared for each road actor: a global profile, one for 1998, and another for 2019. Results: The mortality profiles are different for pedestrians and cyclists, and, in turn, there are also demographic, geographic, and socioeconomic conditions in each type of road actor, which determine higher mortality risks. High population density, younger age group in the cyclists and adults among the pedestrians, low schooling levels and absence of health insurance are suggested as key factors in these profiles. Related to sex, for men is not possible to establish a profile. Women's cases are commonly related to health insurance, age, and population density. Conclusions: Several contextual and demographic characteristics in pedestrians and cyclists allow delimiting mortality profiles. The profiles that were identified suggest the need to articulate road safety policies with other social and development policies in order to coordinate and integrate intersectoral actions that reduce mortality in these road actors.", "keywords": [ "Traffic accident", "mortality", "pedestrian", "cyclist", "Multiple Correspondence Analysis", "Road Traffic Injury" ], "content": "Introduction\n\nTraffic accidents account for 50 million injuries and cause 1.3 million deaths across the globe.1 It is estimated that 942 disability-adjusted life years are lost in the world, with a higher rate in low-income countries (1,068 for every 100,000 individuals) than in high-income countries (593 for every 100,000 people).2 Low- and middle-income countries concentrate 90% of the mortality due to traffic accidents.3 Due to the associated costs, it can push families into poverty or into facing significant psychological, physical, and social harm.4 Thus, it has been pointed out that traffic accidents are an important public health issue,5 as well as one of the threats to sustainable development.3\n\nTarget 3.6 from the Sustainable Development Goals (SDGs)6 set out to reduce mortality due to traffic accidents by 50% by 2020 across the globe6; however, only a 15.40% reduction has been achieved between 2015 and 2019.7 Therefore, the deadline to achieve this target, among others, has been extended to 2030, instructing the countries to implement intersectoral, integrated, and comprehensive interventions to attain safe and sustainable transportation.5 The aforementioned implies that the road safety agenda should be linked to other political plans, such as children’s health, weather-related actions, gender, and equality, among others.3\n\nIn Colombia, it has been estimated that the number of deaths due to traffic accidents between 2015 and 2021 was 47,916. It is the fourth most common cause of death among people aged from 15 to 49 years old, and it is estimated that its incidence implies 918 disability-adjusted life years lost.8 The costs related to traffic accidents were around USD 815.5 million for 2016.9\n\nGiven the behavior in terms of the number of traffic accident victims, motorcyclists, pedestrians, and cyclists have been recognized as the most vulnerable road actors.1 One-third of the deaths in the country corresponds to pedestrians and cyclists: the number of deaths in the last five years has been reduced by 10.1% in the former but has presented a 29.1% increase in the case of cyclists during the same period.10\n\nIn the context of the decade of action for road safety 2020-2031, member states of the United Nations have been instructed to strengthen research in this field in order to understand the nature of the problem, as well as to identify effective solutions and strategies in road safety.3,11 Additionally, in Colombia, research in the road safety field has been acknowledged as the basis for formulating and implementing strategies to prevent and mitigate the impacts of traffic accidents.12\n\nIn this sense, studying profiles of the road actors considered vulnerable provides information that allows for analyzing the phenomenon comprehensively and adapting road safety policies that, in addition to viewing road actors in their singularity, consider them in their full complexity.\n\nTo the present day, there is no knowledge about studies in Colombia addressing the analysis of mortality due to traffic accidents from this perspective. Therefore, the main objective of this study was to analyze the profiles of pedestrians and cyclists who died as a result of traffic accidents in Colombia during the 1998-2019 period.\n\n\nMethods\n\nAn observational and descriptive study was conducted, focused on the deaths due to traffic accidents in Colombia between 1998 and 2019. Secondary data were taken from the Vital statistics of Colombia (EEVV, in Spanish), published by Departamento Administrativo Nacional de Estadística (DANE) (freely available online here). The STROBE guidelines (Strengthening the Reporting of Observational Studies in Epidemiology) were followed for the present study.\n\nOnly deaths among pedestrians and cyclists were considered. The records included were those in which the basic cause of death was recorded with the following ICD-10 codes: V010 to V099 for deaths among pedestrians; and V100 to V199 in the case of deaths among cyclists.\n\nFor the characterization, the death year and the municipality of occurrence were considered to elaborate the “population density” variable, adopting the number of inhabitants for 2010 (approximately half of the period under analysis) and the size of the municipality. The number of inhabitants for 2010 was taken from population projections published by Departamento Administrativo Nacional de Estadística (DANE), Municipal series of the population by area for the period 1985-2017 (freely available online here); the size of the municipality was taken from Municipios de Colombia (freely available online here). Subsequently, based on these data, the population density for each municipality was calculated as follows: population/km2. Subsequently, the quartiles were obtained considering the density of all the municipalities to classify them into municipalities with low, moderate, high, and very high population density based. This measure was calculated by the authors (freely available in online here). Other sociodemographic variables were also used, such as sex, age, schooling level, and health insurance regime. Four major groups were assembled for the “age” variable: group 1 (<25y); group 2 (25-44y); group 3 (45-59y); group 4(≥60y).\n\nIn Colombia, health services are provided through the affiliation of the population to the Social Security General System (Sistema General de Seguridad Social, SGSSS). In health, this is divided into three affiliation regimes which, among other elements, are related to the link of the individuals into the labor market and their ability to pay a fee monthly.13 The subsidized regime includes people lacking formal employment and those who cannot pay a monthly fee. The contributory regime encompasses those with a job contract or who work autonomously and are able to pay a monthly fee. The special regime includes those who work in the armed forces or who teach in the public sector, among others.13 In this study, the “affiliation regime” variable was dichotomized into two groups: subsidized and contributory. This latter incorporates the individuals in the special regime, as it represents less than 5% of the population enrolled in the SGSSS.14\n\nWe performed a trend analysis of the number of deaths during the period under study for road actors stratified by sex to identify potential trends. Absolute and relative frequency measures were used for the characterization, and they were analyzed for each road actor (pedestrians and cyclists separately). Subsequently, multiple correspondence analysis (HOMALS, homogeneity analysis through alternating least squares) was used to identify the profiles of pedestrians and cyclists who die in traffic accidents. This statistical technique allows the representation of the relationship between categories of different variables in perceptual space. The principal advantage is representing columns and rows in the same space; the dimensions are characteristics not observable that allow the objects to gather in a multidimensional space. The principal variable method was used for normalization.15 The main syntaxis to develop Multiple Correspondence Analyses are freely available here.\n\nThe results are presented in the form of bidimensional graphs, where the distances between the points show the relationships between the categories, and the similar categories are indicated as close to each other. The first dimension contains most of the information. The percentage of information explained by each of the dimensions is represented by the eigenvalue. For each model, the variance magnitude value was obtained as an indicator of the importance degree of each dimension in the global solution.\n\nIn order to observe changes in the profile of deaths among pedestrians and cyclists throughout the period, three profiles were prepared, one for each road actor: a global profile, one for 1998, and another for 2019. The IBM SPSSS Statistics program, Windows version 24.0 (Licensed to Universidad CES) (IBM Corp, 2016) (RRID:SCR_002865), was used to process the data and prepare the graphs.31\n\n\nResults\n\nIn the period from 1998 to 2019, there were 52,226 deaths due to traffic accidents in Colombia: 44,203 pedestrians and 8,023 cyclists. A 48% reduction in the number of deaths among pedestrians was observed in the period analyzed; the year with the highest number of deaths was 1998 (2,854) the one with the fewest was 2017 (1,431). The behavior was different for the deaths among cyclists, showing variations over time and noticing that the highest number of deaths was in 2001 (462) and the lowest in 2013 (294); in general, the increase was 24% when comparing the number of deaths between 1998 to 2019.\n\nThe results corresponding to the death trend among pedestrians and cyclists in traffic accidents, both for men and women, are presented in Figure 1. The number of deaths among men was higher than among women, both for pedestrians and cyclists. The highest number of deaths among male pedestrians was recorded in 1998, whereas it was in 1999 for women; throughout the period, there were three deaths of male pedestrians for every death of a female one. Regarding cyclists, the highest numbers of deaths among men and women were recorded in 2001 and in 2004, respectively; the difference between sex was much higher, noticing that there were 13 deaths among men for every death of a woman throughout the period.\n\nIn 83.1% of the deaths, pedestrians were in municipalities with high population density. The highest proportion of deaths was among individuals aged over 60 years old, followed by people aged between 25 and 44 (22.3%). In terms of schooling, 52.7% of the deaths among pedestrians were recorded in people with Elementary School as their highest education level. 38.0% of pedestrians who died in traffic accidents were not enrolled in the health system.\n\nOn the other hand, most of the deaths among cyclists (88.3%) were in municipalities with very high population densities. Unlike what was observed in pedestrians, the proportion of deaths among cyclists was higher in individuals aged less than 25 years old; 53.5% of these deaths corresponded to people with Elementary School, and 35.6% were not enrolled in the health system (Table 1).\n\nThree important profiles that represent the main characteristics of the pedestrians who died due to traffic accidents were observed. A profile represented by the deaths in municipalities with low, moderate, and high population density, these cases corresponded mainly to people under 25 years of age. The deaths in municipalities with very high population density were mainly among individuals aged between 45 and 49 years old and were enrolled in the contributory health regime. On the other hand, the deaths among female pedestrians showed the affiliation to the subsidized health regime and Elementary School education as common elements. For males, it was not possible to establish a profile.\n\nThe profile of the deaths among pedestrians is shown in Figure 2; this model explains 68.1% of the variance, with Dimension 1 and Dimension 2 explaining 34.6% and 33.5%, respectively. The eigenvalues of both dimensions were relatively close to each other, which indicates that they have similar relevance for the model (5.89 and 5.69, respectively). According to the discrimination measures, the most important variable in Dimension 1 was “population density”, whereas it was “age group” for the second dimension. On the other hand, the variable that most contributed to explaining the total variance was “age group”, followed by “population density”.\n\nThe behavior of the deaths among pedestrians was compared between 1998 and 2019. For 1998, two profiles mainly differentiated by the population density of the municipality where the accidents happened and by the pedestrians’ age groups were identified; in this sense, the deaths in the municipalities with low and average population density were mainly in people aged less than 25 years old, with no schooling or with Elementary School as the highest level, affiliated to the subsidized regime or uninsured. On the other hand, the deaths in municipalities with very high population density were mainly in people aged between 45 and 59 years old (Figure 3). In contrast, in 2019, the deaths in municipalities with very high population density corresponded to people enrolled in the contributory system and with a professional schooling level. Also in this year, the pedestrians aged more than 60 years old who died due to traffic accidents belonged mainly to the subsidized health regime and had Elementary School as their highest schooling level (Figure 4).\n\nAmong the cyclists, the deaths due to traffic accidents differed mainly by age group. It is noticed that the deaths among cyclists aged less than 25 years old were characterized as females, with Elementary School as the highest schooling level. On the other hand, the cyclists aged between 25 and 44 years old had attained professional schooling levels, whereas the victims over 45 years old had Elementary School as their highest educational level. In contrast, the deaths in municipalities with low, moderate, and high population density corresponded to individuals that were illiterate and belonged to the subsidized affiliation regime.\n\nThe model obtained for the profile of the deaths among cyclists due to traffic accidents was able to explain a total variance of 60.5%, distributed in 31.1% explained by Dimension 1 and 29.4% by Dimension 2. The eigenvalues of both dimensions were relatively close to each other, which indicates that they have similar relevance for the model (5.92 and 5.58, respectively). According to the discrimination measures, it was observed that the most important variables for Dimension 1 were “schooling level” and “affiliation regime”, whereas it was “age group” for the second dimension. Sex and population density failed to discriminate well between both dimensions. On the other hand, the variable that most contributed to explaining the total variance was “age group” (Figure 5).\n\nIn 1998, the deaths among cyclists in municipalities with average population density were mainly in women aged less than 45 years old, with Elementary School as the highest schooling level. On the other hand, in the municipalities with high population density, these deaths were represented by people aged between 45 and 59 years old with professional studies (Figure 6). In contrast with the above, for 2019, the deaths in municipalities with high population density were in people aged between 25 and 44 years old, with professional studies, from the contributory regime, and mainly women. In addition, it is possible to establish a profile for the cyclists aged more than 60 years old who die in traffic accidents: they mainly belong to the subsidized regime and have Elementary School as the highest schooling level (Figure 7).\n\nThe deaths of male pedestrians and cyclists were variable. They did not reflect the presence of a specific profile that allows for determining the characteristics of the men that die on the streets due to traffic accidents.\n\n\nDiscussion\n\nThe objective of this article was to analyze the profiles of pedestrians and cyclists who died as a result of traffic accidents in Colombia during the 1998-2019 period. Mortality was much higher among men than among women: three men for every woman in the case of the pedestrians and 13 men for every woman in the case of the cyclists. Despite the aforementioned, some profiles were identified that describe mortality in women; however, the variability of the characteristics of the men who die in traffic accidents did not allow for identifying a profile associated with men. Both for cyclists and pedestrians, the highest number of deaths was recorded in cities with high population density. 38.0% of pedestrians were over 60 years old, and, in the case of the cyclists, three out of ten were aged less than 25 years old. For both types of road actors, half of the victims had Elementary School as their highest level of schooling.\n\nAlthough riding a bicycle and walking have been promoted as active transportation means to improve health and environmental conditions throughout the world,16,17 there are few research studies focused on these road actors in low-middle countries,16 perhaps due to the significant attention directed to the accidents involving motorcyclists, drivers and passengers of vehicles.\n\nThe higher mortality rate due to traffic accidents among men reported in this study is consistent with the global behavior18 and showed no variation between the road actors. In the case of cyclists, it has been shown in other studies that men, mainly young ones, are a high-risk group related to greater exposure and lethality19 as a result of risky behaviors such as rule infringements, distractions, and lack of control,20 the person’s skill level,20 riding a bicycle at night and without a helmet, and consumption of alcohol and psychoactive substances,21 which are determinants for the accidents involving bicycles.22\n\nA comparative study of mortality due to traffic accidents showed that contrary to Spain and The United States,23 Colombia has failed to achieve significant reductions and that there is a marked increase in mortality among men, mainly in those under 25 (an increase 17.6%). However, a reduction between 20% to 68% of mortality was evidenced among the women belonging to the same age groups.23 This is congruent with our results; women had reductions in pedestrians by around 47% and in cyclists by 17%.\n\nParticularly in our study, we found that the number of deaths among pedestrians has shown a reduction over time, almost by half, specifically in Colombia, although the reduction percentages have been higher in other countries, close to 60%.24\n\nWe found the deaths among pedestrians are concentrated in older adults. In a study developed in Brazil, it has been described that they correspond to almost one-third of the overall mortality due to traffic accidents. On the other hand, pedestrians aged at least 60 years old present approximately 9.6 and 4.2 more risks of dying than people aged 0-19 and 20-59 years, respectively.25\n\nAmong other reasons, the risk derives from the existence of a traffic environment that is essentially dangerous and challenging for pedestrians and cyclists.24 Consequently, improving road safety for pedestrians is substantial, as it can be a representative element of the population’s quality of life.25\n\nIn relation to the mortality profiles found, important differences were observed between municipalities with high, moderate, and low population density when compared to those with very high population density. Contrary to our findings, previous evidence has shown that population density has been inversely correlated with the number of deaths due to this cause.26 This might be expected in areas where the interaction between vehicles and people would demand greater control, surveillance, and traffic signs to restrict the vehicles’ speed and protect pedestrians.\n\nThe common characteristics among the pedestrians who die in traffic accidents are mainly marked by age group and by the population density of the municipality where the accidents happen. However, they were also linked by schooling level, affiliation to the health system, and age group of the cyclists. In our study, we find that deaths by traffic accidents in pedestrians and cyclists are diverse and consider sociodemographic characteristics, similar to other studies.27–29 Among others, it has been described that traffic accidents are more frequent in the lowest socioeconomic strata, as people belonging to these groups in the social hierarchy tend to indulge in more risky behaviors and because, on the other hand, their access to health services is more precarious.30\n\nAnother factor associated with socioeconomic conditions is related affiliation to the health system. It has been shown that the delays in detecting the need to offer assistance and to provide care to traffic accident victims increase the severity of the injuries and, therefore, the probability of death.18 Treatment of these traumas may demand critical time frames: a delay of only a few minutes can preclude saving a life.18 In order to improve the care to be provided after the accidents, it is necessary to ensure that access to pre-hospital assistance is provided and to improve the quality of this care.18\n\nThe spatial separation of the transportation means might improve people’s sensation of safety and prevent accidents and collisions.16 Accident prevention might increase the willingness to walk and ride bicycles.16 To such end, strategies that allow for improving road design, road education, and citizen culture should be adopted. It can be very useful to adapt to the local reality of successful experiences from countries such as Spain, which, although still reporting significant mortality rates, have shown effective strategies to reduce accidents and mortality due to this cause.16\n\nRegarding the socioeconomic conditions, many low- and middle-income countries lack policies to improve safety for pedestrians and cyclists, or such policies are not complied with (or enforced) by the various actors.26 Especially in these countries, walking is a popular daily activity that offers extensive benefits for health and which, in addition, represents for many their only option to commute to the places they need for social functioning (schools, work, family, recreation).26 Approximately 91 countries, 9.0% of them of high income, have policies to promote walking or riding bicycles26; however, if these strategies are not accompanied by others, such as effective speed control and accessibility for pedestrians and cyclists, they might lead to an increase in the number of injuries due to traffic accidents.26\n\nA key strategy for a safe traffic system both for pedestrians and cyclists is to separate these users from the drivers of motor vehicles.25 Other studies have also shown that reducing speed is more important than improving the design of the vehicles in order to decrease the severity of the pedestrians’ injuries; the existence of regulations and speed limit monitoring, and strict law enforcement are important to reduce the number of injuries among pedestrians and cyclists. More coordinated education in safety is required, combined with community safety promotion activities.26\n\nOne of the limitations while developing this study was the lack of information regarding other variables that are a fundamental component of this complex system to understand the factors influencing traffic accidents. For example, the probability of death can change according to the type of vehicle involved in the pedestrian’s or cyclist’s death; in addition, there are several differences in the collision factors and in the injury patterns between the collisions involving cyclists and pedestrians with and without motor vehicles.\n\nHowever, the data reconstruction performed from 1998 to 2019 with essential variables in terms of inequalities is important, such as population density, sex, schooling level, and health insurance affiliation. This analysis and the profiles prepared to contribute to implementing evidence-based safety interventions. It has already been documented that these actions might prevent between 25% and 40% of all fatal injuries related to traffic accidents at the global level.\n\nThe main strength of this study is understanding differential mortality mechanisms for each road actor during an important period of time, including the characteristics (age, sex, Educational level, health insurance, and population density) of each one. The aforementioned becomes information for more reasonable decision-making processes when devising prevention strategies and, consequently, good results in reducing the mortality rates due to traffic accidents. This is in consequence of the challenges in road safety.4\n\nThis study was developed with an analysis of death data sets that are openly published and available online (here).\n\nIn order to ensure data privacy, the records are anonymous. This study is the result of the research project: Mortality trends (1992-2017) due to road incidents in Colombia according to road actors: Educational inequities, rural/urban inequalities, a differential burden on life expectancy, and retrospective evaluation of public policies in cities, from the CES University and the Ministry of Science and Technology through call 844-2019. This project has the endorsement of the Institutional Human Research Ethics Committee of CES University (Act No. 172 of 2021).\n\n\nAuthors’ contributions\n\nGino Montenegro-Martinez participated in conceptualization, formal analysis, Funding acquisition, investigation, methodology, project administration, supervision, the writing of the original draft, and the manuscript review & editing. Maite-Catalina Agudelo-Cifuentes participated in data curation, formal analysis, investigation, methodology, the writing of the original draft, and the manuscript review & editing. Diana-Isabel Muñoz-Rodriguez participated in formal analysis, investigation, writing of the original draft, and manuscript review & editing.", "appendix": "Data availability\n\nNo primary data are associated with this article. The secondary data used for this research, taken from the Vital statistics of Colombia, are freely available from the Departamento Administrativo Nacional de Estadística (DANE), freely available here. The data used for this study are available in the National Data File of Colombia. On this page, DANE makes available the anonymized open data from the different annual surveys carried out in the country. Users can access databases in specialized formats, such as SPSS, and general use formats, such as TXT, with many variables, which they can use unlimited. To access this data, you must enter this link, then go to “Citizen Service,” “Open data: microdata and macro data.” In the “Society” menu, select “Demographics and population” and enter the “EEVV Vital Statistics” option.\n\nFor the characterization, the death year and the municipality of occurrence were considered to elaborate the “population density” variable, adopting the number of inhabitants for 2010 (approximately half of the period under analysis) and the size of the municipality. The number of inhabitants for 2010 was taken from population projections published by Departamento Administrativo Nacional de Estadística (DANE), Municipal series of the population by area for the period 1985-2017 (freely available online here); the size of the municipality was taken from Municipios de Colombia (freely available online here). Subsequently, based on these data, the population density for each municipality was calculated as follows: population/km2. Subsequently, the quartiles were obtained considering the density of all the municipalities to classify them into municipalities with low, moderate, high, and very high population density based.\n\nMendeley Data: Multiple Correspondence Analysis Syntax for profiling analysis. https://doi.org/10.17632/tj6xkjh5vk.1. 31\n\nThis project contains the following extended data:\n\n- Sintaxis.docx (main syntaxis to develop multiple correspondence analysis)\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\nWorld Health Organization: Global status report on road safety 2018. World Health Organization; 2018. Reference Source\n\nInstitute for Health Metrics and Evaluation: DALYs by road injuries. Institute for Health Metrics and Evaluation.Reference Source\n\nWorld Health Organization-United Nations: Decade for Action for Road Safety 2021-2030. World Health Organization; 2021. Reference Source\n\nHyder AA, Hoe C, Hijar M, et al.: The political and social contexts of global road safety: challenges for the next decade. Lancet. 2022; 400: 127–136. S0140-6736(22)00917-5. PubMed Abstract \| Publisher Full Text\n\nUnited Nations: Resolution Improving global road safety, A/RES/72/299. United Nations; 2020. Reference Source\n\nUnited Nations: Sustainable Development Goals. United Nations; 2015. Reference Source\n\nInstitute for Health Metrics and Evaluation: Death by road injuries. Institute for Health Metrics and Evaluation. Reference Source\n\nInstitute for Health Metrics and Evaluation: DALYs road traffic injuries in Colombia. Institute for Health Metrics and Evaluation; Reference Source\n\nFasecolda: Costos de la accidentalidad vial en Colombia. Fasecolda; 2018. Reference Source\n\nAgencia Nacional para la Seguridad Vial: Observatorio -Estadísticas: Comparativo internacional.2022. Reference Source\n\nWorld Health Organization: Save LIVES: a road technical package. World Health Organization; 2017. Reference Source\n\nMinisterio de transporte Colombia: Proyecto Decreto “Plan Nacional de Seguridad Vial 2022-2031”. Ministerio de transporte Colombia; 2022. Reference Source\n\nRepública de Colombia: Ley 100 de 1993. Por la cual se crea el sistema de seguridad social integral y se dictan otras disposiciones.Reference Source\n\nRepública de Colombia y Ministerio de Salud y Protección Social: Comportamiento aseguramiento 1995-2020.Reference Source\n\nElías C: Elner Osmín: Análisis Multivariante: aplicaciones con SPSS. 1 ed.San salvador: UFG editores; 2016.\n\nFabricius V, Habibovic A, Rizgary D, et al.: Interactions Between Heavy Trucks and Vulnerable Road Users-A Systematic Review to Inform the Interactive Capabilities of Highly Automated Trucks. Front. Robot. AI. 2022 Mar 4; 9: 818019. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGildea K, Simms C: Characteristics of cyclist collisions in Ireland: Analysis of a self-reported survey. Accid. Anal. Prev. 2021; 151: 105948. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization: Road Traffic injuries. World Health Organization; 2022. Reference Source\n\nMartínez-Ruiz V: Contribution of exposure, risk of crash and fatality to explain age- and sex-related differences in traffic-related cyclist mortality rates. Accid. Anal. Prev. 2015; 76: 152–158. Publisher Full Text\n\nFrancke A, Anke J, Lißner S, et al.: Are you an ambitious cyclist? Results of the cyclist profile questionnaire in Germany. Traffic Inj. Prev. 2019; 20(sup3): 10–15. PubMed Abstract \| Publisher Full Text\n\nO’Hern O: Fatal cyclist crashes in Australia. Traffic Inj. Prev. 2018; 19(sup2): S27–S31. PubMed Abstract \| Publisher Full Text\n\nWang C: Aberrant behaviours in relation to the self-reported crashes of bicyclists in China: Development of the Chinese Cycling Behaviour Questionnaire. Transp. Res. Part F Traffic Psychol. Behav. 2019; 66: 63–75. Publisher Full Text\n\nAlarcón JD, Gich Saladich I, Vallejo Cuellar L, et al.: Bonfill Cosp X: Mortality caused by traffic accidents in Colombia. Comparison with other countries. Rev. Esp. Salud Pública. 2018; 92.\n\nMontero G: Mortalidad por accidentes de tránsito: su determinación social. Distrito Metropolitano de Quito, 2013. Rev. Cienc. Salud. 2020; 18: 1. Publisher Full Text\n\nFernandes CM, Boing AC: Mortalidade de pedestres em acidentes de trânsito no Brasil: análise de tendência temporal, 1996-2015. Epidemiol. Serv. Saúde. 2019; 28(1): e2018079. PubMed Abstract \| Publisher Full Text\n\nEid HO, Abu-Zidan FM: Pedestrian Injuries-Related Deaths: A Global Evaluation. World J. Surg. 2015; 39: 776–781. PubMed Abstract \| Publisher Full Text\n\nRoshanfekr P, Khodaie-Ardakani M, Sajjadi H, et al.: Income-Related Inequality in Traffic Accident Health Outcomes (Injury, Disability and Mortality): Evidence from the Nationwide Survey in Iran. Iran. J. Public Health. 2020; 49(4): 718–726. PubMed Abstract\n\nLomia N, Berdzuli N, Sharashidze N, et al.: Socio-Demographic Determinants of Road Traffic Fatalities in Women of Reproductive Age in the Republic of Georgia: Evidence from the National Reproductive Age Mortality Study 2014. Int. J. Women’s Health. 2020; 12: 527–537. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMokdad AA, Wolf LL, Pandya S, et al.: Road Traffic Accidents and Disparities in Child Mortality. Pediatrics. 2020; 146(5): e20193009. PubMed Abstract \| Publisher Full Text\n\nSehat M, Naieni KH, Asadi-Lari M, et al.: Socioeconomic Status and Incidence of Traffic Accidents in Metropolitan Tehran: A Population-based Study. Int. J. Prev. Med. 2012; 3(3): 181–190. PubMed Abstract\n\nMontenegro-Martínez G, Cifuentes A, Catalina M, et al.: Multiple Correspondence Analysis Syntax for profiling analysis. Mendeley Data. 2023; V1. Publisher Full Text" }	[ { "id": "169239", "date": "11 May 2023", "name": "Wilson Giovanni Jiménez Barbosa", "expertise": [ "Reviewer Expertise Health care policies" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIt is very interesting research that addresses a critical problem for Colombian public health. The mortality of cyclists and pedestrians generates impacts on the well-being of the population and on the costs of the health system.\nThe methodology used is clear and concise. Use reliable and verifiable official sources.\nIt is desirable that the results describe the number of bicyclist and pedestrian fatalities for each year in each one of the four defined groups of cities.\nAmong the results there is a finding that is not given due relevance: the high percentage of deaths, both cyclists and passers-by without affiliation to the health system. This finding would warrant further analysis to determine its behavior in each year of the period, since the number of people not affiliated with the health system has been constantly decreasing.\nI believe that the description of the profiles of deceased cyclists and passers-by could be presented by comparing the differences in the profiles of deceased between the years 1998 and 2019 for each group of cities. This would give a more specific perspective of the changes in the social characteristics of the deceased during the period.\nI suggest that in the introduction and in the discussion the history of the impulse that has been given to the use of bicycles in the country, particularly in Bogotá, be described as an alternative means of transport that reduces pollution, traffic congestion and that brings health benefits to its users.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "9885", "date": "25 Jul 2023", "name": "Maite Catalina Agudelo Cifuentes", "role": "Author Response", "response": "We appreciate your suggestions to improve the article. In the next lines, we describe each of the adjustments made considering your recommendations: 1. It is desirable that the results describe the number of bicyclist and pedestrian fatalities for each year in each one of the four defined groups of cities. Response: We agree with the evaluator; we made additional analysis guided to show the behavior of deaths of pedestrians and cyclists by population density for each year analyzed. 2. Among the results there is a finding that is not given due relevance: the high percentage of deaths, both cyclists and passers-by without affiliation to the health system. This finding would warrant further analysis to determine its behavior in each year of the period, since the number of people not affiliated with the health system has been constantly decreasing. Response: We agree with the evaluator; we analyzed the number and percentage of pedestrians and cyclists by health insurance regime. Particularly the number of people uninsurance has decreased by year; between 1998 to 2019, we report a decrease of 96.90%. This behavior is not exclusive to people who died on the roads; according to the data Health Ministry of Colombia is similar to health insurance behavior in the general population of Colombia. 3. I believe that the description of the profiles of deceased cyclists and passers-by could be presented by comparing the differences in the profiles of deceased between the years 1998 and 2019 for each group of cities. This would give a more specific perspective of the changes in the social characteristics of the deceased during the period. Response: We agree with the evaluator; it is relevant that profiles highlight the possible differences by population density. In other papers, this relation was reported. Following the literature review that supported the methodology of this article, it was relevant to highlight that mortality by road accidents is a multifactorial phenomenon involving different variables. In this sense, population density is a variable we consider for the profile's construction in pedestrians and cyclists. Therefore, we consider it unnecessary to show profiles stratified by population density because this variable is one of the other variables explaining the behavior of mortality by road accidents, which is evidenced in our analysis. 4. I suggest that in the introduction and in the discussion the history of the impulse that has been given to the use of bicycles in the country, particularly in Bogotá, be described as an alternative means of transport that reduces pollution, traffic congestion, and that brings health benefits to its users. Response: We agree with the evaluator, considering that in this article, we included an analysis of the behavior of cyclists' mortality, and recently, the bicycle, as a means of transport, has been promoted as an alternative to motor vehicles; we included some contextual data on the development of bicycle infrastructure and their use in our country." } ] } ]	1	https://f1000research.com/articles/12-360
https://f1000research.com/articles/12-878/v1	25 Jul 23	{ "type": "Research Article", "title": "Play and dance therapy: a review of theories, techniques and didactic methodologies for the motor recovery of children with disabilities", "authors": [ "Manuela Valentini", "Laura Teloni", "Anna Prokopiak", "Manuela Valentini", "Laura Teloni" ], "abstract": "Background: This research is aimed at analysing the effectiveness of play activities and dance-therapy programmes in improving the psycho-physical condition and increasing the well-being of individuals with disabilities. Methods: Online search engines (e.g., EBSCOhost, PubMed, the American Journal of Dance) were consulted using parameters such as \"physical disabilities\" or \"dance with music\" or \"childhood\" and excluding protocols published before 2010. Eleven intervention protocols were analysed. These concerned play and dance-therapy courses targeted at disabled subjects under 14 years of age. Results: It was found that at the end of the play sessions, higher muscular activation and improvement of quality of communication exchanges with the family members was found. With regard to the dance-therapy protocols, improvement was reported in general coordination, balance ability and a decrease in maladaptive behaviour in children with disabilities. Conclusions: With the improvement in physical performance, an increase in the subjects' state of well-being is also noted, underlining a strong body-mind connection. For future studies, it is recommended that the number of participants in individual studies should be larger and to include a control group to make the results generalisable on a large scale.", "keywords": [ "disabilities", "play sessions", "dance-therapy", "childhood", "technological devices", "well-being" ], "content": "Introduction\n\nThis research project originated from the observation that there are still problems for individuals with disabilities at both the physical and social level: in fact, while on the theoretical level of the scientific debate, it is widely accepted that all individuals with special needs should receive support and have the opportunity to improve their psycho-physical state, in reality teachers and caregivers encounter obstacles.\n\nIn 2006, the United Nations General Assembly promoted the Convention on the Rights of Persons with Disabilities:\n\n“(e) Recognising that disability is an evolving concept and that disability is the result of the interaction between persons with impairments and behavioural and environmental barriers, which prevent their full and effective participation in society on an equal basis with others.” (Preamble, paragraph E)\n\nThe disability is no longer conceived as an objective condition, but it is generated by the close connection with the characteristics of the social and cultural organisation of reference (Gaspari, 2017). The focus is placed on the overcoming various obstacles that children with disabilities can encounter in interpersonal relations: educational personnel must be aware of the influence that the social organisation has on the individual in a situation of disability (Cottini, 2017). From this perspective, social inclusion of children with disabilities is realised when there is an opportunity to create relationships with other children through play as a fundamental activity for learning about the world at a developmental age (United Nations, General Assembly, 2006).\n\nThe research project LUDI. Play for children with disabilities (Allodi & Zappaterra, 2019) investigated if the dimension of play is an integral part of daily life of individuals with disabilities with the focus on the concept of “Play for the sake of play”, which can be defined as the set of all those playful actions whose aim and object is play itself: the concept of “Play for the sake of play” has been widely recognised as fundamental, but at the same time individuals with disabilities find it difficult to have a fulfilling experience of play, also due to a lack of places and trained staff (Allodi & Zappaterra, 2019).\n\nIn order to make play accessible to all, there is the possibility of using technological devices such as the PALMIBER: a robotic vehicle that adapts to the subject’s level of mobility, so the children with disability can drive and move in space autonomously, interact with objects and take part in play activities with companions independently (Raya et al., 2015). The IROMEC robot acts as a mediator in social exchanges, helping children with disabilities to have a fulfilling experience of symbolic play and to understand respect for their turn and greater awareness of space and body (Besio et al., 2008). Finally, there are movement sensors (Kinect-sensors) that allow the projection of real children’s movements onto figures represented on the screen: during play sessions, the muscles of the hemiplegic limbs are activated in subjects with infantile cerebral palsy (Howcroft et al., 2012); in subjects with Autism Spectrum Disorder, play intensifies communicative exchanges as well as the ability to relate to peers and therapists. Participants also experienced positive emotions and attitudes of curiosity towards new technologies (Stancheva-Popkostadinova & Andreeva, 2018).\n\nIn addition to play, a further strategy for promoting the well-being of individuals with disabilities and promoting cohesion and a sense of belonging to a group concerns dance-therapy. In 1945, the dance teacher Marian Chace first used dance as a treatment for psychosis in a patient at St. Elizabeth’s Hospital in Washington DC, U.S. She wrote a report entitled “Classes in Rhythmic Movement,” in which she described her efforts to relate psychological theory to dance lessons (Cruz, 2016).\n\nIn March 1966, the American Dance Therapy Association (ADTA) was founded with the aim of investigating whether and to what extent movement and dance could have positive-curative repercussions for people with disabilities. Studies on dance therapy have studied the neuro-psychology/physiology/rehabilitation dimension, but also treatments for both physical and psychological trauma and the use of dance therapy in people with psychiatric and other disorders, such as depression and cancer treatment (Cruz, 2016).\n\nSzymanska-Kierlandczyk proves that dance is present in all spheres of human life. The special qualities of dance contribute to human development and have an impact on a person’s psycho-physical well-being. Dance often exhibits therapeutic properties. Dance absorbs the sense of sight, movement and balance. The pyramidal system, the extrapyramidal system and the cerebellum are involved in the movement activity. Dancing activates the entire brain: the sensory, cognitive and emotional executive functions (Szymańska-Kierlańczyk, 2022).\n\nDance-therapy is considered a science. As shown in research, movements can reflect the personality of the subject. During dance therapy sessions, a relationship is created between the therapist and the patient, and a change in movement patterns also results in a change in thought patterns. Furthermore, as dance therapy does not require the use of speech, it is also effective in all those situations where language difficulties are present: by means of movement, the child with disabilities can express needs while feeling accepted (Panagiotopoulou, 2011).\n\nThe aim of the following systematic review is to analyse the effectiveness of alternative techniques to medical-pharmacological treatment, such as play sessions and dance therapy, in improving the living conditions of persons with developmental disabilities.\n\nFirstly, three keywords are identified as coordinates for this research: disability, play, dance-therapy. Consequently, benchmarks like “physical disabilities”, “Intellectual disabilities”, “development”, “childhood”, “movement”, “play session”, “videogame”, “wellbeing”, “exercises” or “dance with music” are employed.\n\nThe search engines consulted were the university library system UrbIS (Urbino Integrated Search), EBSCOhost, PubMed, the American Journal of Dance (Springer Link), DIRImè, European Journal of Physical Education and Sport Science as well as book publications on the topic.\n\nThe inclusion criteria for the protocol selection was as follows:\n\n• Target audience pre-school age (3-6 years) and attending the first cycle of education (Primary school, up to Secondary school).\n\n• Publication date of the protocol between 2010 and 2022 so as to collect the most up-to-date information.\n\n• Adherence of the protocol content to the highlighted keywords.\n\n• Use of a “pre-test - intervention - post-test” methodology.\n\nTherefore, excluded from the survey were protocols involving participants attending secondary school and above, which had been written and published prior to 2010, and which did not adhere to the subject area of interest, or for which the research team had not implemented the “pre-test - intervention - post-test” technique.\n\nAs far as the presence of possible biases is concerned, reference is made to the confirmation bias: the research implementation process may in fact run the risk of inadvertent preference for protocols and studies supporting the assumption (i.e., “dance and play are alternative strategies with positive results in overcoming situations of disability”), rather than taking into consideration studies disproving the underlying assumption. Consequently, in an attempt to minimise this risk of bias, in the first consultation of each protocol, the reading was interrupted before reaching the results so as not to be influenced by the outcomes. Only at a second phase, the reading of the intervention protocols was completed.\n\nA total of 30 protocols were considered, of which 11 were included in the review, while 19 were excluded.\n\n\nMethods\n\nThe qualitative research conducted by Allodi and Zappaterra (2019) involved parents of children with intellectual disability (19%), autism spectrum disorder (17%), communication and speech disorders (15%), multiple disabilities (14%), motor disabilities (12%), visual impairment to the point of blindness (9%), hearing impairment to the point of deafness (8%) and other (6%) including Down syndrome, cerebral palsy, dyspraxia and attention deficit hyperactivity disorder. In addition, the 0-5 age range constitutes the 21% of subjects involved the 6-9 age range is the most numerous with 33%, followed by the 24% of children in the 10-13 range, ending with 22% of individuals aged between 14 and 18 years old. The two questionnaires about the children’s playing conditions show that when asked about the presence of adequate opportunities for play, 42% of children with disabilities answered “a little,” while 31% “No”. Furthermore, although the concept of Play for the sake of play is recognised as important by all family members, 64% of the relatives describe themselves as unhappy about the children’s play practices because they do not know how to interact with their sons and daughters. More specifically, the answers to the question “As a parent of a child with disabilities, please write the first three ideas/word that come to your mind when you think about your child’s play” were divided in two categories the “positive emotions” and the “negative emotions”: the first one contains words such as joy, respect, concentration, laughter, freedom; the second one includes concepts such as frustration, boredom, isolation, lack of concentration. It was pointed out that very often the playmates of people with disabilities are adults, rather than peers, due to the need for supervision by an adult, due to intellectual or motor difficulties that may occur. In conclusion, this qualitative research emphasises the need for children with disabilities to interact with peers and people of the same age, to increase the time available for play also because of the fact that they are often engaged in therapy or well-structured activities, and to take part in games that respect their level of psycho-physical development so they can experience fulfilling play situations.\n\nWhen approaching the issue of electronic devices used to support muscle activation during play sessions, Stancheva-Popkostadinova & Andreeva (2018) used the Kinect-sensor with children with Autism Spectrum Disorder (ASD) (3), hearing impairments (3) and cerebral palsy (4). Concerning the children with ASD, the play phase lasted between 6 and 10 minutes: they understood the instructions, implemented the correct movements to complete the delivery, their attention was adequately supported, and they also interacted verbally to ask for support during play. All three children with hearing impairment sustained the game for about 12 minutes, during which they understood the rules and they were easily involved in the actions: their attention was adequate throughout the duration of the game, and they were well-focused on guiding the figure on the screen. As for the children with cerebral palsy, they played for 10 minutes: the two with mild impairment played continuously and interacted with adults (one of them even tried to move his right hand affected by paralysis), while the other two children with moderate impairment were in constant need of support from professionals, and their movements were insecure. As a result, it can be stated that favourable outcomes were found: the children had an opportunity to work on gross motor skills in presence of disabilities while having fun.\n\nIn correlation, the following study, conducted by Howcroft et al. (2012) aimed to measure the muscle activation in 17 children with cerebral palsy aged 8–12 years during dance, tennis, boxing and bowling sessions using movement sensor. After each child has played all four sports, the measurements taken during the post-tests showed an increase in muscle strength. This was particularly the case with boxing and dance sessions as these sports engage the lower limbs in a more active manner, and which require a tighter rhythm of movement patterns, depending on the ability to move arms and legs simultaneously. At the same time, bowling was found to be the sport with the least muscular involvement as it requires simpler movements of the lower limbs and torso, followed by oscillations of the dominant arm. In conclusion, regarding the OMNI and PACES questionnaires, the researchers found a high level of involvement and enjoyment during the physical activity, which are determining factors for successful interventions.\n\nThe two following protocols being part of the DIRimè Project (Developmental-Individual-Relationship based model and Integration of Developmental Models), applied during play sessions, investigated the social behaviour of children with autism spectrum disorders by actively involving family members (Mirzakhani et al., 2022; Mahoney and Solomon, 2016), as autism spectrum disorder can be defined as “A multifactorial disorder: a consequence of the influence of genetic and environmental factors” (Prokopiak, 2022).\n\nThe study carried out by Mirzakhani et al. (2022) involved 60 children with ASD, aged 6-8, and their respective family members throughout a three-month period during which parents took part in play sessions. Although the Floor-time programme proved to be more fruitful than the Son-Rise one, the GARS-2 and ASSP scales showed that there were overall positive outcomes with a non-statistically significant variation between post-test and follow-up, demonstrating the stability of the improvements obtained over the time. More specifically, the research team found a significant decrease with respect to the stereotyped behaviour observed; these two approaches proved to be useful in increasing the communication skills of ASD subjects with a consequent improvement in the ability to establish social relationships. The second study about the DIRimè project conducted by Mahoney and Solomon (2016) included home-game sessions interspersed with hospital-game sessions, engaging 112 ASD 3-6-years-old children for one year. In post-tests, using the ADOS-G scale, positive effects were found on the children’s social involvement compared to the control group participants, while the CBRS and FEAS scales revealed a positive reciprocal influence between the responsive/affective behaviour of family members and improvements in the affective area of children with ASD. Therefore, in the long term, it can be stated that the difficulties typical of the Autistic Spectrum Disorder regarding social relationships can be improved through an intervention that actively involves the family environment and that is pervasive of the ASD subject’s daily life.\n\nIn the second part of the systematic review, the following studies are reported regarding the effectiveness of dance-therapy protocols. Takahashi et al. (2022) have outlined a dance-therapy protocol for 21 children with intellectual disabilities, ageing 3 to 6 years, carried out in a rehabilitation setting (control group: n.10 subjects; experimental group: n.11 subjects). After a cycle of 10 one-hour dance sessions, the HHD post-test registered an increase in the strength of the extensors of both knees for all 11 participants. Concerning the “one-leg stand” test, measurements of 9 of the 11 participants are considered: the results show that seven of the nine measurements considered increased the time during which they are able to be in balance on one leg only, while five out of nine gained less than one second on both legs. The third measurement, the TUG test, showed that, among of the eight eligible results, three children showed an increase in the time spent to carry out the movements, while five showed a decrease: as a consequence, the results of this test are not statistically significant. To conclude, the improvements in muscular and static balance, the decrease in maladaptive behaviour and anxiety-related disorders were possible thanks to specific DMT (Dance-Movement Therapy) interventions, such as listening to music, a continuous weight shift with a consequent change in the centre of gravity, improving the ability to maintain balance and the ability to synchronise their movements with those of the dance-experts. In addition, the risk of injury is significantly reduced.\n\nThe aim of this following dance-therapy intervention (Takahashi et al., 2020) is to evaluate the effectiveness of dance in improving the well-being of children with Williams syndrome, a rare genetic disorder that causes intellectual impairment, cardio-vascular abnormalities and physical-motor difficulties. Due to the very low incidence rate, only 4 children were involved ageing 5 to 10 years. During the post-tests sessions, the posturography shows a decrease in the total length of body oscillations (the measurements were taken both with closed and open eyes). Regarding the HHD test, all four participants showed improvements in the extensor muscles, while three out of four showed improvements in the knee flexor muscles. Two participants increased their left plantar flexor strength, while one on the right one. Two participants enhanced the dorsiflexion ability of the left ankle, none on the right one and three out of four participants recorded an increase in muscle strength in hip extension. The post-test TUG showed that only one participant (a 5-year-old girl) decreased the recorded time by 1.45s, while the other three participants recorded a change of <1s. In conclusion, being aware of the small sample due to the rarity of the syndrome and the fact that this kind of intervention was not preceded by other previous specific studies, it can be stated that this report proposes methodologies with related highly valuable results, encouraging for future research since improvements have been identified, especially with regard to the ability to maintain balance and increase the strength of the knee muscles.\n\nIn the following study, conducted by McGuire et al. (2019), the experimental group consisted of six children with Down Syndrome aged 7 to 13 years. After the conclusion of a 20-minute dance session, in order to verify the extent of improvements/worsening of the psycho-physical conditions of the subjects involved, the research team used the measuring instruments from the pre-tests (GMFM-88 and COPM). With regard to the GMFM-88 scale, dimensions D-E, improvements were observed in all participants, with particular emphasis on case no. 5, (a 4-year-old girl with DS who also attended swimming lessons). On the COPM scale, improvement was recorded for five participants out of six with an average deviation of 2.36 points for the “Performance” section and of 3.36 points for the “Satisfaction” section. On the contrary, for the sixth participant (a 13-year-old girl) there was a deterioration in performance of 1.2 points and in satisfaction by 0.2 points. In conclusion, for individuals with DS, this protocol identified an adapted dance programme as a good basis on which to set future interventions with a focus on the improvement of gross-motor skills.\n\nThe ninth study was carried out by López-Ortiz et al. (2016) and included 11 children with Cerebral Palsy ageing 7 to 14 years (control group: n.6 subjects; experimental group: n.5 subjects). Firstly, one week and then one month after the end of the dance-therapy, the post-tests were administered using the same rating scales: the PBS scale recorded statistically significant improvements in the ability to maintain static and dynamic balance. Conversely, the QUEST test did not show statistically significant results, since either the situation remained unchanged or there were minimal increases in upper limb movement and control skills. In conclusion, it was observed that a greater improvement in the execution of the movements concerns younger subjects than the other children involved: this aspect reflects a trend, already highlighted in the scientific literature, whereby subjects with CP, for the first 7 years, are capable of significant improvements in their development of physical abilities, followed by a stabilisation.\n\nAithal et al. (2021) investigated the use of dance-therapy to promote the wellbeing of 26 ASD 8-13-year-old children using the crossover method:\n\n‐ First phase “Experimental group 1, control group 2”: about the SCQ scale, for the pre-crossover interventions in the results of the post-tests of experimental group 1 there was a decrease of 1.8 points, whereas the values reported for control group 2 remained almost unchanged compared to the pre-tests. Concerning the SDQ scale, before the crossover, experimental group 1 reported a decrease of 1.7 points compared to the pre-test and control group 2’s situation did not change.\n\n‐ Second phase “Control group 1, experimental group 2”: about the SCQ scale for the post-crossover interventions, experimental group 2 saw a decrease of 1.6 points compared to the pre-test, while for control group 1 the score remained unchanged. With regard to the SDQ, following the crossover, experimental group 2’s post-test reported a decrease of 2.3 points compared to the pre-test, while control group 1 did not fluctuate in values.\n\nThe last research, conducted by Marouli et al. (2021) investigated the effectiveness of Greek traditional dance in 8 ASD 6-14-year-old children (control group: n.4 subjects; experimental group: n.4 subjects). Using the BOT-2 scale, all participants in the experimental group increased their performance on both the item “Tapping feet and finger” by 3.5 points on average and “Standing on a balance beam” by 1.8 points on average. Three out of four participants reported an average increase of 1.5 points for “Copying a square”, by 1 point on “Walking forward on a line” and by 2.25 points on “Jumping with one leg”. For the two items “Drawing a line on a zigzag path” and “Folding a paper” no improvement was noted, while, conversely, in ‘Transferring pennies’ an optimisation of the gesture was reported for all participants in control group A. Thus, although the sample taken is not large, it can be stated that the traditional Greek dance-therapy programme had positive effects on movements involving static and dynamic balance, gross gross-motor skills and motor co-ordination, while fine motor skills were found to be still deficient.\n\n\nSummary and conclusion\n\nWith regard to play, electronic devices have been shown to be effective in supporting both whole-body muscle activation accompanied by improved communicative exchanges (Howcroft et al., 2012; Stancheva-Popkostadinova & Andreeva, 2018); Furthermore, in the two DIRimè projects aimed at ASD subjects, the involvement of family members has been shown to be effective in improving the quality of behaviours enacted by subjects with Autism Spectrum Disorder (Mahoney & Solomon, 2016; Mirzakhani et al., 2022).\n\nThe interventions realised through dance-therapy sessions have shown that, when the goal of improving physical performance is achieved, an increase in the subjects’ state of well-being is also noted. This is possible, in fact, thanks to the solid body-mind connection, present in every subject regardless of the presence or absence of deficits (Aithal et al., 2021).\n\nConsequently, motor activity, in this particular case experienced through dance and play, must no longer be conceived only as a rehabilitative methodology at a muscular level, but its social impact must also be taken into account: if a person with disabilities is able to move more easily and have control over his or her movements, he or she will also be able to participate in social life in a more fulfilling manner.\n\nFinally, with regard to future research developments, it is desirable to involve an increasing number of participants in individual studies and to add a control group where possible so as to extrapolate the results onto a large scale (McGuire et al., 2019).\n\nHereafter is reported a table summarising all the protocols considered, the children involved, the type of intervention and the type of evidence registered (Table 1).", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAithal S, Karkou V, Makris S, et al.: A Dance Movement Psychotherapy Intervention for the Wellbeing of Children With an Autism Spectrum Disorder: A Pilot Intervention Study. Front. Psychol. 2021; 12: 588418. pp. 1-15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAllodi MW, Zappaterra T: Users’ Needs Report on Play for Children with Disabilities: Parents’ and Children’s Views. De Gruyter Poland Ltd; 2019. (A c. Di). part of Walter de Gruyter GmbH (pp. 4-14: Encarnação, P. and Saridaki, M.), (pp. 15-20: Encarnação, P.), (pp. 29-42: Allodi, M. W., et al.), (pp. 42-69: Allodi, M. W., et al.)\n\nBesio S, Caprino F, Laudanna E: Lecture Notes in Computer Science.2008; pp. 545–552.\n\nCottini L: Didattica speciale e inclusione scolastica. Carocci editore S.p.A.2017; pp. 36–41.\n\nCruz RF: Dance/Movement Therapy and Developments in Empirical Research: The First 50 Years. Am. J. Dance Ther. 2016; 38(2): 297–302. Publisher Full Text\n\nGaspari P: Per una pedagogia speciale oltre la medicalizzazione. Milano: Guerini scientifica; 2017; 26.\n\nHowcroft J, Klejman S, Fehlings D, et al.: Active Video Game Play in Children With Cerebral Palsy: Potential for Physical Activity Promotion and Rehabilitation Therapies. Arch. Phys. Med. Rehabil. 2012; 93(8): 1448–1456. PubMed Abstract \| Publisher Full Text\n\nLópez-Ortiz C, Egan T, Gaebler-Spira DJ: Pilot Study of a Targeted Dance Class for Physical Rehabilitation in Children with Cerebral Palsy. SAGE Open Med. 2016; 4: 1–5. 205031211667092. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMahoney G, Solomon R: Mechanism of Developmental Change in the PLAY Project Home Consultation Program: Evidence from a Randomized Control Trial. J. Autism Dev. Disord. 2016; 46(5): 1860–1871. PubMed Abstract \| Publisher Full Text\n\nMarouli E-A, Kaioglou V, Karfis V, et al.: The Effect of a Greek Traditional Dance Program on the Motor Competence of Children with Autism Spectrum Disorder. Eur. J. Phys. Educ. Sports Sci. 2021; 7(3): 1–14. Publisher Full Text\n\nMcGuire M, Long J, Esbensen AJ, et al.: Adapted Dance Improves Motor Abilities and Participation in Children With Down Syndrome: A Pilot Study. Pediatr. Phys. Ther. 2019; 31(1): 76–82. PubMed Abstract \| Publisher Full Text\n\nMirzakhani N, Asadzandi S, Ahmadi MS, et al.: The Effect of Son-Rise and Floor-Time Programs on Social Interaction Skills and Stereotyped Behaviours of Children with Autism Spectrum Disorders: A Clinical Trial. Cad. Bras. Ter. Ocup. 2022; 30: e3253. Publisher Full Text\n\nPanagiotopoulou E: Dance Therapy Models: An Anthropological Perspective. Am. J. Dance Ther. 2011; 33(2): 91–110. Publisher Full Text\n\nProkopiak A: Kelly Hunter Heartbeat Method in Theatre Work with People with Autism Spectrum Disorders. Special School. 2022; LXXXIII: 47–55. Publisher Full Text\n\nRaya R, Rocon E, Urendes E, et al.: Assistive Robots for Physical and Cognitive Rehabilitation in Cerebral Palsy.Mohammed S, Moreno JC, Kong K, et al., editors. Intelligent Assistive Robots. Springer International Publishing; 2015; (Vol. 106. : pp. 133–156). (A c. Di). (pp. 140-142). Publisher Full Text\n\nStancheva-Popkostadinova V, Andreeva A: Piloting Interactive Kinect-based Game in Children with Disabilities. Today’s Children, Tomorrow’s Parents. 2018; 47-48: 86–99.\n\nSzymańska-Kierlańczyk A: Terapia tańcem w autyzmie.Pietras T, Podgórska-Jachnik D, Sipowicz K, et al., editors. Spektrum autyzmu – od diagnozy i terapii do integracji i inkluzji. Wrocław: Wydawnictwo Continuo; 2022; pp. 641–657.\n\nTakahashi H, An M, Matsumura T, et al.: Effectiveness of Dance/Movement Therapy Intervention for Children with Intellectual Disability at an Early Childhood Special Education Preschool. Am. J. Dance Ther. 2022; 2–21. Publisher Full Text\n\nTakahashi H, Seki M, Matsumura T, et al.: The Effectiveness of Dance/Movement Therapy in Children with Williams Syndrome: A Pilot Study. Am. J. Dance Ther. 2020; 42(1): 33–60. Publisher Full Text\n\nUnited Nations, General Assembly: Convention on the Rights of Person with Disabilities.2006; p. 5." }	[ { "id": "245565", "date": "27 Mar 2024", "name": "Tatiana Ogourtsova", "expertise": [ "Reviewer Expertise systematic reviews/scoping reviews", "pediatrics", "developmental disability", "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 manuscript is a systematic review on the effects of play and dance therapy on psycho-physical condition and well-being in children with disabilities. While reviewing the manuscript, several areas where improvements could enhance the overall quality and impact of the work were noted:\nThe rationale for conducting a systematic review in this area could be made clearer. It would be helpful to discuss any previous reviews on this subject to contextualize your contribution. Consider structuring your research question in a PICO format and provide clear operational definitions for terms such as \"living conditions\" to enhance clarity and precision. Clearly delineate your population of interest as part of the research question. Present a comprehensive search strategy to ensure transparency and replicability in your literature review process. Could be presented as an appendix. Adherence to PRISMA guidelines is essential for systematic reviews. Ensure that your manuscript explicitly references these guidelines and follows them in both its methodology and reporting. Revise the flow chart to align with PRISMA standards, providing a clear visual representation of the study selection process. Consider utilizing two raters for the search and data extraction processes to enhance reliability and mitigate bias. It is essential to assess the quality of the studies included in a systematic review. Incorporating a quality assessment tool and reporting its findings would strengthen the rigor of your analysis. Enhance the comprehensiveness of your data extraction process to ensure that all relevant information is captured accurately. While not always feasible, conducting a meta-analysis can provide valuable insights by quantitatively synthesizing data from included studies. Consider whether this approach is appropriate given the available data. Strengthen the discussion section by contextualizing your findings within the existing literature and acknowledging the limitations of your study. Providing insights into future research directions can also enrich the discussion.\nOverall, addressing these areas will contribute to the robustness and impact of your manuscript, enhancing its value to the scientific community.\"\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? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-878
https://f1000research.com/articles/12-872/v1	24 Jul 23	{ "type": "Research Article", "title": "Comparative evaluation of platelet rich fibrin matrix (PRFM) membrane and platelet rich fibrin (PRF) membrane using the vestibular incision subperiosteal tunnel access (VISTA) approach technique for the treatment of multiple gingival recession in humans: A double-blind, parallel-group, randomized controlled clinical trial", "authors": [ "Safiya Hassan", "Prasad Dhadse", "Pavan Bajaj", "Kiran Sethiya", "Chitrika Subhadarsanee", "Ranu Oza", "Prasad Dhadse", "Pavan Bajaj", "Kiran Sethiya", "Chitrika Subhadarsanee", "Ranu Oza" ], "abstract": "Background: In this evolutionary era of dentistry, newer techniques have evolved for complete coverage of multiple recession defects (MRDs). Since 2012, MRDs have been treated using the vestibular incision subperiosteal tunnel access (VISTA) approach and a variety of regenerating membranes with varying degrees of success. Platelet‑rich fibrin matrix (PRFM) membrane has shown a robust release of growth factors and was known to enhance the healing process. Thus, in this study we have evaluated the effectiveness of platelet-rich fibrin matrix (PRFM) with that of platelet-rich fibrin (PRF) membrane using the vestibular incision subperiosteal tunnel access (VISTA) technique in Miller Class I and II multiple gingival recession defects. Methods: This randomized, parallel designed, controlled, clinical study was conducted in 20 subjects (10 male and 10 female) having class I/II MGR defects either buccally or labially. The test group was treated with VISTA and PRFM membrane while the control group was treated with VISTA and PRF membrane. The clinical measurements such as plaque index, papillary bleeding index, probing pocket depth, relative attachment level (RAL) and relative gingival marginal level (R-GML), width of keratinized gingiva (WKG), gingival recession (REC) and gingival thickness (GT) were measured at baseline, three and six months. A Student’s paired t-test was utilized to analyse data from the day of surgery to six months. Results: Ten patients in the test group (89.23±15.04) and 10 patients in the control group (85.06±17.71) showed marked root coverage compared to baseline. Conclusions: Both test and control groups showed statistically significant enhancement in root coverage. However, no statistically significant difference was found when a comparison was made between the two groups in terms of PD, relative RAL, R-GML and REC reduction, gain in WKG, and increase in GT. Trial registration: CTRI/2021/07/035240, registered 29 July 2021.", "keywords": [ "vestibular incision subperiosteal tunnel access", "VISTA", "platelet rich fibrin matrix", "PRFM", "platelet rich fibrin", "PRF", "gingival recession", "randomized controlled trial" ], "content": "Introduction\n\nGingival recession (GR) is a common patient related complaint, which occurs when the position of the marginal gingiva shifts unfavorably. Recession presentation has been observed to follow two broad patterns: localized and multiple types. Multiple gingival recession (MGR) is more common than its localized variation with higher aesthetic demand because of the more common traumatic origin. The large areas of the avascular root surface that needs to be covered further complicates the MGR management.1 Management of single or MGR with various surgical techniques relies on a variety of parameters, including the extent of the defect, whether or not keratinized tissue surrounds the defect, the thickness of the gingiva surrounding the defect, and the patient compliance.2\n\nThe fundamental goal of treating buccal or labial recession defects is to reconstruct the gingival architecture, and whether efforts are made to enhance tissue properties. Traditionally, pedicle grafts, free soft-tissue grafts, and guided tissue regeneration (GTR) have all been used to address recession defects. The decision to choose one modality over another from the variety depends on the number, type, and patient-related aspects of the defects.1 The critical patient element to be considered before choosing a particular procedure is high aesthetic demand with a requirement for low postoperative distress. Both bilaminar and coronally advanced flap (CAF) methods have been used to correct MGR. According to a systematic review, the clinical parameters can be improved by CAF with or without a connective tissue graft (CTG).2 Amongst them, CAF with CTG is regarded as the gold standard for periodontal root coverage (RC) and soft tissue augmentation. It has some drawbacks, including the need to harvest from a donor tissue, the scarcity of available tissue, and the increased risk of post-harvest morbidity.3\n\nThe tunneling technique introduced by Allen in 1994 is yet another significant addition in CAF.4 Since its introduction in 1994, numerous procedural changes have been suggested. Vestibular incision subperiosteal tunnel access (VISTA), a minimally invasive subperiosteal tunnel approach, was introduced by Zadeh in 2011. It allows access to multiple teeth through a single vertical incision.3 It also simplifies the tunneling method and enhances the profile of wound healing.5,6 Additionally, the VISTA in combination with different graft materials produced intriguing results.3,7–9 The successful treatment of multiple recession defects (MRD) can be achieved with the minimally invasive VISTA approach which has several benefits. The possibility of lacerating the gingiva of the teeth being treated is decreased by the vertical incision made medial to the defect. Additionally, subperiosteal dissection minimizes gingival margin (GM) tension during coronal advancement and keeps the interdental papillae blood supply intact. GR coverage is improved with the VISTA procedure when the GM is moved coronally to the cemento-enamel junction (CEJ) with an augmented graft or membrane and fixed in a secure position to avoid recurrence at an early stage of recovery.10\n\nClinicians are always on a quest for an appropriate bioactive surgical adjuvant that can control inflammation while simultaneously promoting healing. The events that follow the postoperative period determine complex wound remodeling and tissue survival. Recombinant growth factors, for example, have been demonstrated to promote periodontal wound healing when used as an adjuvant.11 A second-generation platelet concentrate called platelet rich fibrin (PRF) was introduced in 2005 by Choukroun et al.12 One such bio-healing substance that is important for both effective hard- and soft-tissue repair is PRF. It delivers vital healing dynamics that lead to reduced postoperative pain and advanced tissue recovery.12 Multiple cell lines with immunological activity have shown a good response to PRF, and viable platelets in PRF release the six required growth factors.13 The advantages of PRF in different surgical procedures have been assessed and found to be adequate.13,14 Additionally, its beneficial effects on many cell lines, particularly the fibroblastic cell line, have been ascertained.15 Recent histological research examined CTG with or without PRF in treating recession and said that the PRF group had early vascularity and tissue maturation.16\n\nAutologous platelet concentrates are a promising new approach to periodontal regenerative therapy. Numerous studies have examined the efficiency of platelet rich plasma (PRP) and PRF in a variety of therapeutic conditions that demand rapid healing and have discovered favorable clinical and radiographic findings.17–19 Due to these encouraging results, it is necessary to compare and contrast PRF with the recently created platelet rich fibrin matrix (PRFM), which involves a streamlined technique without artificial biomodification. The creation of autologous PRFM as a growth factor delivery method is an advancement in the dental field. It consists solely of centrifuged blood without any additions or biochemical processing. PRFM is a therapeutic biomaterial with great capability for bone and soft tissue regeneration, which combines the qualities of fibrin, platelets, leukocytes, growth factors, and cytokines.20 Compared to a typical human blood clot, the autologous biomaterial PRFM contains a dense concentration of platelets. Growth factors found in its alpha granules impact every cell and the development of every tissue involved in wound healing. It releases growth factors (GF) abundantly and these are essential elements in the course of wound healing through signaling transduction mechanisms. Soft tissue and bone regeneration have demonstrated an immense potential role in regenerative therapy.21 In vitro research by Carroll et al.22 from 2005 revealed that viable platelets in PRFM released six GFs throughout their seven-day study, primarily platelet-derived growth factor (PDGF), vascular endothelial growth factor (VEGF), epidermal growth factor (EGF), and fibroblast growth factor (FGF).\n\nThe present study was undertaken to compare the efficacy of the PRFM membrane with that of the PRF membrane using the VISTA approach for obtaining RC in patients with Miller’s class I/II MRDs. Since the minimally invasive VISTA approach permits better access, gingival margin stabilization and coronal positioning, PRFM and PRF overcome the drawbacks of CTG.\n\n\nMethods\n\nThe current randomized, controlled, parallel designed clinical study was conducted in 20 subjects as determined by a sample size calculator (OpenEpi, version 3, open-source calculator – SSMean) by comparing two means at 95% confidence interval and a computer-generated random number was generated (10 male and 10 female). We adhered to the CONSORT checklist for reporting clinical trial protocols.23 Patients with an age range of 25 to 50 years (mean age of 33.7 ± 7.11) with MGR defects on the buccal and/or labial surfaces of the teeth were enrolled in the outpatient department of Periodontics, Sharad Pawar Dental College and Hospital, Wardha, Maharashtra. Approval for the research protocol was given by the Institutional Ethics Committee (DMIMS) Wardha, Maharashtra, (IEC No. DMIMS (DU)/IEC/2020-21/9415, date of approval: 24/12/2020). Clinical trial registration: CTRI/2021/07/035240, registered 29 July 2021.\n\nThe purpose and essence of the research were explained to each subject before starting the technique, and the written informed consent of each subject was obtained.\n\nParticipants were recruited from the outpatient department of Periodontics, Sharad Pawar Dental College and Hospital, Wardha, Maharashtra.\n\nHealthy subjects without any systemic illness with MGR (>1) on their labial/buccal surfaces, GR depth ≥ 2 mm, and presence of adequate width of keratinized gingiva (WKG) were included. To match all the characteristics of included subjects at baseline the age group of the subjects was in the range of 25 to 50 years.\n\nSubjects with poor oral hygiene following “etiotropic/phase I periodontal therapy” and exhibiting plaque scores greater than or equal to 1, mobile teeth, any systemic diseases, suspected or known allergies to drugs or study materials, use of tobacco in any form, immune-compromised subjects, alcoholics, lactating or pregnant women, and subjects with compromised immune systems were excluded.\n\nAfter initial therapy and before surgery for this study, all subjects with at least two or more adjacent GR defects were chosen. A computer-generated random number (Research Randomizer software (Version 4.0) (an open-access alternative is Random Allocation Software (Version 2.0))) was generated following a simple randomization technique, with an equal number of subjects allocated in the test and control groups. Once the allocation sequence was generated, a single examiner (CS) allocated the patients into two groups. A second examiner (SH) was blinded to the allocation sequence and the examiner who gave the intervention was blinded. Participants and the examiner were both blinded during the allocation system. The test group was managed by VISTA and PRFM membrane (n = 10) while the control group was treated with VISTA and PRF membrane (n = 12). A re-evaluation was performed at three and six months of therapy for the estimation of outcomes.\n\nCustom made occlusal acrylic stents were made to standardize the probe position and angulations. Alginate impression was prepared to make a cast model of both jaws. An acrylic stent was prepared on the cast model at baseline and six months. The occlusal stent was covering the occlusal surfaces of the teeth and occlusal surface of at least one tooth distal and mesial to it. At the deepest site of the involved tooth a reference point was made for positioning of the UNC 15 periodontal probe (University of North Carolina, Hu-Friedy, Chicago, USA). The apical margin of the stent was considered as a fixed reference point. (To prevent measurement variability, a fixed reference point was established at baseline to duplicate the same location during the subsequent visits.) Assessment of the primary outcomes was carried out with the help of the following clinical measurements. The probing pocket depth (PPD), relative gingival margin level (RGML), and relative attachment level (RAL) was assessed with a UNC-15 calibrated periodontal probe (University of North Carolina, Hufriedy) and rounded up to the nearest millimetre marking – in case of doubt, lower values were considered. All probing measurements were recorded in the individual tooth at peak recession depth (mid-facially). These clinical recordings were noted at baseline and at the six months recall visit.\n\nThe UNC-15 calibrated periodontal probe was positioned in the slot given on the custom-made stent and a measurement was taken from the stent’s bottom edge to the gingival margin, which corresponds to the RGML. The distance to the lower border of the prefabricated stent was then noted as the RAL while the probe was still held at the base of the pocket. By subtracting the RGML from the RAL value, PPD was recorded. WKG was recorded from the most apical portion of mucogingival junction (MGJ) to the margin of gingiva on the mid labial aspect of the experimental teeth with the help of William’s graduated probe (GDC Single End Probes #3 (Pcpunc15). REC was calculated from the CEJ to the gingival margin with the help of a UNC-15. Gingival thickness (GT) was calculated 3 mm below the gingival margin, under topical anesthesia and using an endodontic reamer with a rubber stopper.\n\nFor a detailed description please refer to the research protocol in the underlying data.24,25\n\nFor the production of PRFM, 10 mL of blood was obtained from the antecubital vein through venipuncture for one minute from the patients. Within 30 seconds, the samples were transferred to the Meresis PRFM kit (*R-4C, REMI Laboratory Instruments, Mumbai, India) and positioned in the centrifuge. A single-spin centrifuge (Remi R-8C 16×15 ml Laboratory Centrifuge with Angle Rotor Head) was used to centrifuge the sample for 10 minutes at 3000 rpm. The upper layer of PRFM clot was obtained and placed in a PRFM box after centrifugation and pressed to produce PRFM membranes.22\n\nA sample of 10 mL of blood was collected from the antecubital vein of each patient, placed in sterile glass test tube and centrifugated at 3000 rpm for 13 minutes in a centrifuge machine (Remi R-8C 16×15 ml Laboratory Centrifuge with Angle Rotor Head). After centrifugation, a fibrin clot from the upper layer was obtained, and the remaining red blood cells were removed. To obtain the PRF membrane, the clot was transferred to a PRF box and compressed (Choukroun et al. 2006).26\n\nAll the patients were educated to use oral rinse 0.2% chlorhexidine gluconate (CHX) (Hexidine Mouthwash ICPA health products LTD) for 30 seconds before the treatment. Infection control and full asepsis were maintained during the surgical process. After a 2% Xylocaine containing 1:80,000 concentration of epinephrine (Ligno-Ad local anesthetic, Proxim Remedies, India) anesthetic was administered, the denuded root surfaces were thoroughly cleaned and planed using curettes and an ultrasonic device (Woodpecker HW-3H). Gingival recession seen with three teeth numbered as 23, 24, 25 as shown in Figure 1 and gingival recession seen with two teeth numbered as 14, 15 as shown in Figure 2. Crevicular incision given as shown in Figure 3 and Figure 4. In the vestibule mesial/distal to the surgical site, a full-thickness vertical incision 8–10 mm in length was made as shown in Figures 5 and 6. The vertical incision was not extended all the way to the gingival edge but functioned as a portal for the expansion of the subperiosteal tunnel. The osseous plate was exposed, and a blunt Orban’s knife was used to expand the tunnel up to one or two teeth beyond the surgically corrected recession location. Furthermore, without penetrating the papillary tip, the sub-periosteal tunnel was expanded into the inter-papillary area. The slow apical motion of the knife via the papillary area connects to the vestibular tunnel, allowing the mucogingival covering the MRD to migrate coronally. This subperiosteal tunnel was moved coronally and passively placed over CEJ, which will cover the MRD. Coronal anchoring sutures were engaged 2–3 mm apically to the gingival border of each tooth. To avoid apical displacement of the marginal gingiva, the suture was joined with a resin composite button at the mid-coronal position of each tooth’s buccal aspect as shown in Figures 7 and 8. After coronal stabilization, using a small periosteal elevator, a freshly made PRFM membrane was inserted into the tunnel in the test group (as shown in Figure 9) and a PRF was inserted in the control group (as shown in Figure 10) and they were uniformly distributed throughout all defects. The vertically placed incision was sutured for the primary closure when the membrane had fully adapted as shown in Figures 11 and 12. A Coe pack was used to cover the whole surgical site. A pre- and post-operative view of the test group at six months is shown in Figures 13 and 14. Figures 15 and 16 show a pre- and post-operative view of the control group at six months.\n\nAfter the procedure, a non-steroidal anti-inflammatory, consisting of a blend of Ibuprofen 400 mg and Paracetamol 325 mg and antibiotic Amoxicillin 500 mg TID were prescribed for five days. For three weeks following surgery, participants were instructed not to brush their teeth at the treated areas. For 14 days, all individuals were asked to oral rinse with 0.2% CHX two times daily. Patients were informed to avoid any damage to the pack. Removal of the periodontal pack was done after seven days followed by suture removal after 14 days, healing was observed. Proper care was taken while saline irrigation and polishing with rubber-cup & polishing paste, to avoid damage to the involved sites. Patients were asked to clean the treated area with 0.2% CHX soaked cotton, for additional seven days before brushing using Charter’s approach. The recall periods were set at one, three and six month intervals after the surgical procedure.\n\nThe mean and standard deviation (Mean ± SD) scores for all clinical measures were documented. The statistical significance of the mean data was assessed using conventional statistical techniques. Student-paired t-tests were applied for data comparison within each group from baseline to six months, whereas student unpaired t-tests were utilized for data comparison across groups. If the probability value (p) was ≤0.05 it was significant and ≥0.05 it was non-significant. All data were assessed using SPSS 11.0 (SPSS Inc, 2003) (RRID:SCR_019096) software.\n\n\nResults\n\nTwenty-eight patients were screened of which eight patients did not fulfill the inclusion criteria. Randomization of 20 patients were done and 10 patients were allocated to each group. No patients were lost to follow-up and 20 patients were analyzed at three and six months as shown in Figure 17.\n\nTwenty systemically healthy patients with a mean age of 33.7 ± 7.11 in the test group and 35.1 ± 8.23 in control group (Age range: 25 to 50 years) presenting with 48 labial/buccal multiple (≥2 teeth) GR defects (>2mm) were treated in the present study.\n\nThe healing process was uneventful throughout the research. Until the first postoperative visit, the periodontal dressing remained in place. No patient had any post-operative complications. None of the participants withdrew before the completion of study and all were pleased with the outcome.\n\nTable 1 displays the mean full mouth plaque index (FMPI) and full mouth papillary bleeding index (FMPBI) score at baseline and six months for both groups. We found a statistically significant decrease in FMPI and FMPBI score at six months (p < 0.05) in both groups. The mean FMPI scores during the six-month study period remained low (<1), in both groups which could be because of reinforcement of oral hygiene instructions.\n\n(Mean ± SD in mm).\n\nAll the investigated parameters in both groups at baseline were observed to be statistically non-significant (p >0.05), indicating the same starting point for both procedures. Clinical parameters RGML, REC, RAL, PPD, WKG and GT revealed a significant reduction (p < 0.05) after six months compared to baseline in both groups (Tables 2 and 3).\n\n(Mean ± SD in mm).\n\n(Mean ± SD in mm).\n\nThe comparison between mean RGML reduction in the test (2.58 ± 0.50 mm) and control groups (2.37 ± 0.49 mm) at six months indicated no significant difference (p = 0.23) in both groups by 0.20 ± 0.83 mm. Comparison of mean CAL gain among groups at six months indicated no statistically significant difference (0.20 ± 1.06 mm). The mean reduction of PPD for the test group was 0.5 ± 0.51 mm when compared to the control group 0.5 ± 0.51 mm at six months, and no significance difference was found (p > 0.50). At six months, the comparison of the mean increase in WKG in the test group (2.04 ± 1.36 mm) with the mean gain in WKG in the control group (1.5 ± 1.35 mm) showed no significant difference (p-0.18). The difference between the mean GT rise in the test group (0.77 ± 0.15 mm) and the mean GT rise in the control group (0.82 ± 0.17 mm) was statistically non-significant. At six months, when comparing mean REC between both the groups, a reduction in the test group was observed but it was non-significant (Tables 4 and 5).\n\n(Mean ± SD in mm).\n\n(Mean ± SD in mm).\n\nIn the test group, mean percentage of defect coverage was 89.23 ± 15.04% and the predictability for complete CRC was 61.6 ± 43.11% i.e., 14 of 25 defects demonstrated 100% CRC. In the control group, mean percentage of defect coverage was 85.06 ± 17.71% and the predictability for CRC was 55 ± 19.45% i.e., 8 of 24 defects treated showed 100% CRC (Table 6).\n\n(Mean ± SD in mm).\n\n\nDiscussion\n\nClinicians face significant therapeutic challenges in managing GR defects including restoring the protective anatomy of the MGJ complex, reestablishing the aesthetic harmony between soft tissues and neighboring tooth structures, and ideally regenerating alveolar bone, periodontal ligament, and cementum, which is lost. Such therapeutic challenges become even greater when treating MRD, where challenges include inadequate tissue availability and increased post-harvesting morbidity. In the treatment of gingival recession defects, platelet concentrates have emerged as an alternative, which contain cytokines, platelets, stem cells giving a more predictable and reproducible outcome to restore the amount of keratinized tissue, RC and aesthetic outcome.27 In recent years, the usage of autologous blood derivatives (PRP/PRF/PRFM) for periodontal defects has also aimed to provide a novel and highly efficient technique for regeneration in root coverage procedures with less patient morbidity and fewer post-operative complications. Since the PRP/PRF era derivatives have been used for various soft tissue augmentation procedures. In the current study, 24 recession defects were treated with PRFM membrane with the VISTA approach in the test category whereas 24 recession defects were managed with PRF membrane using the VISTA technique in control group.\n\nZadeh (2011)3 observed complete root coverage for all GF mediated, minimally invasive VISTA treated teeth, as well as 1 to 2 mm gains in keratinized gingiva after a 12-month follow-up period. At the 20-month observation period these improvements were sustained. According to the findings of our study, both groups had significantly improved clinical parameters after six months. At six months, both treatment groups showed a significant GR reduction (2.58 ± 0.50 mm in the test group and 2.37 ± 0.49 mm in the control group).\n\nJankovic et al. (2012)28 carried out an RCT and reported that utilizing PRF membrane accelerated wound healing and this occurs by the virtue of growth factors trapped in the PRF mesh, which are gradually released, accelerating the regenerative capability. The fibrin network structure is crucial to the enhanced PRF healing process20 and reduces subjective discomfort of patients and provides acceptable clinical results in GR treatment compared to CTG. The use of CTG versus PRF in the management of Miller Class I and II GR using conventional RC techniques was compared in several systematic reviews.29–31 Both the types of above-mentioned treatment modalities have shown improvement in the condition of GR defects, with regard to CAL gain, RD reduction and increase in keratinized tissue.\n\nTo the best of our knowledge, the use of PRFM membrane in RC is rare, with just a few case studies documenting its usage especially in socket preservation, GR, and depigmentation. The outcome of a single case report utilizing the CAF method using peripheral blood mesenchymal stem cells and PRFM corresponds to RC of 60.0% and CAL gain of 3 mm at three months. (Belludi, et al., 2020).32 The present study yielded better results. Additionally, there aren’t enough clinical studies that use PRFM for RC. The findings of the above-mentioned study are in congruence with the outcomes obtained in the present investigation.\n\nTherefore, in order to achieve RC, the current investigation was conducted to evaluate the effectiveness of the VISTA+PRFM membrane to manage MRD. A statistically significant reduction in mean recession defects was seen in the test group six months after surgery in comparison to the baseline. At six months, the mean GR in the test group reduced from 3 ± 0.83 mm to 0.41 ± 0.58 mm, reflecting a mean RC of 89.23% and a CRC of 14 out of 24 recession defects treated (61.6%).\n\nSix months after surgery, the mean RD in the control group decreased from 2.91 mm to 0.54 mm, correlating to a mean of 85.06% recession defect coverage. The CRC was present in 13 out of 24 (55%) corrected recession defects. A study by Garg et al. (2017)33 compared the effects of VISTA with or without PRF membrane for the treatment of Class I and III MRD and it can be used to compare the outcomes of this research for the usage of PRF membrane utilizing the VISTA approach to treat multiple GR. The authors concluded that for Class III recession defects, VISTA along with PRF-membrane provides better results in terms of reduction in recession depth that ranged from 50% to 80%.\n\nThe mean CAL gain after six months in the current study was 2.95 ± 0.69 mm in the test group and 2.75 ± 0.89 mm in the control group,24 which was statistically not significant. Since no histological findings are obtainable due to ethical considerations, it is only possible to hypothesize the healing type achieved in the test group (VISTA+PRFM membrane). Debnath and Chatterjee (2018),34 on the third day after depigmentation, found that all the patients presented with good healing in PRF and PRFM, in comparison to seven patients with a poor healing score of 63.6% and four patients with a good healing score. Both groups in the present research had mean PPD reductions of 0.5 mm and 0.5 mm at six months, which were statistically not significant. Other authors have discussed related findings in the literature, for example, Geeti et al.7\n\nThe mean WKG in both experiment (VISTA+PRFM membrane group: 2.04 ± 1.36mm) and control group (VISTA+PRF membrane group: 1.5 ± 1.35mm) at six months was not significant in the current study. Mohamed et al. (2020),35 in their study evaluated VISTA + PRF for root coverage and concluded similar results.\n\nThe significance of GT for describing or achieving RC and clinical outcome stability has been underlined by recent studies. GT increased statistically in the current research in both the test (0.77 ± 0.15 mm) and control (0.82 ± 0.17 mm) groups. This increase may be the result of the membrane’s spacing impact or the effect of GF on the proliferation of PDL and gingival fibroblasts. Thamaraiselvan et al. (2015)36 assessed the clinical outcome of PRF membrane in GR and observed a significant increase in GT from 0.95 ± 0.14 to 1.25 ± 0.23 mm.\n\nThe test and control site outcomes for RC, PPD, CAL, REC, WKG, and GT were similar, according to the study’s overall assessment, while PRFM showed slightly better results for RC, WKG, CAL gain, and REC reduction. This can be ascribed to the VISTA approach, a minimally invasive procedure that lowers trauma to the surgical site while simultaneously preserving the major blood arteries of the flap and the blood supply to the area, improving the nourishment of the placed membrane. This may be partially attributed to the positive group results, the small sample size, and defects (Miller’s Class I and II), which are known to exhibit predictable RC.\n\n\nConclusions\n\nTreatment with VISTA+PFRM membrane is effective for multiple gingival recession defects in terms of significant coverage of gingival recession, which corresponds to 89.23%. However, VISTA+PRF corresponds to 85.06% of root coverage.\n\n\nConsent\n\nWritten informed consent for publication of the patients’ details and their images was obtained from the patients.", "appendix": "Data availability\n\nFigshare: Underlying data for ‘Comparative evaluation of platelet rich fibrin matrix (PRFM) membrane and platelet rich fibrin (PRF) membrane using the vestibular incision subperiosteal tunnel access (VISTA) approach technique for the treatment of multiple gingival recession in humans: A double-blind, parallel-group, randomized controlled clinical trial’, https://www.doi.org/10.6084/m9.figshare.22354444. 24\n\nFigshare: CONSORT checklist for ‘Comparative evaluation of platelet rich fibrin matrix (PRFM) membrane and platelet rich fibrin (PRF) membrane using the vestibular incision subperiosteal tunnel access (VISTA) approach technique for the treatment of multiple gingival recession in humans: A double-blind, parallel-group, randomized controlled clinical trial’, https://www.doi.org/10.6084/m9.figshare.22354435. 23\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nReferences\n\nZucchelli G, Mounssif I: Periodontal plastic surgery. Periodontology 2000. 2015; 68(1): 333–368. Publisher Full Text\n\nChatterjee A, Sharma E, Gundanavar G, et al.: Treatment of multiple gingival recessions with vista technique: A case series. J. Indian Soc. Periodontol. 2015; 19(2): 232–235. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZadeh HH: Minimally invasive treatment of maxillary anterior gingival recession defects by vestibular incision subperiosteal tunnel access and platelet-derived growth factor BB. Int. J. Periodontics Restorative Dent. 2011; 31(6): 653–660. PubMed Abstract\n\nAllen AL: Use of the supraperiosteal envelope in soft tissue grafting for root coverage. I. Rationale and technique. Int. J. Periodontics Restorative Dent. 1994; 14(3): 216–227. PubMed Abstract\n\nZabalegui I, Sicilia A, Cambra J, et al.: Treatment of multiple adjacent gingival recessions with the tunnel subepithelial connective tissue graft: a clinical report. Int. J. Periodontics Restorative Dent. 1999; 19(2): 199–206. PubMed Abstract\n\nAroca S, Molnár B, Windisch P, et al.: Treatment of multiple adjacent Miller class I and II gingival recessions with a Modified Coronally Advanced Tunnel (MCAT) technique and a collagen matrix or palatal connective tissue graft: a randomized, controlled clinical trial. J. Clin. Periodontol. 2013; 40(7): 713–720. PubMed Abstract \| Publisher Full Text\n\nGupta G, Puri K, Bansal M, et al.: Platelet-Rich Fibrin–Reinforced Vestibular Incision Subperiosteal Tunnel Access Technique for Recession Coverage. Clin. Adv. Periodontics. 2015; 5(4): 248–253. Publisher Full Text\n\nDandu SR, Murthy KRV: Multiple Gingival Recession Defects Treated with Coronally Advanced Flap and Either the VISTA Technique Enhanced with GEM 21S or Periosteal Pedicle Graft: A 9-Month Clinical Study. Int. J. Periodontics Restorative Dent. 2016; 36(2): 231–237. PubMed Abstract \| Publisher Full Text\n\nKumar TA, Gowda TM, Mehta DS, et al.: Management of Multiple Gingival Recessions with the VISTA Technique: An 18-Month Clinical Case Series. Int. J. Periodontics Restorative Dent. 2018; 38(2): 245–251. Publisher Full Text\n\nJamwal D, Waghmare P, Mali A, et al.: Vestibular incision subperiosteal tunnel access (VISTA) for root coverage with platelet-rich fibrin (PRF): A case report. Int. J. Recent Sci. Res. 2017; 8(10): 21081–21083.\n\nAniruddha Deshpande BDS, Koudale MSB, Bhongade ML: A comparative evaluation of rhPDGF-BB+ ß-TCP and subepithelial connective tissue graft for the treatment of multiple gingival recession defects in humans. Dent. 2014; 34: 241–249.\n\nAleksić Z, Janković S, Dimitrijević B, et al.: The use of platelet-rich fibrin membrane in gingival recession treatment. Srp. Arh. Celok. Lek. 2010; 138(1–2): 11–18. Publisher Full Text\n\nAli S, Bakry SA, Abd-Elhakam H: Platelet-rich fibrin in maxillary sinus augmentation: a systematic review. J. Oral Implantol. 2015; 41(6): 746–753. PubMed Abstract \| Publisher Full Text\n\nKotsakis GA, Boufidou F, Hinrichs JE, et al.: Extraction socket management utilizing platelet rich fibrin: a proof-of-principle study of the “Accelerated-early implant placement” concept. J. Oral Implantol. 2016; 42(2): 164–168. PubMed Abstract \| Publisher Full Text\n\nEhrenfest DMD, Diss A, Odin G, et al.: In vitro effects of Choukroun’s PRF (platelet-rich fibrin) on human gingival fibroblasts, dermal prekeratinocytes, preadipocytes, and maxillofacial osteoblasts in primary cultures. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2009; 108(3): 341–352. PubMed Abstract \| Publisher Full Text\n\nEren G, Kantarcı A, Sculean A, et al.: Vascularization after treatment of gingival recession defects with platelet-rich fibrin or connective tissue graft. Clin. Oral Investig. 2016; 20(8): 2045–2053. Publisher Full Text\n\nKökdere NN, Baykul T, Findik Y: The use of platelet-rich fibrin (PRF) and PRF-mixed particulated autogenous bone graft in the treatment of bone defects: An experimental and histomorphometrical study. Dent. Res. J. 2015; 12(5): 418–424. PubMed Abstract \| Publisher Full Text\n\nMiron RJ, Fujioka-Kobayashi M, Bishara M, et al.: Platelet-rich fibrin and soft tissue wound healing: a systematic review. Tissue Eng. Part B Rev. 2017; 23(1): 83–99. PubMed Abstract \| Publisher Full Text\n\nSimonpieri A, Del Corso M, Vervelle A, et al.: Current knowledge and perspectives for the use of platelet-rich plasma (PRP) and platelet-rich fibrin (PRF) in oral and maxillofacial surgery part 2: Bone graft, implant and reconstructive surgery. Curr. Pharm. Biotechnol. 2012; 13(7): 1231–1256. PubMed Abstract \| Publisher Full Text\n\nChoukroun J, Diss A, Simonpieri A, et al.: Platelet-rich fibrin (PRF): a second-generation platelet concentrate. Part IV: clinical effects on tissue healing. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2006; 101(3): e56–e60. PubMed Abstract \| Publisher Full Text\n\nMarx RE, Carlson ER, Eichstaedt RM, et al.: Platelet-rich plasma: Growth factor enhancement for bone grafts. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 1998; 85(6): 638–646. Publisher Full Text\n\nCarroll RJ, Arnoczky SP, Graham S, et al.: Characterization of autologous growth factors in Cascade platelet rich fibrin matrix (PRFM). Edison, NJ: Musculoskeletal Transplant Foundation; 2005.\n\nHassan S, Dhadse PV, Bajaj P, et al.: Consort checklist. [Dataset]. figshare. 2023. Publisher Full Text\n\nHassan S, Dhadse Prasad V, Bajaj P, et al.: Master chart. [Dataset]. figshare. 2023. Publisher Full Text\n\nHassan S, Dhadse PV: Evaluation of Effectiveness of Platelet Rich Fibrin Matrix (PRFM) Membrane and Platelet Rich Fibrin (PRF) Membrane using Vestibular Incision Subperiosteal Tunnel Access (VISTA) Approach Technique for the Treatment of Multiple Gingival Recession Defects in Humans–A Study Protocol. J. Pharm. Res. Int. 2021; 33(62A): 9–15. Publisher Full Text\n\nChoukroun J, Diss A, Simonpieri A, et al.: Platelet-rich fibrin (PRF): A second-generation platelet concentrate. Part IV: Clinical effects on tissue healing. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2006 Mar; 101(3): e56–e60. PubMed Abstract \| Publisher Full Text\n\nSubbareddy BV, Gautami PS, Dwarakanath CD, et al.: Vestibular incision subperiosteal tunnel access technique with platelet-rich fibrin compared to subepithelial connective tissue graft for the treatment of multiple gingival recessions: A randomized controlled clinical trial. Contemp. Clin. Dent. 2020; 11(3): 249–255. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJankovic S, Aleksic Z, Klokkevold P, et al.: Use of Platelet-Rich Fibrin Membrane Following Treatment of Gingival Recession: A Randomized Clinical Trial. Restor. Dent. 2012; 32(2): 10.\n\nMancini L, Tarallo F, Quinzi V, et al.: Platelet-rich fibrin in single and multiple coronally advanced flap for type 1 recession: An updated systematic review and meta-analysis. Medicina. 2021; 57(2): 144.\n\nMiron RJ, Moraschini V, Del Fabbro M, et al.: Use of platelet-rich fibrin for the treatment of gingival recessions: a systematic review and meta-analysis. Clin. Oral Investig. 2020; 24(8): 2543–2557. PubMed Abstract \| Publisher Full Text\n\nRodas MAR, de Paula BL , Pazmiño VFC, et al.: Platelet-rich fibrin in coverage of gingival recession: A systematic review and meta-analysis. European. J. Dent. 2020; 14(02): 315–326.\n\nBelludi SA, Laveena Singhal BDS: Peripheral Blood Mesenchymal Stem Cells and Platelet Rich Fibrin Matrix in the Management of Class II Gingival Recession: A Case Report. J. Dent. 2021; 22(1): 67–70. PubMed Abstract \| Publisher Full Text\n\nGarg S, Arora SA, Chhina S, et al.: Multiple gingival recession coverage treated with vestibular incision subperiosteal tunnel access approach with or without platelet-rich fibrin-A case series. Contemp. Clin. Dent. 2017; 8(3): 464–468. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDebnath K, Chatterjee A: Clinical and histological evaluation on application of platelet concentrates on depigmented gingival epithelium. J. Indian Soc. Periodontol. 2018; 22(2): 150–157. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMohamed AD, Marssafy LH: Comparative clinical study between tunnel and VISTA approaches for the treatment of multiple gingival recessions with acellular dermal matrix allograft. Egypt. Dent. J. 2020; 66(1-January (Oral Medicine, X-Ray, Oral Biology&Oral Pathology)): 247–259. Publisher Full Text\n\nThamaraiselvan M, Elavarasu S, Thangakumaran S, et al.: Comparative clinical evaluation of coronally advanced flap with or without platelet rich fibrin membrane in the treatment of isolated gingival recession. J. Indian Soc. Periodontol. 2015; 19(1): 66–71. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "197108", "date": "17 Aug 2023", "name": "Gustavo Vicentis de Oliveira Fernandes", "expertise": [ "Reviewer Expertise Periodontics", "Biomaterials", "Implants", "Clinical Trial", "Systematic review", "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\nI evaluated the article titled \"Comparative evaluation of platelet rich fibrin matrix (PRFM) membrane and platelet rich fibrin (PRF) membrane using the vestibular incision subperiosteal tunnel access (VISTA) approach technique for the treatment of multiple gingival recession in humans: A double-blind, parallel-group, randomized controlled clinical trial”.\nThe goal was \"compare the efficacy of the PRFM membrane with that of the PRF membrane using the VISTA approach for obtaining RC in patients with Miller’s class I/II MRDs”.\nConcerns raised:\nABSTRACT\n- Results were poorly presented\nINTRO\nPlease revise the following phrase: \"A second-generation platelet concentrate called platelet rich fibrin (PRF) was introduced in 2005 by Choukroun\"\nIf the authors intend to talk about the subject, please refer to it correctly.\nM&M\nthere were fatal mistakes in the preparation of the PRFs. The authors did not use the same standard proposed for preparation.\n\nAs the article discusses PRF membrane, citing Choukroun, the same protocol MUST be followed.\nThe authors cannot use the PRF group as a control. I suggest including a group of CTG as a control.\nThe figures presented did not show the original VISTA technique. Please, review the technique used.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "235338", "date": "15 Feb 2024", "name": "Shiva Shankar Gummaluri", "expertise": [ "Reviewer Expertise Periodontolgy", "Implantology", "Mucogingival surgery", "Platelet Concentrates" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 written and I appreciate the authors for their effort. The following changes should be made: 1. Please rectify the figures because figure 1 legends were wrong and for the same thing provide the immediate post op and follow up post-operative images. 2. Collage of images will be better than presenting individual figures. Please depict in the form of collage. 2. Follow up is short which is 6 months. Please provide a valid reference where 6 months follow up is sufficient for giving a conclusion.\nI would suggest to approve the manuscript after these revisions.\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": "235337", "date": "15 Feb 2024", "name": "Abhaya Chandra Das", "expertise": [ "Reviewer Expertise Platelet concentrate", "Implant", "Peridodontal medicine", "regenerative periodntal surgery", "Stem cells in dental 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\n1. Figure 1 is not teeth number 23,24,25. The wrong figure was given. It seems like a lateral incisor (12), etc. 2. While the study focuses on clinical measurements, it may benefit from including patient-reported outcomes and subjective assessments of aesthetic improvement. This would provide a more comprehensive evaluation of the intervention's impact on patients' quality of life. 3. It's not clear from the provided information whether the assessors or participants were blinded to the treatment allocation. Lack of blinding can introduce bias into the study. 4. Preparation of PRF membrane was not used in Chukroun's centrifuge machine, which is the real standard machine. 5. The study doesn't mention the occurrence or monitoring of adverse events related to the interventions. Reporting adverse events is essential for a complete understanding of the safety profile of the treatments..\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-872
https://f1000research.com/articles/12-871/v1	24 Jul 23	{ "type": "Case Report", "title": "Case Report: Total intragastric mesh migration six years after diaphragmatic rupture and hiatal hernia surgery", "authors": [ "Asma Sghaier", "Mohamed Amine Elghali", "Abdelrahmen Daadoucha", "Amal Letaief", "Itimed GHARBI", "Fehmi Hamila", "Sabri Youssef", "Mohamed Amine Elghali", "Abdelrahmen Daadoucha", "Amal Letaief", "Itimed GHARBI", "Fehmi Hamila", "Sabri Youssef" ], "abstract": "Background: Mesh implementation to repair the hiatal space is already justified. Nevertheless, the use of this procedure is debated in regard of complications that may occur. Mesh erosion and migration are considered the most serious complications of mesh repairs. Case presentation: It has not yet been well described in the literature. We describe a case of mesh erosion of\n\nstomach, many years later after a prosthetic repair of a diaphragmatic rupture associated to hiatal hernia, is presented here because of its rarity. Conclusion: Few explanations have been put forward to explain this incident. Could it be due to inflammatory processes, or to the composition of the Meshes? As yet, there is no definitive explanation.", "keywords": [ "diaphragmatic rupture", "hiatal hernia", "mesh repair", "complications" ], "content": "Introduction\n\nDelayed presentation of traumatic diaphragmatic rupture is a challenging diagnostic and treatment with necessity of mesh reinforcement.1 Mesh repair can also be proposed for hiatal hernia.2 There are a few published observational studies supporting the use of mesh, convincing lower rates of recurrence with lack of long-term follow-up. Likewise, there are sparse published studies proving the complications associated with mesh in the long-term,3 which provided the importance for this case. Limited related complications of mesh in such localization have been described. We describe one case of late dysphagia due to intragastric mesh migration six year after surgical reparation for diaphragmatic rupture associated with hiatal hernia.\n\n\nCase report\n\nA 52-year-old white man, with history of epigastric pain and gastroesophageal reflux disease, was operated for mixt hiatal hernia (Type III). During the operation we found that it was a left diaphragmatic rupture with a large collar with gastric migration into the thorax. The diaphragmatic hernia is located 5 cm from a wide hiatus with a sliding hiatal hernia (Figure 1).\n\nIntraperitoneal gastric reduction and Nissen fundoplication was performed. A two-face mesh 15×15 cm was put in place covering the orifice of the diaphragmatic rupture and the hiatal orifice by tying the esophagus (Figure 2). Fixation was performed by crown tacks. Post-operative course was simple. The patient required level I analgesics. Transit was restored after 24 hours. The patient described no complaints, particularly no dysphagia, and the physical examination was normal.\n\nBy interviewing the patient post-operatively, we discovered that the patient, who belongs to the forces of order. He was a security officer and he was a victim of an accident during a pursuit and was violently struck with the wheel of his car. He consulted as a matter of emergency and had an abdominal ultrasound and was put out with analgesic treatment.\n\nThe patient remained asymptomatic for more than six years postoperatively. When, he had progressive complaints of dysphagia and weight loss. An upper gastro-intestinal endoscopy showed a dilated esophagus, crossed cardia easily without protrusion with evidence of anti-reflux montage and migration of mesh into the stomach. Pneumatic dilation of antireflux montage with a 30-mm balloon was performed (Figure 3).\n\nAn attempt at endoscopic removal of the mesh had failed. A magnetic resonance imaging examination had not described any signs in favor of a diaphragmatic defect.\n\nThe decision was then made to operate the patient laparoscopically and to remove the mesh.\n\nThe patient was operated on, the per operative exploration discovered the presence of several adhesions at the supra meso-colic level. A longitudinal gastrotomy was carried out which made it possible to reveal the mesh that was inside and to extract it with the few staples that were attached (Figure 4).\n\nThe postoperative course was simple. The patient was discharged at day six.\n\n\nDiscussion\n\nMesh repair is becoming increasingly necessary to manage large diaphragmatic rupture.4 But use of mesh at the hiatus is yet controversial because of possible complications that may occur.5–7 Recommendation with a fairly high level of evidence concerning indications of prosthetic mesh does not clearly developed. Many procedures were proposed. Tension-free procedure consist of mesh setting without tight suture to procure excessive tension whereas the on-lay technique with consolidation of the defect closure by mesh. The materiel could be placed in an anterior, posterior, or circular position with a hole for the passage of the esophagus.7\n\nThe mesh used for hiatal reinforcement are made usually of non-resorbable material. It should have a very low risk of post-operative adhesions, and can be easy to be manipulate proceeding by laparoscopic approach.\n\nPolypropylene mesh seems to offer most of these requirements; however, it is susceptible to be responsible of intraperitoneal adhesions and also sometimes fistulas.8 Prosthetic reinforcement, though associated with a low rate of hernia recurrence, has particular drawbacks like this case of migration into stomach that we described in this article. Indeed, there are two considerable complications due to meshes: Parietal erosion and esophageal stenosis. The incidences of these two main complications ranged in literature between 0%–0.49%8 and 3.9%9 respectively depending on the series. However, surgical management is crucial to treat both conditions. A predisposition to esophageal stenosis succeeding the setting up of meshes produced by biological materials and toward parietal erosion after the use of polytetrafluoroethylene and polypropylene meshes has been developed by retrospective studies.10 Furthermore, stitches around a mesh placed above the fundoplication may be responsible of dysphagia, and contact of the mesh with the esophagus may leads to erosion, as illustrated in our case. Moreover, a surgical approach might provide a crucial role in decreasing the incidence of complications due to mesh.10 The techniques proposed for this purpose are tension-free repair with mesh placement without crus suturing to avoid excessive tension and the on-lay technique with reinforcement of the crucial closure by mesh. The on-lay technique is usually performed in all cases of hiatal hernia, independently of hernia size.11\n\nFurther recent studies concluded that mesh might be associated with fewer short-term recurrences, and the biological mesh was involved with improved short-term quality of life. Nevertheless, these advantages were offset by more dysphagia,12 which is why most experienced practitioners recommend mesh use exclusively for carefully selected cases.13 For our patient we could not explain this intragastric migration of the Mesh. Would it be related to the fixation by the tackers and the nature of the Mesh? We do not have valid proof and explanations.\n\n\nConclusions\n\nOur case, even though it is rare, demonstrates this, as we are led to re-operate a patient and to be faced with technical difficulties and often even a conversion to open surgery to retrieve the mesh that migrated inside the digestive tract. The mesh type may provide a role in the complication rate, with synthetic mesh being more implicated. The simultaneous co-existence of an intraperitoneal infection may also be responsible, although that must be proven by well-conducted studies and further controlled randomized trials.\n\n\nConsent for publication\n\nWritten informed consent was obtained from the patient for publication of this case report and accompanying images.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAl-Nouri O, Hartman B, Freedman R, et al.: Diaphragmatic rupture: Is management with biological mesh feasible? Int. J. Surg. Case Rep. 2012; 3(8): 349–353. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSpiro C, Quarmby N, Gananadha S: Mesh-related complications in paraoesophageal repair: a systematic review. Surg. Endosc. 2020 Oct; 34(10): 4257–4280. PubMed Abstract \| Publisher Full Text\n\nBernabé MQ, Adelina EC: Use of absorbable meshes in laparoscopic paraesophageal hernia repair World. J. Gastrointest. Surg. 2019 October 27; 11(10): 388–394. Publisher Full Text\n\nSirbu H, Busch T, Spillner J, et al.: Late bilateral diaphragmatic rupture: challenging diagnostic and surgical repair. Hernia. 2005 Mar; 9(1): 90–92. PubMed Abstract \| Publisher Full Text\n\nVeronique M, Marc Z, Myriam D, et al.: Complications of Mesh Repair in Hiatal Surgery: About 3 Cases and Review of the Literature. Surg. Laparosc. Endosc. Percutan. Tech. 2012; 22: 222–225.\n\nIdrissi A, Mouni O, Bouziane M, et al.: Intraesophageal Migration of a Paraesophageal Hernia Mesh: A Case Report. Cureus. 2022 Apr 21; 14(4): e24339. PubMed Abstract \| Publisher Full Text\n\nTam V, Winger DG, Nason KS: A systematic review and meta-analysis of mesh versus suture cruroplasty in laparoscopic large hiatal hernia repair. Am. J. Surg. 2016 January; 211(1): 226–238. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPriego P, Ruiz-Tovar J, Pérez de Oteyza J: Long-term results of giant hiatal hernia mesh repair and antireflux laparoscopic surgery for gastroesophageal reflux disease. J. Laparoendosc. Adv. Surg. Tech. A. 2012; 22(2): 139–141. PubMed Abstract \| Publisher Full Text\n\nStadlhuber RJ, Sherif AE, Mittal SK, et al.: Mesh complications after prosthetic reinforcement of hiatal closure: A 28-case series. Surg. Endosc. 2009; 23(6): 1219–1226. PubMed Abstract \| Publisher Full Text\n\nGriffith PS, Valenti V, Qurashi K, et al.: Rejection of goretex mesh used in prosthetic cruroplasty: A case series. Int. J. Surg. 2008; 6(2): 106–109. PubMed Abstract \| Publisher Full Text\n\nWei-T L, Zhi-Wei H, Zhong-G W, et al.: Mesh-related complications after hiatal hernia repair: two case reports. Gastroenterol. Nurs. 2015; 38(3): 226–229.\n\nKöckerling F, Schug-Pass C, Bittner R: A word of caution: never use tacks for mesh fixation to the diaphragm! Surg. Endosc. 2018: Jul; 32(7): 3295–3302. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBalagué C, Fdez-Ananín S, Sacoto D, et al.: Paraesophageal hernia: to mesh or not to mesh? The controversy continues. J. Laparoendosc. Adv. Surg. Tech. A. 2020; 30: 140–146. Publisher Full Text" }	[ { "id": "205919", "date": "10 Oct 2023", "name": "Ivan Romic", "expertise": [ "Reviewer Expertise Abdominal surgery", "gastric 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\nVery interesting article on rare complication of hiatal hernia surgery. It provides details of diagnostic and management.\n\nI suggest to state what kind of MESH was used, which material and company.\n\nAlso, reformulate 'belongs' to 'belonged'.\n\n\"2. Our case, even though it is rare, demonstrates this, as we are led to re-operate a patient and to be faced with technical difficulties and often even a conversion to open surgery to retrieve the mesh that migrated inside the digestive tract.\" - this is unclear, reformulate.\n\nPlease find and cite all articles on MESH migration. One of them is attached1.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] }, { "id": "234856", "date": "29 Jan 2024", "name": "Nir Messer", "expertise": [ "Reviewer Expertise Abdominal Wall reconstruction", "paraesophageal hernia repair", "endocrine surgery", "and general surgery." ], "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\nTotal intragastric mesh migration six years after diaphragmatic rupture and hiatal hernia surgery\nI value the opportunity to assess the study \"Total intragastric mesh migration six years after diaphragmatic rupture and hiatal hernia surgery\". The manuscript presents a case study involving mesh migration following diaphragmatic rupture and hiatal hernia repair with permanent mesh. I find this case to be interesting and challenging, and I would like to provide the following comments:\n\nCase presentation\n\" A 52-year-old white man, with history of epigastric pain and gastroesophageal reflux disease, was operated for mixt hiatal hernia (Type III)\". The presentation is confusing. The authors initially label the patient with type III paraesophageal hernia, yet later, it is characterized as a sliding hiatal hernia (type I). Kindly provide an accurate clarification regarding the suspected and confirmed diagnosis for the patient. Please specify the preoperative diagnostic procedures employed for the patient. \"Intraperitoneal gastric reduction and Nissen fundoplication were performed\". Was there concurrent hiatal hernia repair involving hernia sac reduction and crural reapproximation? \"A two-face mesh 15×15 cm was put\". Kindly specify the precise type of mesh utilized in the procedure.\n\nDiscussion\n\"Polypropylene mesh seems to offer most of these requirements; however, it is susceptible to be responsible of intraperitoneal adhesions and also sometimes fistulas\". Polypropylene mesh is generally not recommended for intraabdominal application unless it is coated with an anti-adhesive material, attributed to its elevated adhesion and bowel erosion characteristics. \"The techniques proposed for this purpose are tension-free repair with mesh placement without crus suturing to avoid excessive tension and the on-lay technique with reinforcement of the crucial closure by mesh. The on-lay technique is usually performed in all cases of hiatal hernia, independently of hernia size\". As highlighted in numerous studies, the predominant method for para-esophageal hernia repair involves crural reapproximation, even when incorporating mesh. The term \"on-lay technique\" is inaccurately applied in this context.\n\"whereas the on-lay technique with the consolidation of the defect closure by mesh\". This sentence lacks clarity. Additionally, the term \"on-lay\" is typically employed to describe mesh positioning in abdominal wall hernias, not diaphragmatic hernias.\nGeneral comments\nThe manuscript lacks clarity, requiring repeated readings for comprehension. Furthermore, authors utilize inappropriate surgical jargon for diaphragmatic hernia repairs and attempt to extrapolate motives from abdominal wall hernia repairs to diaphragmatic hernias, a mismatch that warrants attention. The figures lack clarity and fail to enhance the comprehension of the presented case.\n\nIs the background of the case’s history and progression described in sufficient detail? No\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? No", "responses": [] } ]	1	https://f1000research.com/articles/12-871
https://f1000research.com/articles/10-393/v1	17 May 21	{ "type": "Research Article", "title": "Correlation between anti-hypertensive drugs and disease progression among moderate, severe, and critically ill COVID-19 patients in the second referral hospital in Surbaya: A retrospective cohort study", "authors": [ "Satriyo Dwi Suryantoro", "Mochammad Thaha", "Mutiara Rizky Hayati", "Mochammad Yusuf", "Budi Susetyo Pikir", "Hendri Susilo", "Satriyo Dwi Suryantoro", "Mutiara Rizky Hayati", "Mochammad Yusuf", "Budi Susetyo Pikir", "Hendri Susilo" ], "abstract": "Background: Hypertension, as the comorbidity accompanying COVID-19, is related to angiotensin-converting enzyme 2 receptor (ACE-2R) and endothelial dysregulation which have an important role in blood pressure regulation. Other anti-hypertensive agents are believed to trigger the hyperinflammation process. We aimed to figure out the association between the use of anti-hypertensive drugs and the disease progression of COVID-19 patients.\n\nMethods: This study is an observational cohort study among COVID-19 adult patients from moderate to critically ill admitted to Universitas Airlangga Hospital (UAH) Surabaya with history of hypertension and receiving anti-hypertensive drugs.\n\nResults: Patients receiving beta blockers only had a longer length of stay than angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ACEI/ARB) or calcium channel blockers alone (17, 13.36, and 13.73 respectively), had the higher rate of intensive care unit (ICU) admission than ACEi/ARB (p 0.04), and had the highest mortality rate (54.55%). There were no significant differences in length of stay, ICU admission, mortality rate, and days of death among the single, double, and triple anti-hypertensive groups. The mortality rate in groups taking ACEi/ARB was lower than other combination.\n\nConclusions: Hypertension can increase the severity of COVID-19. The use of ACEI/ARBs in ACE-2 receptor regulation which is thought to aggravate the condition of COVID-19 patients has not yet been proven. This is consistent with findings in other anti-hypertensive groups.", "keywords": [ "COVID-19", "Severity", "Progression", "Hypertension", "Anti-hypertensive drugs", "Infectious disease" ], "content": "Introduction\n\nCoronavirus disease (COVID-19) had become a pandemic since almost one year ago. (Huang et al., 2020) Over 90 million cases and 1.5 million death-cases had happened during 2020 and several comorbidities associated with an increase in COVID-19 cases. Cardiovascular disease had become one of the most frequent comorbidities among COVID-19 patients which had a poor prognosis and high mortality rate. (WHO, 2021)\n\nThe mechanism of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection is associated with the angiotensin-converting enzyme 2 receptor (ACE-2R) in the host cell and related with endothelial dysregulation. (Saha et al., 2021) Angiotensin-converting enzyme 2 (ACE2) plays a crucial role in renin-angiotensin-aldosterone system (RAAS) that regulate the blood pressure and main cause of hypertension. Hence, hypertension, and all complication-caused by hypertension, is associated with increased incidence and severity or risk of death in COVID-19. ( Ferrario et al., 2005; Li et al., 2020b)\n\nOne of the most common drugs for hypertension are angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARB). Some evidence had suggested the use of angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ACEIs/ARB) in increasing the expression of ACE2 and hypothetically worsening the outcome of COVID-19 patients. (Li et al., 2020b; Ren et al., 2021; Sanders et al., 2020) Several anti-hypertensive drugs had been studied about the relation of increasing inflammatory markers like C-reactive protein in cardiovascular disease. In COVID-19, there was an evidence of hyper-inflammation process that caused acute respiratory distress syndrome (ARDS) via the cytokine storm mechanism. (Bas et al., 2005; Moore & June, 2020) Therefore, in several studies, the use of anti-hypertensive drugs had become a debate in the occurrence of worsening disease progression in COVID-19 patients. (Li et al., 2020b; Li et al., 2020d; Palvesky et al., 2020; Parveen et al., 2020; Ren et al., 2021; Sunden-Cullberg, 2020; Zuin et al., 2020) We hypothesize that the use of ACEI/ARBs might be correlated to ICU admission rate and length of stay, and may influence the inflammatory markers in COVID-19 patients.\n\nAlthough several studies had associated few anti-hypertensive drugs to the severity and risk of death due to COVID-19, we aim to test for an association between the use of anti-hypertensive drugs and the disease progression from moderate, severe, and critically ill COVID-19 patients in Universitas Airlangga Hospital (UAH). We used the UAH COVID-19 database that we had built since March 15, 2020.\n\n\nMethods\n\nWe conducted a retrospective cohort study with consecutive sampling and eligibility criteria COVID-19 adult patients from moderate to critically ill patients admitted to Universitas Airlangga Hospital (UAH) Surabaya during March 15, 2020 to August 31, 2020 through hospital medical records. Universitas Airlangga Hospital is a teaching hospital and one of the referral hospitals for COVID-19 in Surabaya, East Java. Our inclusive sample consisted of patients with a medical history of hypertension with moderate to critically ill COVID-19. Diagnosis of COVID-19 was made based on WHO guidelines and the Indonesian Ministry of Health guidelines, which were proven by oropharyngeal and nasopharyngeal swabs for SARS-CoV-2 PCR. Grouping of anti-hypertensive drugs based on three main groups ACEIs or ARBs (ACEI/ARB), calcium channel blockers (CCB) and beta blockers (BB) and we divided it into subgroups: single anti-hypertensive drugs, double anti-hypertensive drugs, and triple anti-hypertensive drugs. The outcome of this study were mortality rate, ICU admission and days of death. The potential confounding was multiple comotbidities of population. To minimize bias we eliminated patient without a history of antihypertensive and had serial clinical and laboratory examinations until patient discharged or died. The study size wsa decribed at Figure 1. Serial chest x-ray and laboratory inflammatory marker evaluation was performed, and we grouped it into three periods of time evaluation. The first time was when the patient came to the hospital; means of second time evaluation was at day six, and the third time was when the patient was either discharged or died (mean time 13 days).\n\nACEI/ARB: angiotensin-converting enzyme inhibitors and angiotensin receptor blockers; CCB: calcium channel blocker.\n\nData was collected from medical records from March 15, 2020 to August 31, 2020. We had 218 patients with moderate to critically ill COVID-19 and medical records with incomplete clinical, laboratory, and radiology data were excluded. Clinical characteristics were divided according to the medical history of hypertension and anti-hypertensive drugs. We grouped anti-hypertensive drugs as single, double, and triple treatment. For single use anti-hypertensive drugs, we divided them into ACEI/ARB, CCB, and BB.\n\nFor severe COVID-19, moderate case definitions were defined as: 1) clinical sign of pneumonia (fever, cough, dyspnea, tachypnea) and 2) Oxygen saturation ≥93% free air. Severe case definitions are if there were clinically sign of pneumonia, and one of this are the following: 1) respiration rate >30 times per minutes, or 2) severe respiratory distress, or 3) oxygen saturation < 93% free air. The critical condition is upright when symptoms are present that supports the diagnosis of acute respiratory distress syndrome (ARDS) and septic shock.(Burhan et al., 2020)\n\nThe severity score of COVID-19 pneumonia was assessed by simplifying the radiographic assessment of lung edema (RALE) score proposed by Warren et al. The RALE score assesses lung involvement into score zero as no involvement of the lung, score one for less than 25% involvement, score two for 25%–50% involvement of the lung, score three for 50%–75% involvement of the lung, and score four for more than 75% involvement of the lung. The results were divided into four categories: normal, mild (score one-two), moderate (score three-five), and severe (score six-eight). (Warren et al., 2018)\n\nInflammatory marker evaluation was based on the following criteria : 1) white blood cell count (WBC) >6.16x103 cells/μL; (Feng et al., 2020) 2) neutrophil-lymphocyte ratio (NLR) >6.5; (Li et al., 2020c) 3) Absolute lymphocyte count (ALC) < 1.0x103 cells/ μL; (Wagner et al., 2020) 4) C-reactive protein (CRP) >41.8 mg/L; (Liu et al., 2020) and 5) procalcitonin (PCT) > 0,07 ng/mL. (Liu et al., 2020)\n\nThis research was previously approved by the subjects with informed consent and was reviewed by ethical committee of Universitas Airlangga Hospital, Surabaya, Indonesia, number 179/KEP/2020. The study complies with the Declaration of Helsinki (Ethical Principles for Medical Research Involving Human Subjects) version 2013.\n\nData were analyzed with SPSS version 24.0 (Chicago, IL, USA). Descriptive statistics included categorical variables reported as number (%) and continuous variables as mean (standard deviation). To control confounding, we did selection data by antihypertensive groups and severity. For missing data, we used list wise deletion or univariable and multivariable analysis. Chi-square test and Mann-Whitney test were applied according to the type of variable or subgroup interactions. Categorical variables were shown as number (%) and continuous variables as mean (standard deviation) or median (range) depending on whether the data are normally distributed. Statistical significance was assessed by means of chi-squared for dichotomous variables, or by means of the two independent sample t-test or the Mann-Whitney U test for continuous variable depending on whether the data are normally distributed. Analysis for the mean difference between the first, second and third evaluations of the lab results, radiology score severity, and length of stay using the ANOVA test. We calculated the risk ratio (RR) among subgroup analysis anti-hypertensive drugs to evaluate the outcome. Additionally, for the evaluation of disease progression among anti-hypertensive drugs group, we conducted a Cox-regression test. Kaplan-Meier curves were constructed for time survival in 30 days.\n\nThe strengthening the reporting of observational studies in epidemiology (STROBE) statement checklist was used for our report in this study.\n\n\nResults\n\nFrom 218 moderate to critically ill COVID-19 patients, 77 patients were inclusive of our criteria (see Figure 1). Forty-two patients were male (54.5%) and 35 were female (45.5%) with means aged 58.26 ± 12.59 years old. Although 55.84% severity of COVID-19 was moderate but based on RALE score 46.75% were included in severe and critically ill. The majority of comorbidities of the patients were hypertension (50.65%), diabetes mellitus (49.35%), geriatric (age > 60 years old) (40.26%), heart disease (10.39%), chronic kidney disease (7.79%), and obesity (2.6%).\n\nChief complaints in the admission such as dyspnea, fever, nauseous, vomit, diarrhea, malaise, runny nose and headache were mentioned. The findings of laboratory data showed that almost all inflammatory markers increased as could be seen in WBC counts 10,360/uL, neutrophil-lymphocyte ratio (NLR) 7.05, C-reactive protein (CRP) 72.5 mg/L, procalcitonin 4.48 ng/mL, creatinine serum 1.97mg/dL, and D-dimer 2.13 mcg/mL. We had been following all of the patients since the admission day up till the day of discharge, and data showed that the average length of hospital stay was 13.73 ± 6.69 days. During the follow up, 18 (23.4%) patients experienced deterioration in their condition and then they were admitted to the ICU, 15 patients (19.5%) had an acute respiratory distress syndrome (ARDS), and 12 (15,6%) were getting ventilated. For the characteristics of the patients see Table 1.\n\nACEI/ARB: angiotensin-converting enzyme inhibitors and angiotensin receptor blockers; CCB: calcium channel blocker; BB: beta blocker; ICU: intensive care unit; HT: hypertension.\n\nDM, diabetes mellitus; HT, hypertension; ACE, angiotensin-converting enzyme inhibitors; ARB, angiotensin receptor blockers; BB, beta blocker; CCB, calcium channel blocker; ICU, intensive Care Unit; SD, standard deviation.\n\nBased on the characteristics, each group of anti-hypertensive drugs had comorbidities. In the single anti-hypertensive group, patients grouped in the CCB and BB had several significant comorbidities, e.g. elderly>60 years, diabetes mellitus, and hypertension. Among those three groups of single anti-hypertensive therapy, patients grouped in the ACEI/ARB and BB had controlled blood pressure. Differences in systolic blood pressure of patients were discovered among these three groups, which were 136.43 mmHg in ACEI/ARB group, 142.91 mmHg in CCB groups, and 117.91 mmHg in BB group (p 0.05), whereas other clinical parameters such as diastolic blood pressure, pulse, respiration rate, temperature and oxygen saturation showed no significant differences. Radiological evaluation showed that ACEI/ARB, CCB, and BB group were in the moderate category, although ACEI/ARB seemed to have the lowest radiological severity score.\n\nAn increase of the inflammatory markers such as WBC count, NLR, ALC, CRP, PCT creatinine serum, and D-dimer were recorded after periodical follow-ups of all groups. ACEI/ARB group showed the elevation of white blood cell counts along with the CRP and PCT. It might be hypothesized that the initial character of patients in ACEI/ARB group had previously high numbers of inflammatory markers with the possibility of secondary infection. ACEI/ARB also did not deteriorate the renal function of moderately to critically ill patients who were prone to experience systemic vasodilation. This was indicated by the return of serum creatinine after episodes of acute kidney injury in the third treatment evaluation.\n\nThe WBC and CRP counts in CCB group were only slightly detected if compared to other two groups. This might be related to a low level of procalcitonin at two previous evaluations. However, the group treated with CCB was more susceptible to developing acute kidney injuries as evidenced by the increase in serum creatinine levels. Patients with COVID-19 being treated with BBs also showed the highest numbers of some inflammatory markers such as NLR, CRP, and SCr in the second evaluation. The major comorbidities of the BB-treated group were diabetes mellitus (DM) type 2 (54.55%), hypertension (HT) (36.36%), and geriatic (age > 60 years old) (36.36%), and minor comorbidities were heart disease and obesity. (9.09%)\n\nPatients taking double anti-hypertensive agents were also categorized into ACEI/ARB and CCB group, ACEI/ARB and BB group, and CCB and BB group. In groups involving ACEI/ARB, laboratory markers showed lower level of NLR (3.13 and 6.15), than in groups taking BB and CCB (12.04). Otherwise, D-dimer levels surged in the group of patients taking BB and CCB.\n\nWe then expanded the group into larger ones of patients taking single, double and anti-hypertension groups. Elderly patients, diabetes mellitus, and hypertension were comorbidities found in all these three groups. In accordance with the characteristics of blood pressure, patients who took more anti-hypertension drugs had poorer blood pressure control, patients in the single anti-hypertension group presented 135.13 mmHg of systolic blood pressure, 147.13 mmHg in the double anti-hypertension group and 159.67 mmHg in the triple anti-hypertension group and were statistically different (p 0.038). Significant differences between groups were also seen in the CRP results at baseline admission (p 0.005) and the first evaluation of oxygen fraction (p 0.032).\n\nBased on the inflammatory markers and evaluation on the case severity using x-ray follow ups, it is crucial to discuss the effect of hypertension to the clinical outcome of patients with COVID-19. Based on the single anti-hypertension analysis, patients who received only BBs had a longer length of stay than ACEI/ARB or CCB alone (17, 13.36, and 13.73 respectively). After the evaluation, patients who received anti-hypertension BBs also had the highest rates of ICU admission (63.64). This rate is quite high in number when compared to ACEI/ARB or CCB (p 0.04). Nevertheless, although ACEI / ARB had a fairly high rate for ICU admission (28.57), the discharge rate was also quite high (71.43%) with a mortality rate of 7.14%. The highest mortality was found in the BB group (54.55%) with a discharge rate of 45.45% (p 0.032) (see Table 2 and Figure 2).\n\nACEI/ARB: angiotensin-converting enzyme inhibitors and angiotensin receptor blockers; CCB: calcium channel blocker; BB: beta blocker.\n\nDM, diabetes mellitus; HT, hypertension; ACE, angiotensin-converting enzyme inhibitors; ARB, angiotensin receptor blockers; BB, beta blocker; CCB, calcium channel blocker; ICU, intensive Care Unit; SD, standard deviation\n\nACE, angiotensin-converting enzyme inhibitors; ARB, angiotensin receptor blockers; BB, beta blocker; CCB, calcium channel blocker; RALE, radiographic assessment of lung edema\n\nWBC, white blood cells; ALC, absolute lymphocyte count; NLR, neutrophil to lymphocyte ratio; Plt, platelet; CRP, C-reactive protein; PCT, procalcitonine;\n\nBUN, blood urea nitrogen; SCr, serum creatinine; SGOT, Serum Glutamic Oxaloacetic Transaminase; SGPT, Serum Glutamic Pyruvic Transaminase; P/F ratio, PO2/FiO2 ratio\n\nACEI/ARB: angiotensin-converting enzyme inhibitors and angiotensin receptor blockers; CCB: calcium channel blocker; BB: beta blocker; ICU: intensive care unit; RALE: radiographic assessment of lung edema.\n\n\n\nDisease progression can be observed through number patients died and days of death (time from first admission to death) from comorbidity, anti-hypertensive drugs, severity of chest x-ray, and inflammatory markers. It showed that heart disease (25%) and being geriatric (19.35%) contributed to a higher mortality rate than the others’ comorbidities. Nevertheless, all comorbidities were not significantly different for the days of death. No mortality had occurred in patients with CKD. Compared to the anti-hypertensive drugs used, there was significance in single use BBs for mortality events and days of death (RR: 9.82; 95% CI: 2.3–41.89; HR: 6.64; 95% CI: 1.3–33.04) (see Table 3 and Figure 3). Comparing single, double and triple anti-hypertensive drugs groups, there were no significant differences in length of stay, ICU admission, mortality rate, and days of death. Even though patients taking ACEI/ARB in both the single and combination groups had quite a high number of inflammatory marker variables, the mortality rate was still lower when compared to other anti-HT drug combinations. This suggests that ACEI/ARB has a protective effect (see Table 2 and Table 3). Additionally, more severe chest x-ray findings and higher inflammatory markers correlated to a higher mortality rate but had no significant effect on days of death.\n\nACEI/ARB: angiotensin-converting enzyme inhibitors and angiotensin receptor blockers; CCB: calcium channel blocker; BB: beta blocker; CI: confidence interval.\n\nDM, diabetes mellitus; HT, hypertension; ACE, angiotensin-converting enzyme inhibitors; ARB, angiotensin receptor blockers; BB, beta blocker; CCB, calcium channel blocker; ICU, intensive Care Unit; SD, standard deviation; NLR, Neutrophil-lymphocyte ratio; ALC, Absolute Lymphocyte Count; CRP, C- Reactive Protein\n\nACEI/ARB: angiotensin-converting enzyme inhibitors and angiotensin receptor blockers; CCB: calcium channel blocker; BB: beta blocker.\n\n\nDiscussion\n\nAccording to the results of our study, COVID-19 confirmed cases may appear with multiple comorbidities, inducing significant inflammatory markers that affect the clinical outcomes of the patients. We analyzed the results by grouping the antihypertension agents into three groups: ACEI/ARB, CCB, and BB. Hypertension is believed to be one of the most common comorbidities. Patients involved in this research had a medical history of hypertension and was previously given the anti-hypertension agent before or during the hospital care. Most of the patients with a previous history of hypertension along with other comorbidities, such as heart failure, diabetes mellitus and received BBs. Although BB seems to be frequently used by patients with heart failure, it is also vastly used to lower the blood pressure in diabetes mellitus patients.\n\nCOVID-19 has been known to stimulate an inflammation cascade. Immune responses of critically ill patients with sepsis can be classified into three patterns: macrophage-activation syndrome (MAS), sepsis-induced immune-paralysis characterized by low expression of the human leukocyte antigen D related (HLA-DR) on CD14 monocytes, and an intermediate functional state of the immune system lacking obvious dysregulation. A preceding result states that approximately one-fourth of patients with septic condition have MAS and that most patients suffer from immune dysregulation dominated by low expression of HLA-DR on CD14 monocytes, which is triggered by monocyte hyperactivation, excessive release of interleukin-6 (IL-6), and profound lymphopenia. Addtionally, lower absolute lymphocyte count (ALC) (< 1.0x103 cells/μL) could be a prognostic factor for COVID-19. (Giamarellos-Bourboulis et al., 2020; Wagner et al., 2020)\n\nIt has been shown that proinflammatory cytokines and chemokines including tumor necrosis factor (TNF) α, interleukin 1β (IL-1β), IL-6, granulocyte-colony stimulating factor, interferon gamma-induced protein-10, monocyte chemoattractant protein-1, and macrophage inflammatory proteins 1-α were significantly elevated in COVID-19 patients. It is characterized by sustained and substantial reduction of the peripheral lymphocyte counts, mainly CD4-T and CD8-T cells in COVID-19 patients, and is associated with a high risk of developing secondary bacterial infection. (Li et al., 2020a)\n\nOur study showed that high levels of inflammatory markers, such as WBC, PCT, and NLR, were correlated with higher mortality rates but showed no diffrerences for days of death. CRP levels were higher in the ACEI/ARB group, both single and double, but the mortality rate wasn’t higher than BB groups.\n\nHypertension, as stated by the American Heart Association, is defined as the rise of systolic blood pressure to the point of 140 mmHg and above, and/or diastolic blood pressure to 90mmHg and above. (PERHI, 2019) Hypertension is the leading cause of mortality globally. Approximately one-third of adults were estimated to have hypertension worldwide in 2010. Since the emerge of SARS-CoV-2 infection, hypertension has been frequently observed as a major comorbidity in patients with COVID-19. (Casucci et al., 2020; Yang et al., 2020) SARS-CoV2 virus penetrates into the cell through the ACE2 receptor. ACE2 was recognized as an enzyme having a role in the renin-angiotensin system (RAS) regulation. The transport of ACE2 to SARS-Cov-2 virus escalates the activity of the protein containing disintegrin domain and metalloproteinase domain-containing protein 17 (ADAM17). ADAM17 induces the release of ACE-2 ectodomain and produces soluble ACE-2 in the blood circulation. The low expression of ACE2 in the cell surface might lower the possibility for the infection to occur. The strong inhibition of ACE2 by SARS-CoV2 leading to increased vascular permeability and pulmonary edema (Yang et al., 2020). Early investigations in SARS-CoV suggest that ACE2 may have both a pathogenic role in facilitating virus infection and a protective effect in limiting lung injury during SARS-CoV-2 infection. As we know, ACE2 is recognized as a critical enzyme that regulates blood pressure, fluid and electrolyte balance, and vascular resistance by renin-angiontensi-aldosterone system. Drugs that can upregulate the expression of ACE2, such as ARBs and ACE inhibitors, have been commonly used in patients with hypertension and other cardiovascular diseases to regulate blood pressure and reduce the mortality and morbidity events (Gul et al., 2021; Shibata et al., 2020; Yang et al., 2020).\n\nThe mechanism of hypertension in worsening the clinical outcome has not been yet explained. Several studies declared that ACEI-induced angiodema was associated with increasing CRP and BB was associated with lower CRP level. Nevertheless, Yang et al declared that patients with hypertension came with highly detected inflammatory markers such as CRP (p=0.024), Procalcitonin (p=0.017) and IL6 (p=0.017). Angiotensin II is a renin-angiotensin effector peptide, responsible in pro-inflammatory cytokines induction, e.g IL-6, IL-1 β, TNF-α, IFN-ϒ, IL-17 and IL-23. Therefore, ACE inhibitors and ARBs that are capable of reducing the production of inflammatory cytokines are potential candidate drugs for treatment of patients with COVID-19 and preexisting hypertension. (Bas et al., 2005; Palmas et al., 2007; Yang et al., 2020 )\n\nBased on the known SARS-Cov-2 pathogenesis, there seems to be a strong correlation among hypertension, anti-hypertensive agents, and SARS-Cov-2 infection. The SARS-CoV-2 receptor binds to the angiotensin-converting enzyme 2 (ACE-2) found on the respiratory cells with the help of S protein, which helps in entry and the replication process. After the multiplication process, when the virus reaches the lungs, it causes inflammation in the alveoli or lung sacs leading to pneumonia. Several patients would suffer from severe sepsis, shock, and even ARDS. (Kumar et al., 2020)\n\nThis research shows that the final clinical outcome from each of the group; ACEI/ARB, CCB, and BB might vary despite the similar initial condition. It also has been observed that the patients’ discharge and mortality numbers among these three groups show significant different results. Data shows that the discharge numbers of ACEI/ARB group are high (71.43%) while the ICU admission rate reached a third of the BB group. Comorbidities also play a role in severity and higher mortality rate among groups but isn’t different in days of death.\n\nThis result was similiar with the Ren et al study, which showed that the use of antihypertensive drugs weren’t correlated with the severity and risk of COVID-19. (Ren et al., 2021) Compared to previous local and regional studies, we didn’t find any study that compared antihypertensive drugs with disease progression in COVID-19.\n\nThe use of ACEI/ARB is still a matter of discussion due to the ACE-2 numerous receptor theories. ARBs/ACE inhibitors treatment has been reported to increase the expression of ACE2, which is also the cellular receptor for SARS-CoV-2 infection. It was suggested a protective role of ACE2 upregulation and ARBs/ACE inhibitors treatment in COVID-19 and raised concerns that ARBs/ACE inhibitors treatment could promote SARS- CoV-2 infection by increasing the expression of ACE2. (Yang et al., 2020)\n\nDespite many hypotheses, evidence from a series of cohort studies published recently suggests that previous or current treatment with ACEIs or ARBs does not increase the risk and the complication of COVID-19 infection. ACEI and ARB act by inhibiting the renin-angiotensin-aldosterone system (RAAS). Angiotensinogen is converted to angiotensin I (AngI) by renin, then converted to angiotensin II (AngII) by angiotensin converting enzyme (ACE). Furthermore, angiotensin is converted to angiotensin (1–7) by angiotensin converting enzyme-2 (ACE-2). Angiotensin II activates angiotensin 2 type 1 receptor (AT1R) which stimulates vasoconstriction, pulmonary edema, oxidative effects, inflammation, and fibrosis. Meanwhile, angiotensin 1–7 have anti-inflammatory, anti-apoptotic, and anti-fibrosis effects. Both ACEI and ARB inhibit the ACE, hence the amount of ACE will be detected abundantly in the circulation. ACE in the systemic circulation is thought to have protective effects on the lungs, particularly in preventing the ARDS. At the same time, a decrease in ACE activity will increase Ang II levels, causing the activation of the AT1 receptor that produces ARDS. (Gul et al., 2021; Saha et al., 2020; Yang et al., 2020)\n\nOn the other hand, a study by Trump et al comparing the proportion of critical cases to all other severities of COVID-19 in the different patient groups with hypertension and cardiovascular diseases that receive anti-hypertensive agents, show that ACEI treatment proves to have a more profound decline in critical cases compared to other antihypertensive agent. Also, the results successfully showed the overall increased expression of both ACE2 (P = 0.0025) and TMPRSS2 (P = 0.0002) upon SARS-CoV-2 infection. However, anti-hypertensive treatment did not alter ACE2 expression, in neither patient positive for SARS-CoV-2 nor patients negative for SARS-CoV-2. Therefore, entry factor expression did not predispose ACEI or ARB-treated patients to SARS-CoV-2 infection. This finding is in accordance with observational studies, which did not reveal any effect of ACEI or ARB treatment on SARS-CoV-2 infection risk in individuals with hypertension or other cardiovascular diseases. (Trump et al., 2020)\n\nIn accordance with the guidelines of the European Society of Cardiology, there is no change in anti-hypertensive recommendations for COVID-19 patients. CCBs, both non-dihydropyridine and dihydropyridine can still be considered. Verapamil, a non-dihydropyridine CCB, is able to control heart rate in supraventricular tachycardia (SVT), prevent the migraine attack, and to manage the high blood pressure in patients with atrial fibrillation. This drug can be the drug of choice in hypertension management in COVID-19 patients. Preliminary data from animal studies suggest that verapamil has no effect on ACE2 expression, cardiac involvement, and SARS-Cov-2 related myocarditis. Amlodipine, a CCB dihydropyridine, shows some benefits in COVID-19 patients by inhibiting SARS COV-2 infection in vitro through the role of intracellular Ca2+, inhibiting viral replication at the post entry stage, showing inhibitory effects against SARS-Cov2 replication, and enhancing the anti-viral effect of chloroquine. (ESC, 2020)\n\nThe use of BBs also showed promising benefits in patients with COVID-19. Beta-adrenergic blockers block the entry of SARS-COV-2 via the ACE2 receptor as well as CD147. BBs on the juxtaglomerular cells in the kidney reduce the activity of both arms of the RAAS pathway, thereby it may decrease the ACE2 level. As ACE2 is the receptor for SARS-CoV-2 cellular entry, beta-adrenergic blockers may decrease the SARS-CoV-2 cellular entry. Therefore, beta-adrenergic blocker treatment in COVID-19 will decrease the SARS-CoV-2 cellular entry by downregulation of both ACE2 and CD147. Beta-adrenergic blockers have been shown to decrease a variety of proinflammatory cytokines expression including IL-1β, IL-6, TNFα, IFNγ. The use of beta-adrenergic blockers in COVID-19 patients may reduce the expression of the proinflammatory cytokines and the inflammation associated with it. (Vasanthakumar, 2020)\n\nOur study showed that patients who were treated with single BB had higher ICU admission, mortality rate, and shorten days of death when compared with the others who were treated with only anti-hypertensive drugs. Nevertheless, when compared to double and triple antihypertensive drugs, as a single group, there was no significant difference.\n\nThere are some limitations of our study. First, we only used retrospective data from medical records. Second, the ratio of the population involved in the study using anti hypertension BB is quite small so it might not reflect the general population. Third, there may be an effect of multiple comorbidities in the study population which has the potential to be confounder which may effect the study results.\n\n\nConclusion\n\nCOVID-19, caused by SARS-COV-2 infection, is a disease that can activate the immune system and promotes immune system dysregulation. Hypertension is one of the comorbidities that causes increased severity of COVID-19. The effect of ACEI or ARBs on ACE-2 receptor regulation, which is thought to aggravate the condition of COVID-19 patients has not yet been proven. This is consistent with findings in other anti-hypertensive groups.\n\n\nData availability\n\nFigshare. Data of Anti Hypertensive in COVID-19. DOI: 10.6084/m9.figshare.14130584\n\nThis project contains the following underlying data:\n\n- This .xls dataset contains patients’ history, physical examination, laboratory data, and chest x-ray imaging.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Acknowledgements\n\nWe thank Prof. Dr. Nasronudin, Sp. PD K-PTI for supporting us in completing this study and making the database of COVID-19 patients in Airlangga University Hospital.\n\n\nReferences\n\nBas M, Hoffmann TK, Bier H, et al.: Increased C-reactive protein in ACE-inhibitor-induced angioedema. Br J Clin Pharmacol. 2005; 59(2): 233–238. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBurhan E, Susanto AD, Nasution SA, et al.: Pedoman Tatalaksana COVID-19 5OP Edisi 3 2020. 3 edn. Jakarta, Indonesia: PDPI, PERKI, PAPDI, PERDATIN, IDAI., 2020; 3–6. Reference Source\n\nCasucci G, Acanfora D, Incalzi RA: The Cross-Talk between Age, Hypertension and Inflammation in COVID-19 Patients: Therapeutic Targets. Drugs Aging. 2020; 37(11): 779–785. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nESC: European Society of Cardiology: Guidance for the Diagnosis and Management of CV Disease during the COVID-19 Pandemic. European Heart Journal. 2020; 119. Reference Source\n\nFeng X, Zhu B, Jiang C, et al.: Correlation between White Blood Cell Count at Admission and Mortality in COVID-19 Patients: A Retrospective Study. 2020. Publisher Full Text\n\nFerrario CM, Jessup J, Chappell MC, et al.: Effect of Angiotensin-Converting Enzyme Inhibition and Angiotensin II Receptor Blockers on Cardiac Angiotensin-Converting Enzyme 2. Circulation. 2005; 111(20): 2605–2610. 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Int J Infect Dis. 2020d; 94: 128–132. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu F, Li L, Xu M, et al.: Prognostic value of interleukin-6, C-reactive protein, and procalcitonin in patients with COVID-19. J Clin Virol. 2020; 127: 104370. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMoore JB, June CH: Cytokine release syndrome in severe COVID-19. Science. 2020; 368(6490): 473–474. PubMed Abstract \| Publisher Full Text\n\nPalmas W, Ma S, Psaty B, et al.: Antihypertensive medications and C-reactive protein in the multi-ethnic study of atherosclerosis. Am J Hypertens. 2007; 20(3): 233–41. PubMed Abstract \| Publisher Full Text\n\nPalvesky PM, Radhakrishnan J, Townsend RR: COVID-19: Issues related to acute kidney injury, glomerular disease, and hypertension. UpToDate. 2020. 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Nat Biotechnol. 2020. PubMed Abstract \| Publisher Full Text\n\nVasanthakumar N: Beta-Adrenergic Blockers as a Potential Treatment for COVID-19 Patients. Bioessays. 2020; 42(11): e2000094. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWagner J, DuPont A, Larson S, et al.: Absolute lymphocyte count is a prognostic marker in Covid-19: A retrospective cohort review. Int J Lab Hematol. 2020; 42(6): 761–765. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWarren MA, Zhao Z, Koyama T, et al.: Severity scoring of lung oedema on the chest radiograph is associated with clinical outcomes in ARDS. Thorax. 2018; 73(9): 840–846. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWHO: World Health Organization : Weekly epidemiological update - 5 January 2021. 2021; (Accessed 14 January 2021). 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "85528", "date": "04 Jun 2021", "name": "Dhite Bayu Nugroho", "expertise": [ "Reviewer Expertise Cardiovascular", "adipose tissue angiogenesis", "cardiac hypertrophy", "Senescence", "Endothelin", "Adipokine" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 study talks about the difference in antihypertension drugs (AHD) used in COVID-19 patients with hypertension. Although similar studies have been published, this study emphasizes that the use of ACEI may not differ from other AHD's in the outcome of COVID-19.\nAlthough this might give merit to the knowledge of COVID-19, several issues need to be addressed:\nThe criteria of COVID-19 severity in this study should be clearer and must refer to an acceptable recommendation/guideline. Please provide the reference.\n\nThe difference with other similar studies should be stated clearly.\n\nAuthors are advised to go through the manuscript again to correct the grammatical errors. A language edit is suggested.\nSpecific comments:\nPage 3\nWhat is the impact of UAH being a referral hospital? Did it affect the severity of the admitted patients? Please explain.\n\nIs previous medication with antihypertension drugs also accounted for the inclusion and classification of the patient?\n\n\"Coronavirus disease (COVID-19) had become a pandemic since almost one year ago. (Huang et al., 2020) Over 90 million cases and 1.5 million death-cases had happened during 2020 and several comorbidities associated with an increase in COVID-19 cases. Cardiovascular disease had become one of the most frequent comorbidities among COVID-19 patients which had a poor prognosis and high mortality rate. (WHO, 2021)\" - This paragraph should be revised for its grammatical errors. The authors are advised to use the past tense. Because the data related to this pandemic is rapidly changing, the authors should reference when this data was obtained.\n\n\"Several antihypertensive drugs had been studied about the relation of increasing inflammatory markers like C-reactive protein in cardiovascular disease\" - This sentence is confusing. Please revise.\n\n\"The critical condition is upright when symptoms are present that supports the diagnosis of acute respiratory distress syndrome (ARDS) and septic shock (Burhan et al., 2020).\" - What does it mean by \"upright\"?\n\n\"For severe COVID-19, moderate case definitions were defined as: 1) clinical sign of pneumonia (fever, cough, dyspnea, tachypnea) and 2) Oxygen saturation ≥93% free air. Severe case definitions are if there were clinically sign of pneumonia, and one of this are the following: 1) respiration rate >30 times per minutes, or 2) severe respiratory distress, or 3) oxygen saturation < 93% free air.\" - Please insert citations that recommend this classification of COVID-19 severity.\n\n\"Although several studies had associated few antihypertensive drugs to the severity and risk of death due to COVID-19,...\" - This sentence needs references. What is the difference between this study and other similar ones?\nPage 4\n\"Figure 1\", please explain the abbreviation of \"BB\". Please explain the types of antihypertensive agents in the group receiving triple agents and The rationale for using more than 1 AHD?\n\n\"Although 55.84% severity of COVID-19 was moderate but based on RALE score 46.75% were included in severe and critically ill.\" - Thus, which criteria were used for the classification of moderate vs severe COVID-19? Is it clinical or radiological criteria?\n\nWhat about other medications/ co-medications? Were all subjects received the same medications for COVID-19 other than the antihypertension drugs? Please state it here.\n\nIn the descriptive analysis, data that are not normally distributed should be shown as the median.\n\n\"The strengthening of the reporting of observational studies in epidemiology (STROBE) statement checklist was used for our report in this study.\" - Please add references.\nPage 5\n\n\"Table 1\" - Please give appropriate subtitle for each column. I think \"sex\" is not the best subtitle for this part.\nPage 6-8\n\"Table 2\", a significant p-value, should be marked.\n\n\"Table 2\" - Please explain why there is a missing p-value in table 2 in comparing the use of Antihypertensive agents in the comorbidity group.\n\nPlease explain why the discharge and death outcome parameters have the exact p-value. What variables are the researchers trying to compare on this outcome parameter?\n\nA lot of information in this manuscript refers to the table on page 8 of the pdf version. However, this table is not clearly explained: is this table part of table 2? With different types of information, this table should be dedicated as a separate table. What is meant by evaluations 1,2, and 3? The information displayed is too convoluted, although not much of this information is discussed in the manuscript. We suggest that this table be presented more concisely by displaying only relevant information.\n\nThe outcome associated with the anti-hypertension discussion refers to table 2, but the explanation in the \"Laboratory and radiology characteristics\" section is not clear which table it relates to.\nPage 10\nThe proportional hazards assumption is critical for Cox regression to work correctly. One of the essential assumptions is that the risk ratio between any two persons remains constant over time. In Figure 3, we see the intersection of the Kaplan-Meier curves for the two groups being compared. As a result, Hazard ratio reporting in this group is less precise. We recommend that authors report RR rather than HR unless they have confirmed that the Cox regression assumptions have been satisfied.\nPage 11\n\"figure 3\" - Make sure that all words are written in English.\nPage 13\nThe conclusion does not represent the results of the study. Please be consistent with your results to conform to a conclusion. The authors emphasize the dysregulation of the immune system, but the authors do not sufficiently explain the dysregulation of the immune system in the study's findings or discussions. We recommend that the writer leave this point out of the discussion and conclusion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "6826", "date": "22 Jun 2021", "name": "Satriyo Dwi Suryantoro", "role": "Author Response", "response": "Dear Dr Dhite Thank you for the helpful and considerate advices. We will revise soon." } ] }, { "id": "85479", "date": "02 Jul 2021", "name": "Bertram Pitt", "expertise": [ "Reviewer Expertise Cardiology", "heart failure", "RAAS", "CKD", "hypertension", "diabetes" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 review of the role of antihypertensive medication in patients with COVID-19. There have however been several prior papers pointing out the role of hypertension in COVID-19 and the relative risk of various antihypertensive medications. It would therefore be important to point out what new information this paper provides.\nIt might also be of value to discuss the role of obesity, since obesity is a risk factor for COVID-19 and often co-exists with hypertension.\nIn regards to the the effect of the individual classes of antihypertensive medications in patients with COVID-19, it should be emphasized that the number of patients is rather small and that therefore no definitive conclusions can be drawn. It might be of interest to present statistical power calculations for the sample size that would be needed to reach a significant conclusion in regard to the risk of the individual agents in patients with COVID-19.\nWithout further explanation of what is new in this paper to justify publication, I do not believe it has sufficient priority for indexing.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/10-393
https://f1000research.com/articles/11-1026/v1	09 Sep 22	{ "type": "Systematic Review", "title": "Information and communication integration in smart factory design", "authors": [ "Christian Fauska", "Jaroslava Kniežová", "Jaroslava Kniežová" ], "abstract": "Strategic smart factory design is essential to utilize Industry 4.0 technologies in production environments effectively. Although a series of earlier reviews in the context of smart manufacturing have been published, so far none addresses smart factory design, i. e. the planning and operation of smart factories. This review provides an overview of recent research in the field by systematizing opportunities, risks and success factors of smart factory design as available from recent empirical studies (2018-2022). Businesses are informed how smart factory design should be approached and implemented to realize cost advantages and increase competitiveness. Academic research benefits of a classification of relevant issues and open research fields are outlined.", "keywords": [ "Industry 4.0", "smart factory design", "shop floor management", "information and communication technology" ], "content": "Introduction\n\nSmart factory design has become a buzzword in production engineering in the context of the Industry 4.0 debate: According to a study by PWC (PricewaterhouseCoopers) consultants, 91% of industrial companies are investing in digital factory technology in Europe and 90% of survey participants believe that opportunities of smart factory design outweigh its risks from a business perspective (PWC, 2022).\n\nDigital data processing enables the automation of all production steps and their and autonomous flow integration (Mabkhot et al., 2018; Rejikumar et al., 2019). Intelligent value chains and product life cycles supporting the way of products from design to recycling have been called “Industry 4.0 technologies”. Industry 4.0 is characterized by on-time interoperability of virtual decentral and service oriented modular systems in the supply chain (Rejikumar et al., 2019). This extends to the usage phase of smart products, i.e. intelligent and networked products indicating producers the necessary life cycle data and retrieving operation data automatically through the Internet of Things (Brettel et al., 2014).\n\nSmart factories comprise self-organizing virtually interlinked autonomous supply chain production and delivery environments which integrate production, machinery, and information technology based on decentral information and communication infrastructures (Rejikumar et al., 2019). These cyber-physical systems self-organize essential production flows but also provide interlinks for human intervention and human integration in the work process, which is essential for control and supervision. Social machines collaborate with human beings by retrieving or analyzing provided data and images according to man-defined requirements or supporting human activities physically or informationally (Zavadska & Zavadsky, 2018).\n\nThe integration of information and communication in smart factory environments offers important opportunities to realize economies of scale, save resources and use manpower more efficiently (Oesterreich & Teuteberg, 2016). To implement smart factory designs at the informational level, however, huge amounts of data have to be collected stored, retrieved and analyzed to develop and supervise production routines and order flows autonomously. This puts high requirements on information technology technology development and maintenance.\n\nSmart factory design refers to factory layout, planning and construction aimed to integrate machines and production based on Industry 4.0 information technology (Kagermann et al., 2013). Machinery and equipment communicate via the Internet of Things a virtual networking platform (Osterrieder et al., 2020). Based on that technology, smart factories could span the whole supply and delivery chain: social machines, i.e. communicative self-organized IT technology could communicate across factories and digital production technologies. Different companies could interact locally and self-reliantly (Mabkhot et al., 2018).\n\nThis study evaluates opportunities, challenges and success factors of information and communication in smart factory design based on a systematic literature review of empirical studies to outline the status of existing literature, identify further empirical research fields and inform companies how to make smart factory environments succeed.\n\n\nEarlier related reviews\n\nAlthough a series of topical (2018 and beyond) reviews in the context of Industry 4.0 and smart manufacturing are available, the research field of information and communication integration in smart factory design has not yet been explored: Rejikumar et al. (2019) retrieve distinguishing attributes of Industry 4.0 applications from earlier studies and analyze the content and timeline of publications, but do not explicitly discuss opportunities and challenges of the technologies. Fatorachian and Kazemi (2020) evaluate impacts of Industry 4.0 on supply chain performance, a part sector of smart manufacturing. Erro-Garcés (2019) conducts a meta-analysis of Industry 4.0 studies published between 2005 and 2018 and highlights managerial issues. With its Industry 4.0 focus, this approach is broader than the current study, does not explicitly mention challenges, and does not include the most recent papers. Calabrese et al. (2020) conduct a review of opportunities, difficulties and development goals of Industry 4.0 technologies and systematize nine technologies, among them smart worker and smart equipment technologies which are part of the smart manufacturing process, but does not conclusively describe them. The study lacks an analysis of success factors.\n\nFive recent reviews in the context of smart manufacturing are available: Yang et al. (2018) systematize recent research trends in smart manufacturing based on a review. The review by Osterrieder et al. (2020) of smart factory studies systematizes technical solutions and identifies groups of technologies to outline a digital value stream. Hughes et al. (2020) discuss future potentials of Industry 4.0 applications to manufacturing but do not assess presently available technologies. None of these studies discusses smart factory design, its potentials, risks or success factors.\n\nSome specialized reviews partly address potentials and risks of smart manufacturing in certain contexts: Mabkhot et al. (2018) identify “perspectives of smart factory applications and technical support systems for smart factory implementation” in the form of proprieties of smart production and smart products but does not refer to smart factory planning and construction. The study also neglects potential risks of smart manufacturing. Lee et al. (2018) discuss literature in machine health management (i.e. maintenance and repair) in smart factories, but do not refer to smart factory design. Mittal et al. (2019) critically review the applicability of available smart manufacturing and Industry 4.0 maturity models to SME and diagnose low adaptiveness to small business manufacturing practices. All three studies focus on a part segment of smart manufacturing and are thus narrower in range than the intended study and problem rather than solution focused.\n\nSo far, no review systematically juxtaposes the opportunities and risks of information and communication integration in smart factory design based on a comprehensive analysis of presently available technologies and referring to the most recent studies. This review aims to close this research void.\n\n\nMethods\n\nThis study conducts a systematic review based on a methodology suggested by Synder (2019). The purpose of the study is to identify and analyze topical empirical research in information and communication integration in smart factory design. Three key research questions are meant to be answered:\n\n• What are opportunities of smart factory applications from the perspective of production company applications?\n\n• Which problems of smart factory applications have been observed?\n\n• What can be done to design smart factory applications so that opportunities are fulfilled while problems are avoided?\n\nFigure 1 outlines the literature research process: To identify eligible studies the review uses a systematic research strategy. The review is limited to studies in English published in peer reviewed journals or at academic conferences in the period 2018 to 2022. To systematize the research process, the databases EbscoHost, Web of Knowledge, Science Direct and Scholar Google were consulted using the following homogenous keyword combination: [“smart factory design” OR “smart factory] AND [information OR communication] AND [review OR empirical]” The databases sort by relevance and studies are considered until a point of saturation is reached i.e. no further eligible studies are found or results repeated.\n\nA secondary manual evaluation process deselects reviews and then discards non-empirical studies, studies of minor empirical quality and studies that do not fit content-wise, i.e. do not focus on smart factory applications but are more general, e.g. on Industry 4.0. From the initially identified 54 studies (based on the key word combination), 11 are identified as reviews (see above) and deselected from the core analysis, 27 are discarded due to lacking focus on “smart manufacturing” or lacking empirical evidence, 16 remain for the final review. For a graphical overview of the literature research process (see Figure 1).\n\nFirst the studies are summarized in an author-centric table addressing sample, research method, identified opportunities, limitations and success factors and points of critique. This step corresponds to Webster & Watson’s (2002) content matrix. The study to catalogue the studies and extract relevant major and subcategories, a so-called concept matrix is drafted, which reorganizes the points made by arguments in major and sub-items and structures the textual evaluation (compare appendix). The textual evaluation of the studies follows the organization of the concept tables.\n\nBased on a synthesis of the review results, opportunities and risks of smart factory technologies are juxtaposed. Drawing on the outlined success factors the potentials to resolve inherent risks are discussed. Further research requirements are given if adequate solutions to recognized risks of smart factory design are unavailable.\n\n\nResults: I&C integration in smart factory design\n\nThe appendix provides an overview of the retrieved studies in the form of a content matrix (Table 1). Further classification is seen in concept matrices of opportunities, risks and success factors of smart factory design (Table 2, Table 3 and Table 4 respectively) (Webster & Watson, 2002). The arguments for opportunities, risks and success factors are each classified into technical informational, economic and sustainability (social or environmental) aspects. Technical aspects dominate the discussion and refer to the planning phase and the operation phase of smart factories. This structure guides the following sections:\n\nOnly two studies (Guo et al., 2019; Xia et al., 2021) refer to technical opportunities in the planning stage of smart factories, i.e. the actual design phase, and suggest to develop and refer to a digital twin of the planned factory to simulate the production environment first (Guo et al., 2019). Digital twins are electronic usually 3-dimensional models which are developed and refined in the planning process. They comprise building-related information, machinery equipment data and are extended to simulate production flows and interconnections in the supply chain (Xia et al., 2021). Digital twins allow the flexible analysis of design options and realistic simulation of production conditions. Simulations in the planning stage avoid erroneous designs and avoid ill-designed physical plants (Guo et al., 2019; Xia et al., 2021).\n\nMost evaluated contributions however assess the technical advantages of smart factories in operation as compared to conventional production (Baek, 2021; Ko et al., 2020; Micheler et al., 2019; Braccini & Margherita, 2018; Mantravadi et al., 2020; Lee, 2021; Suebsook et al., 2020). The transition to smart manufacturing by designing a smart factory offers diverse advantages for businesses:\n\nSmart factories contribute to an optimization of production process flows (Ko et al., 2020) and partly enable fully self-organizing shop floors (Micheler et al., 2019), which saves manpower on the shop floor and frees human resources for responsible control and supervision tasks. Production in automated supply and processing chains is adapted to demand at short notice, i.e. is on-time responsive to order flows (Lee, 2021).\n\nSmart manufacturing realizes product quality improvements due to high automation quotas and digital control and planning solutions (Braccini & Margherita, 2018; Ko et al., 2020) Smart factories usually dispose of real time digital failure analysis, which facilitates error detection and avoidance (Baek, 2021). Human workers are discharged of responsibility.\n\nThe advantages of smart factory design at the informational level refer to the informational model backing technical implementation at the manufacturing machines and in the logistics of the production process. Digital media synchronize information flows across workshops, storages and machines on time (Häckel et al., 2019). Machines interact and communicate in a self-organized manner without necessary human intervention (Schaupp & Diab, 2020). Standardized production processes are run through the value chain automatically (Häckel et al., 2019). An extensive informational network systematizes the production process based on earlier flow data (Micheler et al., 2019).\n\nFriction less order flows presuppose the interoperability of the IT systems of production machines and IT manufacturing planning systems (Mantravadi et al., 2022; Suebsook et al., 2020). Information and communication architectures are designed flexible to adapt to different Internet of Things, devices which allows a flexible composition of the production chain (Mantravadi et al., 2022). Work process inventories can be reduced on that basis (Xia et al., 2021) and manpower is saved for responsible extraordinary information management tasks (Micheler et al., 2019).\n\nTechnical and informational opportunities of smart factory design produce economic advantages. As compared to conventional production smart manufacturing sites frequently realize productivity increases (Braccini & Margherita, 2018; Lee, 2021). Demand based production reduces redundancies and allows efficiency gains (Lee, 2021).\n\nSmart manufacturing saves time in the inner organizational order flow (Guo et al., 2019) and equally reduces delivery time due to just-in-time planning (Xia et al., 2021). Realized economies of scale reduce costs and increase business competitiveness (Vestin et al., 2018).\n\nSocial and environmental sustainability of smart manufacturing sites can be increased as compared to conventional production (Micheler et al., 2019) due to higher energy consumption continuity (Braccini & Margherita, 2018). Information technology-supported production machines are worker friendly and service oriented, which improves work conditions and satisfaction on the job (Suebsook et al., 2020).\n\nTechnical risks of smart factory design at the planning stage are often concerned with the excessive complexity of site and equipment layout (Jin & Lee, 2018). Guo et al. (2019) are concerned about the potentially lacking adequacy or over-sophistication of the “digital twin” i.e. building information management model, which impairs its operability and puts the reproducibility of simulation results at risk. Due to rapid planning cycles and dynamic technological development (Häckel et al., 2019) smart manufacturing equipment is threatened by obsolescence (Büchi et al., 2020). Häckel et al. (2019) fear compatibility problems among IT and production machines and incompatibility between the diverse modular units of the plant. Limited availability of measurement data could impair the prognosis and early identification of compatibility issues (Wang & Lee, 2021).\n\nAt the stage of operation, technical problems could emerge due to high function complexity (Häckel et al., 2019), which entails a high number of interactions between modular production devices and the corporate enterprise resource planning architecture (Baek, 2021). Incorrect demand forecasts resulting from technical malalignment could mean a major threat to the implementation of efficient smart manufacturing systems (Ko et al., 2020). Häckel et al. (2019) fear lacking operationality of smart manufacturing equipment due to the failure and temporary unavailability of essential components. The limited operability of individual Industry 4.0 components could endanger the flow of the whole production process if all units are interdependent and automatized (Micheler et al., 2019).\n\nInformational risks of smart factory design are frequently connected to IT security (Häckel et al., 2019). Autonomous and interdependent systems and complex network architectures relying on the web 2.0 as a communication channel have been exposed to hacker attacks and data abuse (Ko et al., 2020). In smart manufacturing, complex network architectures intermesh the whole supply chain. Limited capabilities of supply chain partners (Lee, 2021), can impair the functioning of the whole logistic process and make high sophisticated solution at the core company redundant (Häckel et al., 2019). Studies further discuss low strategic guidance and orientation from inhouse management with regard to the conclusive implementation of smart factory designs (Micheler et al., 2019). Leaders feel a loss of personal control if information and manufacturing technologies interact self-reliantly and are reluctant to admit further digitalization steps (Schaupp & Diab, 2020). According to Vestin et al. (2018), lacking organizational adaptiveness to modern technologies is a major reason for the failure or inadequate implementation of smart factory technologies.\n\nEconomic restrictions to smart factory design are repeatedly mentioned in the retrieved studies (Büchi et al., 2020; Häckel et al., 2019; Lee, 2021). Companies fear that the investment in smart factory architectures will not amortize due to lower-than-expected efficiency gains (Häckel et al., 2019). High investment costs in digital solutions are a major reason to stick to established analogous production systems. Businesses facing resource constraints are partly unable to gain investment partners for innovative Industry 4.0 solutions if the profitability is uncertain (Micheler et al., 2019).\n\nFinally, smart factory design is assumed to be little responsible from a social perspective: Smart manufacturing hardly creates new jobs but makes workers with low qualification redundant (Ko et al., 2020). Human labor is replaced by a network of self-reliant machines and information and communication technology (Schaupp & Diab, 2020).\n\nSuccess factors of smart factory design targeted at controlling technical, informational and economic risks and caveats. At the technical planning stage of smart factories, the real-world fidelity of the digital factory model (digital twin) is essential. It is gradually adapted to real data structures and production flows as planning progresses (Guo et al., 2019). Xia et al. (2021) explained that the development of a digital twin requires a detailed analysis of the product life cycle and extensive data bases of the building information model, which is continuously updated and fed with the most recent production data.\n\nModular systems are resilient to disruptions in the value chain or temporary information lacks since they can accomplish their tasks self-reliantly, even if part of the production network breaks down (Ko et al., 2020). On the other hand, strict modularity based on common technical standards is essential to fit the value creation chain together and interconnect it in virtual space (Büchi et al., 2020). Mantravadi et al. (2022) recommended the application of standardized modular interfaces to ensure adaptiveness when the line’s process flow has to be changed or new equipment is integrated. Hardware and software, e.g. the digital databases, should be fully integrated (Li et al., 2019; Mantravadi et al., 2020), which requires electronic system compatibility across all levels of the value chain (Micheler et al., 2019). Büchi et al. (2020) advise that planning adequate breath, and depth of Industry 4.0 technology is essential to ensure sustainable evolution of the smart factory when novel technologies emerge in future or a redesign of the production process is required.\n\nIn technical operation, smart factories should be equipped with a detailed productivity management system to direct order flows through the system effectively. Baek (2021) emphasizes the relevance of reliable automated prognostic tools to schedule production planning based on a data base (Guo et al., 2019). To keep automated production systems running, accurate parameter validation and control is indispensable which again is based on a gapless information management system (Ko et al., 2020). To ensure high production quality of automated manufacturing systems these should dispose of an equally digitalized quality management concept and rely on standardized work processes as much as possible (Lee, 2021). The detailed supervision of defect rates through that system allows to recognize deviances early and human intervention should be possible without delay in that case (Ko et al., 2020).\n\nThe informational basis is key to operate smart factories without friction, which comprises an effective failure management (Baek, 2021). Wang & Lee (2021) exemplify this by a digital path loss training algorithm based on 5G technology which intervenes in case of erroneous production flows. Maximum IT security standards are required to keep self-reliant smart manufacturing systems safe and running. Access limitations and clear accountability regulations are fundamental to the informational safety of the production line. This includes adequate (human) IT support in case of extraordinary events (Häckel et al., 2019). As Li et al. (2019) observe, smart factory effectiveness and sustainability depend on a conclusive strategic business-IT alignment scheme, which includes supply chain interaction. Micheler et al. (2019) suggest relying on cloud technologies for the storage and sharing of huge data volumes in that inter-business network.\n\nTo make smart factory design an economic success, businesses should dispose of the necessary managerial and cultural preconditions: Business culture should be open to innovation (Büchi et al., 2021), which as Jin & Lee (2018) explain depends on the progressive attitude of the top management. Leaders should be involved and committed to Industry 4.0 technologies to guide businesses on the long way to autonomous production and accept the necessary investments in sustainable technology (Li et al., 2019). An environment of high research and development activity and strongly growing companies is advantageous to the frictionless implementation of smart production systems since companies usually have to rely on innovative lending and investment partners to implement their strategy. A stringent yield management is essential to monitor the efficiency of smart production sites (Ko et al., 2020).\n\n\nDiscussion\n\nSummarizing the review results, smart factory design opportunities, risks, and success factors are conclusively classified into five corresponding categories technical aspects in planning and operation, informational aspects, economic aspects and social/ecological aspects. Businesses benefit of some fundamental advice as to the planning and operation of smart factories.\n\nTo utilize design opportunities in technical planning proactively, businesses are required to control technical complexity at the planning stage, avoid compatibility issues and risks of rapid obsolescence. Digital twin simulation are useful to predict future physical performance and ensure the friction less interaction of all plant components in a modular design.\n\nIn technical operation smart manufacturing technology excels due to real time digital fault analysis, self-organizing shop floor environments and can realize higher quality standards at improved flexibility than conventional technologies. These benefits are threatened by low operability due to high system complexity and interdependency. To avoid these difficulties businesses should standardize operation and quality management routines and establish interlinks for early human intervention in case of difficulties.\n\nAt the informational level, smart factory design allows the automation of communication via self-organizing informational networks. In a real world application, however, IT security risks threaten plant operation and private data could be abused. Businesses risk losing control of production processes, and intervening late in case of failure, which can result in the costly failure of the entire production line. Low in-house competency to monitor and repair the plant, makes businesses dependent on expensive external experts. Businesses can reduce this dependence by developing in-house knowledge on their IT system and by applying tight IT security standards.\n\nAt the economic level, smart factories promise productivity increases, higher quality standards and in effect improved competitiveness. The investment costs to build smart factories, however, are significant. To amortize these expenses, smart production lines should be designed flexible to adapt to different production jobs and volumes. Investment or financing partners should be provided a reliable calculation of expected benefits of the smart factory.\n\nIf planned to requirements, smart factories can save energy, however, threaten unqualified jobs which are substituted by automated processes. Businesses should plan digitalization and automation early to develop their work force so that responsible jobs in machine and computer operation can be taken over by long-standing employees, while job cuts are avoided.\n\nThe evaluation of recent (published 2018 to 2022) studies in smart factory design has provided some general insights in the opportunities, risks and success factors of smart factory design from a business perspective. Essential categories for classifying these issues have been developed, which can be used as a foundation to further empirical research in smart factory design. The literature analysis has found 11 reviews and 16 empirical studies fitting with the research objective, which suggests that available research in Industry 4.0 and smart factory design tends to be theoretical and literature focussed. In available empirical research, practice applications are frequently based on single case studies i.e. smart factory applications in individual companies (Braccini & Margherita, 2018; Lee, 2021; Mantravadi et al., 2022; Vestin et al., 2018; Xia et al., 2021), which impairs the representativeness of these studies. Empirical studies differ in focus and range: Some focus on particular technologies (e.g. Wang & Lee, 2021: 5G communications; Guo et al., 2019: digital twin; Häckel et al., 2019: IT security risks; Baek, 2021: vibration sensor signals in automated storage). Their results apply to specific conditions but are not generally applicable to smart factory design in other contexts. Other studies are very broad in range (e.g. Büchi et al., 2020; Industry 4.0 application in manufacturing units; Jin & Lee, 2018: Smart factory construction in Korea; Micheler et al., 2019: Smart technologies in Industry 4.0). The results of these studies are broadly applicable but little concrete concerning concrete smart factory implementations. Businesses planning smart factory solutions, thus obtain little valuable information from current academic research.\n\nFurther empirical research in smart factory design is required, to systematize available smart manufacturing technologies and empirically analyse implementations of smart factory solutions, ideally in the form of a comparative analysis including several businesses. the issues of smart supply chain integration and man–machine interaction planning have hardly been addressed in recent empirical studies and further research in these fields of smart factory design is desirable.\n\nThis study has provided an overview of recent empirical and review-based publications in smart factory design, has derived advice for businesses investing in the field and has outlined further academic research requirements. However, the insights gained here are limited in range. Only 27 studies (11 reviews and 16 empirical studies) have been referred to due to limitations in range. Publications before 2018 have not been considered. The provided overview on smart factory design research thus is not comprehensive and the inclusion of further studies would be useful to obtain a representative overview of available smart factory technologies and their potential integration.\n\n\nAuthor contributions\n\nCollection and analysis were performed by Christian Fauska. The first draft of the manuscript was written by Christian Fauska, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.\n\n\nData availability\n\nAll data are available as part of the article.\n\nFIGSHARE: PRISMA checklist and flowchart for ‘Information and communication integration in smart factory design: a systematic review’, https://doi.org/10.6084/m9.figshare.20279223.v1 (Fauska & Kniežová, 2022).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nBaek S: System integration for predictive process adjustment and cloud computing-based real-time condition monitoring of vibration sensor signals in automated storage and retrieval systems. Int. J. Adv. Manuf. Technol. 2021; 113(3): 955–966. Publisher Full Text\n\nBraccini AM, Margherita EG: Exploring organizational sustainability of Industry 4.0 under the triple bottom line: The case of a manufacturing company. Sustainability. 2018; 11(1): 36. 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Publisher Full Text\n\nMantravadi S, Srai JS, Brunoe TD, et al.: Exploring Reconfigurability in Manufacturing Through IIoT Connected MES/MOM. 2020 IEEE International Conference on Industrial Engineering and Engineering Management (IEEM). 2020: pp. 161–165. Publisher Full Text\n\nMantravadi S, Møller C, LI C, et al.: Design choices for next-generation IIoT-connected MES/MOM: An empirical study on smart factories. Robot. Comput. Integr. Manuf. 2022; 73: 102225. Publisher Full Text\n\nMicheler S, Goh YM, Lohse N: Innovation landscape and challenges of smart technologies and systems–a European perspective. Prod. Manuf. Res. 2019; 7(1): 503–528. Publisher Full Text\n\nMittal S, et al.: Building blocks for adopting smart manufacturing. Procedia Manuf. 2019; 34: 978–985. 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Publisher Full Text\n\nZavadska Z, Zavadsky J: Quality managers and their future technological expectations related to Industry 4.0. Total Qual. Manag. Bus. Excell. 2018; 1–25." }	[ { "id": "153717", "date": "07 Nov 2022", "name": "Deepika Pandita", "expertise": [ "Reviewer Expertise human resources", "organizational behavior", "entreprenership" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 surely a very interesting one, but the following aspects needs to be worked on by the authors:\n1. The abstract needs to be re-worked very explicitly stating the need and objective of the study. The current abstract talks about only the overview of smart factories.\n2. The literature review is very concise and needs to be elaborated.\n3. Which methods of LR is used in this study? Please mention that very clearly.\n4. Research Questions need to be mentioned very clearly and should be in sync with the research objectives.\n5. The findings are missing. The authors need to mention these as they have studied various literature review papers, so they should include how these studies help to discuss the findings.\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", "responses": [ { "c_id": "9805", "date": "21 Jul 2023", "name": "Christian Fauska", "role": "Author Response", "response": "Hello, Thank you very much for your feedback. I have tried to improve the points in a 2nd version. Some points were, in my opinion, already described. Therefore, a short statement if I have not implemented everything in the point. also, the 2nd Reviwer had partly contrary views. There I tried to mediate: 1. the summary must be revised by explicitly stating the need and the goal of the study. The current summary only gives an overview of smart factories. --> It is described in detail in the introduction. I would also not elaborate on the possibilities of the descent owed here. 2. the literature review is very brief and needs to be elaborated. --> In principle you want a longer overview. I don't want that, because other articles investigate the topics and it is shown that the scientific contribution is finished for me. I will include wieter anlehnungen in other articles 3. what methods of LR are used in this study? Please specify. --> According to Snyder (2019), the method is shown in detail and also graphically in the methods chapter. 4. The research questions must be stated very clearly and should be consistent with the research objectives. --> They are listed under the methods as follows: - What are the opportunities of smart factory applications from the perspective of applications in manufacturing companies? - What problems have been observed in smart factory applications? - What can be done to design smart factory applications to take advantage of the opportunities and avoid the problems? 5. there is a lack of insights. The authors need to mention these as they have studied various literature reviews, so they should state how these studies help to discuss the findings. -->I discuss the findings in the Results chapter and discuss them in detail in the Discussion chapter based on the tabular analyses of the studies." } ] }, { "id": "173434", "date": "02 Jun 2023", "name": "Varun Tripathi", "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\nThe authors reviewed recent research works in the context of smart manufacturing by systematizing opportunities, risks, and success factors of smart factory design as available from recent empirical studies. The manuscript's contents are well short of the standard for publication in a research journal. There are several things that could be improved in the current research work.\nThe authors should include the following suggestions in their manuscript for the manuscript to be considered:\n\nIn the abstract, the authors should clarify the present research work's objective and describe how the study could benefit researchers. The authors should also explain the statement given in the abstract \"So far none addresses smart factory design, i.e. the planning and operation of smart factories\". The abstract must be modified systematically.\n\nThere are several discrepancies in the introduction section, as follows:\na) What is the Research objective? b) What are the needs and current scenario? c) Describe the backgrounds. d) Which types of problems have been faced by researchers in previous research works? e) What is the meaning of the statement given \"So far, no review systematically juxtaposes the opportunities and risks of information and communication integration in smart factory design based on a comprehensive analysis of presently available technologies and referring to the most recent studies\".\n\nThe authors must include the latest research works on smart manufacturing.\n\nThe authors must review the literature extensively to understand the present condition of smart factory design.\n\nThe research outcomes should be described.\n\nWhich data collection and analysis tools/methods have been used?\n\nThe authors should explain the reason for the focus on selecting research studies for 2018–2022.\n\nAccording to the journal standards, the references cited need to be more systematic.\n\nThe authors must add the description of tables 2, 3, and 4.\n\nHow and why the opportunities, risks, and success factors are same?\n\nThe authors should define the results obtained by analyzing opportunities and risks in the discussion section. The authors should describe how the researchers could consider the different categories in smart factory design. Which types of factors and limitations should consider for achieving desired outcomes?\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? No", "responses": [ { "c_id": "9806", "date": "21 Jul 2023", "name": "Christian Fauska", "role": "Author Response", "response": "Hello, Thank you very much for your feedback. I have tried to improve the points in a 2nd version. Some points were, in my opinion, already described. Therefore, a short statement if I have not implemented everything in the point. Also, the 2nd Reviewer had partly contrary views. Therefore I tried to mediate: 1. In the abstract, the authors should clarify the present research work's objective and describe how the study could benefit researchers. The authors should also explain the statement given in the abstract \"So far none addresses smart factory design, i.e. the planning and operation of smart factories\". The abstract must be modified systematically. --> The abstract is based on the possibilities of the journal. It gives only a first overview. In my opinion, all the points raised will only be clarified with the scope of the introduction. 2. There are several discrepancies in the introduction section, as follows: a) What is the Research objective? --> It's here in the Introduction section in the last paragraph b) What are the needs and current scenario? --> As described in the objective: \"This study assesses opportunities, challenges, and success factors of information and communication in designing smart factories based on a systematic literature review of empirical studies to outline the state of the existing literature, identify further empirical research areas, and inform companies on how to successfully design smart factories.\" c) Describe the backgrounds. --> This issue is highlighted in a separate chapter, \"Earlier related reviews.\" d) Which types of problems have been faced by researchers in previous research works? --> It's here in the Introduction section in the last paragraph where it belong e) What is the meaning of the statement given \"So far, no review systematically juxtaposes the opportunities and risks of information and communication integration in smart factory design based on a comprehensive analysis of presently available technologies and referring to the most recent studies\". --> The sentence is correct. Rewritten: “To date, there is no review work that systematically compares the opportunities and risks of information and communication integration in the design of smart factories based on a comprehensive analysis of the currently available technologies and with reference to the latest studies. This review aims to fill this research gap.” 3. The authors must include the latest research works on smart manufacturing. --> The article was written in 2021 and beginning 2022. Published in August 22. It was actually. I will develop to the newest development in other articles. 4. The authors must review the literature extensively to understand the present condition of smart factory design. -->The reviews were even summarized and compared in tabular form. For the sake of simplicity, I have placed the tables at the end of the article. This way, they are a supplement to the body text. 5.The research outcomes should be described. -->I discuss the findings in the Results chapter and discuss them in detail in the Discussion chapter based on the tabular analyses of the studies. 6. Which data collection and analysis tools/methods have been used? --> according to Snyder (2019), the method is shown in detail and also graphically in the methods chapter. 7. The authors should explain the reason for the focus on selecting research studies for 2018–2022. --> the study was written in 2021 and 2022. This is the actual status of research. This u forced also in your point 3. 8. According to the journal standards, the references cited need to be more systematic. --> I have provided detailed tabular lists of all results and their methodological evaluation. This is all that can be systematized. We use a Proven Methodology according to Snyder (2019) and already present the results in detail also in tabular form and derive the whole evaluation text in detail. 9. The authors must add the description of tables 2, 3, and 4. --> The tables are the summary of the chapter. U ca see it as underlining the content. 10. How and why the opportunities, risks, and success factors are same? --> Because they are the key enabler for success. 11. The authors should define the results obtained by analyzing opportunities and risks in the discussion section. The authors should describe how the researchers could consider the different categories in smart factory design. Which types of factors and limitations should consider for achieving desired outcomes? --> They are combined. U can not unique them. U have to understand the whole technical topic with the factettes- opportunities, risks, and success factors – to achieve outcomes." } ] } ]	1	https://f1000research.com/articles/11-1026
https://f1000research.com/articles/11-1555/v1	22 Dec 22	{ "type": "Systematic Review", "title": "The relationship between climate change and malaria in South-East Asia: A systematic review of the evidence", "authors": [ "Ardhi Arsala Rahmani", "Dewi Susanna", "Tommi Febrian", "Ardhi Arsala Rahmani", "Tommi Febrian" ], "abstract": "Background: Climatic change is an inescapable fact that implies alterations in seasons where weather occurrences have their schedules shift from the regular and magnitudes intensify to more extreme variations over a multi-year period. Southeast Asia is one of the many regions experiencing changes in climate and concurrently still has endemicities of malaria. Given that previous studies have suggested the influence of climate on malaria’s vector the Anopheles mosquitoes and parasite the Plasmodium group, this study was conducted to review the evidence of associations made between malaria cases and climatic variables in Southeast Asia throughout a multi-year period. Methods: Our systematic literature review was informed by the PRISMA guidelines and registered in PROSPERO: CRD42022301826 on 5th February 2022. We searched for original articles in English and Indonesian that focused on the associations between climatic variables and malaria cases. Results: The initial identification stage resulted in 535 records of possible relevance and after abstract screening and eligibility assessment we included 19 research articles for the systematic review. Based on the reviewed articles, changing temperatures, precipitation, humidity and windspeed were considered for statistical association across a multi-year period and are correlated with malaria cases in various regions throughout Southeast Asia. Conclusions: According to the review of evidence, climatic variables that exhibited a statistically significant correlation with malaria cases include temperatures, precipitation, and humidity. The strength of each climatic variable varies across studies. Our systematic review of the limited evidence indicates that further research for the Southeast Asia region remains to be explored.", "keywords": [ "climate change", "malaria", "Southeast Asia", "temperature", "precipitation", "windspeed", "humidity", "systematic review" ], "content": "Introduction\n\nClimatic change, as an inescapable fact, refers to the changes in long-term normal weather conditions. Unlike the varying weathers due to seasonality that is of common occurrence in one given year, the climate is indicated by weather pattern types and related classifications such as the Köppen-Geiger, – which subdivides climates into the tropics, temperate, cold and polar.1 The climate normal range is typically measured over a 30-year period but spans of 5- to 25-year periods have also recently been included.2 A changing climate therefore also implies alterations in seasons where weather occurrences have their schedules shift from the regular and magnitudes intensify to more extreme variations over a multi-year period.\n\nNaturally, the climate system has always changed across different geological epochs since our blue planet formed approximately 4.6 billion years ago. The epochs, which are part of a system of chronological dating, so called by geologists, paleontologists and paleoclimatogists, represent periods of geologic history. The current period, known as the Holocene, began around 11,000 years ago following the end of the Pleistocene epoch. The Holocene is marked by a relatively stable climate with averaging global temperature variations of about plus or minus 1°C for every turn of the century so far.3 This marked stability has been advantageous for humanity and has allowed the establishment of modern civilizations, beginning with the advent of agriculture that relied on the very stable climatic conditions of the early Holocene.3\n\nAn important feature of the current epoch is the natural greenhouse effect where the sun’s energy is partially absorbed by the earth’s surface and reflected back into space. The solar radiation is absorbed by naturally occurring greenhouse gas molecules which disperse the energy as heat thereby warming the lower atmosphere and conferring the needed energy and radiation to the biosphere. In the earth’s normal state, greenhouse gases, which include carbon dioxide (CO2), water vapour, nitrous oxides, and other compounds such as methane and ozone naturally exist around us.3 However, with the ascent of industrialized civilization, humans have since caused atmospheric imbalances with increased accumulation of greenhouse gas emissions from anthropogenic activities. This has led to climatic variations and feedback, which include precipitation intensification as well as temperature rises.4,5\n\nThese extreme feedbacks are of concern because they influence the reproduction of infectious agents such as viruses, bacteria and vectors such as mosquitoes and flies as they are sensitive to fluctuations in climatic variables such as temperature.6 In the event of climatic fluctuations that enable reproductive enhancement of infectious agents, the spread of disease amongst humans inevitably increases and overall public health conditions are threatened. An example of this is malaria, wherein climatic fluctuations have been shown to influence the risk factors posed by both the infectious parasitic agent, the Plasmodium group, and Anopheles mosquitoes.7,8\n\nMalaria incidence and prevalence are also determined by variables like urbanization, globalization, migration patterns as well as land-use changes,9 and the disease remains endemic in many parts of the world in spite of sociodemographic developments such as throughout Southeast Asia (WHO, 2020). With regards to the fact that malaria is a climate-dependent disease, it is endemic in many areas across Southeast Asia and the region is experiencing climatic changes like the rest of the world, this study was conducted to critically assess and review the evidence of associations made between malaria cases and climatic variables in the region over a multi-year period, in line with the span of a climate normal range.\n\n\nMethods\n\nThe conduct of this study was guided by the PRISMA 2020 checklist for review studies10,11 and registered in PROSPERO: CRD42022301826 on 5th February 2022. One Indonesian database (Garuda) and three international databases (PubMed, SpringerLink, ProQuest and Scopus) were searched to gather peer-reviewed articles for this review of evidence. The Indonesian database was included to capture additional articles catered in the authors’ local language as previously done in Babaie et al. (2018)12 with the inclusion of Persian databases for a review of Iran and Fischer et al. (2020)13 with the inclusion of German and French articles for a review of Europe. The search strategies applied were deployed in multiple sequences to mitigate any biases arising from missed articles from each database. The articles were then immediately disbursed amongst authors following selection. The keywords for our search included the terms ‘climate’, ‘iklim’, ‘malaria’ and ‘Southeast Asia’ or the 10 Southeast Asian countries searched as ‘Indonesia’, ‘Malaysia’, ‘Singapore’, ‘Philippines’, ‘Thailand’, ‘Myanmar’, ‘Laos’, ‘Cambodia’, ‘Vietnam’ and ‘Brunei’. The search terms and methods along with the appropriate incorporation of truncations and operators specific to each database was discussed and consulted between DS and AR. Our search strategy did not include any limitations on publication periods. The search methods used and respective retrieved results from each database used are detailed as follows:\n\n• PubMed (169 retrieved results): ((“climat”[All Fields]) AND (“malaria”[All Fields]) AND (“Indonesia” OR “Malaysia” OR “Singapore” OR “Philippines” OR “Thailand” OR “Vietnam” OR “Laos” OR “Cambodia” OR “Myanmar” OR “Brunei” OR “Southeast Asia” [All Fields]))\n\n• SpringerLink (126 retrieved results): where the the title contains “climate” AND “malaria” AND (“Indonesia” OR “Malaysia” OR “Singapore” OR “Philippines” OR “Thailand” OR “Vietnam” OR “Laos” OR “Cambodia” OR “Myanmar” OR “Brunei” OR “Southeast Asia”) with Content Type set to Articles\n\n• Scopus (136 retrieved results): TITLE-ABS-KEY ((climat) AND (malaria) AND (Indonesia) OR (Malaysia) OR (Singapore) OR (Philippines) OR (Thailand) OR (Vietnam) OR (Laos) OR (Cambodia) OR (Myanmar) OR (Brunei) OR (Southeast Asia)) AND (LIMIT-TO (DOCTYPE,“ar”))\n\n• ProQuest (94 retrieved results): ALL (climat* AND malaria AND (Indonesia OR Malaysia OR Singapore OR Philippines OR Thailand OR Vietnam OR Laos OR Cambodia OR Myanmar OR Brunei OR Southeast Asia)) with Source Type set to Scholarly Journals\n\n• Garuda (10 retrieved results): “iklim” AND “malaria”\n\nOriginal articles written in Indonesian and English which were analytical ecological studies and utilized longitudinal or time-series data of climatic variables with malaria incidence and/or prevalence in regions across Southeast Asia were included. Additionally, the articles included were studies which quantitatively analyzed the data through correlation, regression and/or mathematical models to infer relationships between multiple meteorological measures to reflect climate change and malaria incidence and/or prevalence. The studies that did not include data from a multi-year period and quantitative models with only one climatic variable were excluded.\n\nThree reviewers were involved in this systematic review of evidence with discussions and decisions conducted online. The selected papers were systematically reviewed thematically, and their methodologies assessed by AR with independent verifications by TF who also ensured no relevant articles were missing in the systematic review. Then, eligibility of the full-text records following screening of abstracts was conducted by AR and further corroborated by DS and TF. The three authors were familiar with reviewing and presenting descriptive assessments of quantitative results which should minimize the potential bias arising from reporting conflicting results. Any differing judgements on the selection of articles and extraction of results were resolved with the expert verdict of DS who also gave the final confirmation on credibility of the synthesis with regards to the climatic variables’ influence on malaria dynamics. AR compiled the retrieved and summarized data of studies selected from the eligibility assessment stage into a separate review table in a shared Microsoft Word document (Version 2207 Build 16.0.15427.20182). DS and TF worked independently in corroborating the extracted data and narrative outlined in the shared review table. The systematic review flowchart to document our research process according to PRISMA conventions is shown in Figure 1.\n\nData was extracted from the studies that met the eligibility conditions. The studies were imported from their respective online databases and managed with the reference management software Zotero (Version 6.0.13, RRID: SCR_013784). The information included in the extractions were title, author and year of publication, location of study, period of study, independent and dependent variables, the scale and measure of the variables, quantative analysis methods, and summary of results. These extracted data were retrieved and summarized for qualitative synthesis within a table in a shared Microsoft Word document that was independently corroborated by the reviewing authors.\n\nThe study utilizes a narrative synthesis method to describe the overarching influence of climatic variables indicated by meteorological measures such as temperature, humidity, wind speed and precipitation on malaria prevalence and/or incidence in countries across Southeast Asia. The strength and direction of the influence between variables is derived from the outcomes and summaries of the quantitative correlation, regression or mathematical models presented in the reviewed studies. Every climatic variable found throughout the review is described in the narrative synthesis irrespective of the number of studies that include them for the quantitative models. The reported outcomes of studies included in the final review are tabulated to group them according the the temperature, precipitation, humidity, and windspeed indicators as a meteorological proxy variables of climate change against their respective effects on malaria. Any incomplete reported outcomes in statistical tables found within the reviewed articles were thoroughly searched in the textual section of the articles with corroborations from the three authors. Categorized tabulations of the summarized articles were made using Microsoft Word’s table features and shared amongst the three authors concurrently.\n\n\nResults\n\nDuring the first stage of the review process, a total of 535 records were identified from four different databases. 10 records were written in Indonesian and 425 in English. We then conducted a deduplication process which then left 391 records for abstract screening. After 391 of the articles were screened from their abstracts, 352 were excluded as they included studies outside the Southeast Asian region, were not ecological analyses or did not indicate the inclusion of more than one climatic variable. We were then left with 39 records for full-text eligibility assessment. In this final stage, 20 full-text articles were excluded as they did not include malaria cases as an outcome variable and did not use multi-year data for analysis in addition to the similar exclusion reasons of the previous stage. This left us with a total of 19 articles selected for the final review which we have summarized categorically and presented in Tables 1–4. A meta-analysis attempt was made following the Hedges-Olin and Hunter-Schmidt method to assess sets of regression and correlation coefficients by way of pooled fixed effects.14–16 However, due to insufficiencies in the reported statistical results and variations in methodologies in the 19 selected articles, a meta-analysis report could not be made in this study as we’ve detailed in our added underlying data.17 This review is therefore only a narrative systematic review.\n\n\n\n• Median temperature at lag 1 (r = 0.38, p = 0.008)\n\n• Median temperature at lag 2 (r = 0.47, p = 0.001)\n\n• Mean temperature at lag 1 (r = 0.38, p = 0.008)\n\n• Mean temperature at lag 2 (r = 0.47, p = 0.001)\n\n\n\n• Mean relative humidity at lag two (r = -0.35, p = 0.019)\n\n• Mean relative humidity at lag three (r = -0.47, p = 0.001)\n\n\n\n• Precipitation at lag 3 (β = 0.0008, SE = 0.0003, p < 0.05).\n\n• Precipitation at lag 12 (β = 0.0009, SE = 0.0003, p < 0.05).\n\n\nDiscussion\n\nTemperatures across different locations in Southeast Asia proved to be a worthy inclusion for analyzing the relationship with malaria cases based on the reviewed studies. Both Anopheles mosquitoes as the vector for malaria and the parasitic agent, Plasmodium group, rely on optimally warm temperatures.18–24 The optimal temperature for Anopheline reproduction according to Mau et al. (2020) is between 25–27°C whilst the Plasmodium group’s extrinsic cycle is optimum within the 20–30°C range.19 This implies that as temperatures become warmer within the optimum range, the duration of incubation is shortened, and mosquitoes become infective much sooner.19,21,23\n\nThat said, the quantitative analyses conducted in the reviewed studies exhibited varying results with temperature variables being averaged over a year, a month, split into maximum and minimum ranges as well as added lagged variations. For instance, in Kiang et al.'s (2006) neural network analysis, the composite use of mean monthly temperature with other climatic variables and vegetation index resulted in a model configuration to assess malaria cases with a training accuracy of 73% and testing accuracy of 53%. The model was developed based on variable data from 19 provinces across Thailand throughout a seven-year period (1994–2001).\n\nMeanwhile, a study of the Koh Chang district in Thailand throughout 2001–2011 indicates that maximum temperature and mean temperature are positively correlated with malaria cases (r = 0.150 and r = 0.190 at α ≤ 0.01) by one year according to the count regression models.26 Similarly, Rejeki et al. (2018) also utilized count models in which maximum and minimum temperatures were included with the addition of lagging by one, two, three and 12 months. The results of their baseline Poisson model suggest that minimum and maximum temperatures have a significant influence on monthly malaria cases at the negative and positive directions respectively. However, after the inclusion of a dispersion parameter and testing for fit, a negative binomial model was selected in Rejeki et al. (2018) in which maximum and minimum temperatures exhibited no significance at α ≤ 0.05.\n\nIn Mau et al. (2020), temperature was also shown to have a significant influence on malaria cases in their linear regression model. The difference being those temperatures were averaged over a year and negatively influenced malaria cases, which were measured as annual parasite incidence (API). The results in Rejeki et al. (2018) and Mau et al. (2020) suggest that further increases of temperatures beyond certain levels will be associated with reductions in malaria cases – in line with the optimum range for both Anopheline reproduction and Plasmodia incubation. In the Rejeki et al. (2018) Purworejo study, maximum temperatures recorded in the study period ranged between 28–30°C,21 while the average temperatures between 2013–2019 at the study site in Mau et al. (2020) ranged between 25.13–27.58°C (which is already the optimum levels for Anopheline reproduction). Interestingly, the studies of Ninphanomchai et al. (2014) and Servadio et al. (2018) have offered their explanatory evidence through a non-linear thresholding effect with spline-fitted models that establish a peak positive effect of temperature at around 30°C.26,27\n\nMoreover, another alternative take on the temperature-malaria case relation is found in studies by Bui et al. (2011), Mercado et al. (2019) and Noppradit et al. (2021) who similarly argue that other factors confound the role temperature plays in variations of malaria cases. In their study of 670 districts across Vietnam between 2007–2008, Bui et al. (2011) found that temperature variables have district specific effects with many regions exhibiting opposite interactions with malaria cases, i.e., in some regions malaria cases soar as temperatures rise while others reduce with increased heat. The same is stated in Kotepui and Kotepui (2018) and Noppradit et al. (2021), where the latter argues that the lack of statistical significance between malaria and temperature variables in their study was due to topographic factors of the study site which were unfavorable to malaria from the commencement of the study.\n\nThe next climatic variable analyzed for its association with malaria in the reviewed studies was precipitation. Although the amount of rain does not directly affect both vector and parasite proliferation, low to medium intensity rain creates reservoirs in the form of pools and puddles for Anopheles to breed.18–24 Aside from forming breeding sites, precipitation also leads to increased relative humidity which prolongs the age of infective adult Anopheles mosquitoes as explained in the following section.19,21–23\n\nAcross the 19 reviewed studies, the measures of precipitation as an independent variable varies. A mean yearly precipitation is used in Sandy & Wike (2019), Mau et al. (2020), Gallalee Sarah et al. (2021), and Noppradit et al. (2021) while mean monthly precipitation is used in Kiang et al. (2006), Jeefoo et al. (2009), Bui et al. (2011), Ninphanomchai et al. (2014), Nurmala (2017), Rejeki et al. (2018), Rejeki et al. (2019), Mercado et al. (2019), and Wangdi et al. (2020). Similar to the latter articles, Jubaidi (2015) also includes mean monthly precipitation in addition to the number of rainy days per month. Suwito et al. (2010) on the other hand uses a precipitation index. They defined the index as the product of the sum of precipitation and number of rainy days within a given month that is then divided by the total number of days in said month.24\n\nThe relationship between precipitation between malaria cases across the reviewed studies was inconclusive as the resultsof some studies did not exhibit statistical significance for the variable.27,29,30,32,35 The study by Suwito et al. (2010) did not statistically associate precipitation index with malaria cases, but their resulting correlation between the former with Anopheles density measured by man-biting rate (MBR) exhibited a positive relationship that was statistically significant. As for direct associations with statistical significance, the correlation and linear regression results in Mau et al. (2020) showed that yearly precipitation has a positively linear relationship with API where their linear regression model implies that for every 1 mm increase in precipitation, API cases increase by 0.028. The negative binomial regression results in Rejeki et al. (2018) also indicate that a 1 mm increase in precipitation has a positive influence on malaria cases by 0.08% and 0.09% with the use of three-month and 12-month lags respectively. However, in contrast to the three previous studies, results in Jubaidi (2015) showcases negative correlations that are statistically significant between monthly precipitation and number of rainy days with monthly malaria incidence (r = -0.431, α ≤ 0.01 and r = -0.349, α ≤ 0.05 respectively). Taking into account the previously mentioned studies, the results in Jubaidi (2015) indicate the need to take precipitation as a lagging indicator for direct associations with malaria cases as suggested in Kim et al. (2012), Krefis et al. (2011), and Wu et al. (2017).36–38\n\nAs previously mentioned, humidity as a meteorological measure of climate is an important indicator for malaria cases as it enables the lifespan of an infective adult Anopheles mosquito – where relative humidities of at least 60% and above optimize the mosquitoes’ activity to bite and infect.20,21,23,24\n\nOnly seven of the reviewed studies had results where humidity was a statistically significant independent variable. That said, the results were inconclusive. In the negative binomial model of Rejekti et al. (2018), results suggest that a 1% increase in maximum relative humidity is associated with a 10.47% decrease in malaria cases after two months. However, the results of Suwito et al. (2010) instead further validate the influence of humidity on Anopheles activity to bite and infect as average humidity is shown to have a statistically significant positive correlation with MBR. Narrative background for humidity posed by the other reviewed studies, where previous prevailing studies are also referred to, would suggest the latter study as being the sounder evidence for humidity’s relationship with malaria cases (albeit indirectly). The authors in the former study unfortunately did not provide any theoretical explanations as to why their two-month lagged maximum humidity was associated with a decrease in malaria cases. However, an argument could be made regarding the range of the maximum humidity throughout the period and location of study. In Purworejo, the maximum humidity between 2005–2014 varied between 83–99%, which is well beyond the 60% necessary optimum for Anopheles mosquito activity. Alternatively, the results in Rejeki et al. (2018) could suggest that the use of humidity as a lagged indicator associated with malaria cases is unwarranted.\n\nOnly two of the reviewed articles included windspeed as a climatic variable that was assessed for its relationship with malaria cases.18,23 Based on references included in their article, Sandy and Wike (2019) state that windspeed has an influence on Anopheles mosquitoes’ flight range, hence enabling an expanded scope of humans to bite. That said, the evidence in both Jubaidi (2015) and Sandy and Wike (2019) indicate that the resulting correlation between windspeed with monthly malaria incidence and API respectively did not exhibit statistical significance. The authors in both attribute the narrow windspeed range across the periods and their respective locations of study as the potential reason for the variable not resulting in statistically significant correlations.\n\n\nConclusions\n\nFollowing previous systematic reviews of evidence on changing climatic variables’ relationship with malaria for a given region such as Babaie et al. (2018),12 Fischer et al. (2020),13 and Bai et al. (2013),39 this review finds that changing temperatures, precipitation and humidity across a multi-year period are correlated with malaria cases in various regions throughout Southeast Asia. The established evidence, however, was only limited to 19 articles with most studies in Indonesia (7), Vietnam (3) and Thailand (7). Many other studies were also excluded from this review as they either utilized only a single meteorological measure, which undercuts the complex dynamics of climatic variables or claimed to assess changing climatic variables despite only analyzing a single-year period, which is not informative for exhibiting a change of climate normals that is indicated by multi-year averages.\n\nHowever, the exhibited evidence for the case of Southeast Asia suggests that further explorations could still be made with regards to the intricate dynamics of changing climatic variables with malaria incidence and/or prevalence across the region. Future research could incorporate added interactons with better inclusion of spatially varying confounders like distance from Anopheles reservoirs as done by Hasyim et al. (2018)40 or changing land-use data through proxies such as the Normalized Difference Vegetation Index (NDVI) as done by Lubinda et al.41 This is in addition to the suggested inclusion of non-climatic confounders such as availability of malaria interventions and programs, regionally specific topographic factors as well as behavioral and sociodemographic variables.20,21,25,28–30,35\n\nIn conclusion, the findings of this systematic review of evidence could serve to inform the environmental ministries and health ministries of the respective Southeast Asian countries for climate change adaptation and malaria elimination strategies amidst climatic exacerbations.\n\n\nData availability\n\nFigshare: Underlying data for ‘The relationship between climate change and malaria in South-East Asia: A systematic review of the evidence’. https://doi.org/10.6084/m9.figshare.20697298.v1.17\n\nFigshare: PRISMA checklist for ‘The relationship between climate change and malaria in South-East Asia: A systematic review of the evidence’. https://doi.org/10.6084/m9.figshare.20489235.v1.10\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nBeck HE, Zimmermann NE, McVicar TR, et al.: Present and future Köppen-Geiger climate classification maps at 1-km resolution. 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Publisher Full Text\n\nJubaidi MG: Studi Ekologi Hubungan Iklim dengan Kejadian Malaria di Kota Bengkulu Tahun 2011-2013. J. Media Kesehat. 2015; 8(1): 1–99.\n\nMau F, Tallan MM, Bullu AK: Fluktuasi iklim dan kejadian malaria sebelum eliminasi di Kabupaten Sumba Timur Provinsi Nusa Tenggara Timur. J. Health Epidemiol. Commun. Dis. 2020; 6(2): 42–48.\n\nNurmala EE: DINAMIKA PERUBAHAN UNSUR IKLIM (SUHU, KELEMBABAN DAN CURAH HUJAN) DAN KEJADIAN MALARIA PADA PENDUDUK PANDEGLANG. J. Dunia Kesmas. 2017; 6(2): 63–69.\n\nRejeki DSS, Nurhayati N, AJI B, et al.: A Time Series Analysis: Weather Factors, Human Migration and Malaria Cases in Endemic Area of Purworejo, Indonesia, 2005-2014. Iran. J. Public Health. 2018; 47(4): 499–509. PubMed Abstract\n\nRejeki DSS, Wijayanti SPM, Octaviana D, et al.: The effect of climate and intervention methods on malaria incidence: A time series analysis. Ann. Trop. Med. Public Health. 2019; 22(11): 123–129. 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PubMed Abstract \| Publisher Full Text\n\nServadio JL, Rosenthal SR, Carlson L, et al.: Climate patterns and mosquito-borne disease outbreaks in South and Southeast Asia. J. Infect. Public Health. 2018; 11(4): 566–571. PubMed Abstract \| Publisher Full Text\n\nBui HM, Clements ACA, Nguyen QT, et al.: Social and environmental determinants of malaria in space and time in Viet Nam. Int. J. Parasitol. 2011; 41(1): 109–116. PubMed Abstract \| Publisher Full Text\n\nMercado CEG, Lawpoolsri S, Sudathip P, et al.: Spatiotemporal epidemiology, environmental correlates, and demography of malaria in Tak Province, Thailand (2012–2015). Malar. J. 2019; 18(1): 240. PubMed Abstract \| Publisher Full Text\n\nNoppradit P, Pradit S, Muenhor D, et al.: Investigation of 37 years weather record and its relation to human health: A case study in Songkhla Province, Southern Thailand. Int. J. Agric. Technol. 2021; 17(4): 1507–1520.\n\nKotepui M, Kotepui KU: Impact of Weekly Climatic Variables on Weekly Malaria Incidence throughout Thailand: A Country-Based Six-Year Retrospective Study. Giuseppe La Torre, ed. J. Environ. Public Health. 2018; 2018: 8. PubMed Abstract \| Publisher Full Text\n\nSarah G, Ward AV, Moe AM, et al.: Factors associated with the decline of malaria in Myanmar’s Ayeyarwady Region between 2013 and 2017. Sci. Rep. Nat. Publ. Group. 2021; 11(1). Publisher Full Text\n\nJeefoo P, Tripathi NK, Souris M, et al.: Exploring geospatial factors contributing to malaria prevalence in kanchanaburi, Thailand. Int. J. Geoinform. 2009; 5(1): 21–26.\n\nWangdi K, Canavati SE, Ngo TD, et al.: Spatial and Temporal Patterns of Malaria in Phu Yen Province, Vietnam, from 2005 to 2016. Am. J. Trop. Med. Hyg. 2020; 103(4): 1540–1548. PubMed Abstract \| Publisher Full Text\n\nKaewpitoon N, Loyd RA, Kaewpitoon SJ, et al.: Malaria risk areas in Thailand border. J. Med. Assoc. Thail. 2015; 98 Suppl 4: S17–S21. PubMed Abstract \| Publisher Full Text\n\nKim YM, Park JW, Cheong HK: Estimated effect of climatic variables on the transmission of plasmodium vivax malaria in the republic of Korea. Environ. Health Perspect. 2012; 120(9): 1314–1319. PubMed Abstract \| Publisher Full Text\n\nKrefis AC, Schwarz NG, Krüger A, et al.: Modeling the Relationship between Precipitation and Malaria Incidence in Children from a Holoendemic Area in Ghana. Am. J. Trop. Med. Hyg. 2011; 84(2): 285–291. PubMed Abstract \| Publisher Full Text\n\nWu Y, Qiao Z, Wang N, et al.: Describing interaction effect between lagged rainfalls on malaria: an epidemiological study in south–west China. Malar. J. 2017; 16(1): 53. PubMed Abstract \| Publisher Full Text\n\nBai L, Morton LC, Liu Q: Climate change and mosquito-borne diseases in China: A review. Glob. Health. 2013; 9(1). PubMed Abstract \| Publisher Full Text\n\nHasyim H, Nursafingi A, Haque U, et al.: Spatial modelling of malaria cases associated with environmental factors in South Sumatra, Indonesia. Malar. J. 2018; 17(1): 87. PubMed Abstract \| Publisher Full Text\n\nLubinda J, Haque U, Bi Y, et al.: Near-term climate change impacts on sub-national malaria transmission. Sci. Rep. 2021; 11(1): 751. PubMed Abstract \| Publisher Full Text\n\nRahmani A, Susanna D, Febrian T: Systematic Review Flowchart. figshare.2022; 144057 Bytes. Publisher Full Text\n\nPhung D, Nguyen HX, Thi Nguyen HL, et al.: The effects of socioecological factors on variation of communicable diseases: A multiple-disease study at the national scale of Vietnam. PLoS One. 2018; 13(3): e0193246. PubMed Abstract \| Publisher Full Text" }	[ { "id": "179112", "date": "10 Jul 2023", "name": "Srinivasa Rao Mutheneni", "expertise": [ "Reviewer Expertise Epidemiology", "Climate Change and Public Health", "Vector-Borne Diseases", "Computational Biology", "and Data Analytics." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nRahmani AA and colleagues present an interesting narrative systematic review of the relationship between climatic factors and malaria cases in the South-East Asia region. In their review analysis authors suggest that changing temperatures, precipitation and humidity across a multi-year period are correlated with malaria cases in various regions throughout Southeast Asia. However, I have some minor concerns about the framing and interpretation of the result. I suggest that authors carefully consider this and include the suggestions in the revision.\nThe need for the present review or the rationale for conducting the review is not clearly explained.\n\nThough the inclusion and exclusion criteria are well defined, is the search strategy is comprehensive and transparent?\n\nIs there any assessment of the risk of bias in the included studies?\n\nIt would have been better if the authors have included the recent and up-to-date literature. All the papers cited in the review used only the statistical methods but there is recent literature which has used machine learning and deep learning models to assess the relationship between climatic factors and malaria cases.\n\nPlease mention Plasmodium in italic throughout the manuscript.\n\nIn the result section, the number of records written in English is misquoted as 425, please change it to 525.\n\nThe review considered the studies conducted only in 3 countries and does not provide a balanced view of the topic.\n\nThough numerous climatic variables influence malaria transmission, the study considered only temperature, precipitation, humidity and wind speed. The inclusion of the majority of the climate variables would provide a better insight into the situation.\n\nSince all the climatic parameters exhibited variation in terms of significance in different regions, the discussion can be improved by mentioning major contributing factors in the specific region.\n\nPlease mention the consequences of the findings in the conclusion section in the context of climate change and malaria?\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": "9931", "date": "29 Nov 2023", "name": "Dewi Susanna", "role": "Author Response", "response": "Dear Srivivasa Rao Mutheneni CSIR-Indian Institute of Chemical Technology, Hyderabad, India Thank you very much for your review reports for our article. Here are our responses in accordance with your comments: 1. The need for the present review or the rationale for conducting the review is not clearly explained. The specific rationale for the review to address a research gap and the basis for the particular attention to Southeast Asia as a grouping for have now been stressed further in the introduction section (Para. 5, Line 2). 2. Though the inclusion and exclusion criteria are well defined, is the search strategy is comprehensive and transparent? Our search strategy in detail, which includes the boolean search terms we’ve used where appropriate is made available to be replicated in Appendix 1 and presented without alterations. 3. Is there any assessment of the risk of bias in the included studies? Prescriptive bias mitigation has been conducted through the rotational review between the three authors of this study who each interpreted the outputs of the 19 reviewed studies. 4. It would have been better if the authors have included the recent and up-to-date literature. All the papers cited in the review used only the statistical methods but there is recent literature which has used machine learning and deep learning models to assess the relationship between climatic factors and malaria cases. Studies that do not fulfil our exclusion and inclusion criteria were omitted as they go beyond the scope of this study. Repeating the search strategies we’ve employed, we find an article by Liu et al. (2022) which warranted full-text assessment. Upon further reading however, the outcome of the study did not meet our systematic review of evidence scope as said study predicted malaria on set of Representative Concentration Pathway (RCP) scenarios instead of specific climatic variables. 5. Please mention Plasmodium in italic throughout the manuscript. We have addressed this review comment where appropriate across the paper and appreciate the reviewer for the thorough correction. 6. In the result section, the number of records written in English is misquoted as 425, please change it to 525. We have addressed this review comment where appropriate across the paper and appreciate the reviewer for the thorough correction. 7. The review considered the studies conducted only in 3 countries and does not provide a balanced view of the topic. Out of all the 19 studies included in this review, a total of 5 countries were covered. These countries are mentioned across Tables 1-4, they include: Indonesia (Jubaidi, 2015; Mau et al., 2020; Nurmala, 2017; Rejeki et al., 2018, 2019), Vietnam (Bui et al., 2011; Phung et al., 2018; Servadio et al., 2018; Wangdi et al., 2016), Thailand (Jeefoo et al., 2009; Kiang, 2021; Kotepui & Kotepui, 2018; Mercado et al., 2019; Ninphanomchai et al., 2014; Noppradit et al., 2021), Myanmar (Gallalee Sarah et al., 2021; Kaewpitoon et al., 2015; Servadio et al., 2018) Cambodia (Kaewpitoon et al., 2015; Servadio et al., 2018) The multiple studies that cover Indonesia, Vietnam, and Thailand also extend beyond a single region, but in various locations throughout said countries. Not all of the studies were inclusive of all the selected climatic variables which would warrant their absence in descriptive analysis of the studies within the discussion sections. That said, we recognize the indications of locations in describing the studies within the discussion section are not always present. We appreciate the feedback by the reviewer and have further indicated the countries of studies across all discussion sections where appropriate. For example, we’ve now highlighted Gallalee Sarah et al. (2021)’s study location in subsection Precipitation and Malaria (Para. 2, Line 2). 8. Though numerous climatic variables influence malaria transmission, the study considered only temperature, precipitation, humidity and wind speed. The inclusion of the majority of the climate variables would provide a better insight into the situation. Mentions of non-climate variables are stated where appropriate and if explanations are made by the reviewed studies. For example, studies that mention topographic factors are described in the subsection Temperature and Malaria (Para. 5, Line 2) 9. Since all the climatic parameters exhibited variation in terms of significance in different regions, the discussion can be improved by mentioning major contributing factors in the specific region. The inclusion of multiple location studies within country addresses the potential variations in malaria response towards climate. Mentions of region specific variables are indicated where appropriate within the summary Tables 1-4 but did not warrant extended elaboration within the discussion sections. 10. Please mention the consequences of the findings in the conclusion section in the context of climate change and malaria? Our emphasis on the results paid particular attention to the regression coefficients or correlation indices given by the reviewed studies. As this is a systematic review of evidence for the relationship between the climatic variables and malaria, said emphasis fits within the scope of this type of study. Our conclusion and the consequences we’ve explained remains concise and brief, leaving room for other research to further specific explorations. Thank you, Best regards." } ] }, { "id": "176897", "date": "10 Jul 2023", "name": "Eleanore Sternberg", "expertise": [ "Reviewer Expertise Vector-borne diseases" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI would simplify the writing and refocus the introduction on malaria. A brief history of the world’s climate is less relevant than covering some of the current literature on climate and malaria (and other vector-borne diseases). There is a substantial body of literature focused on climate change and malaria in Africa that would be relevant, plus modelling results on climate change and infectious disease.\n\n“This implies that as temperatures become warmer within the optimum range, the duration of incubation is shortened, and mosquitoes become infective much sooner” in the discussion is an important point. Once the temperature exceeds the optimal temperature (as it will undoubtedly in some places), that will slow or stop plasmodium development. This could potentially explain why increasing temperature is associated with more malaria in some instances and not in others.\n\nThe results and discussion focuses on significant associations between malaria and climate variables, but the key result would be change over time. Change over time is mentioned in the conclusion, but I don’t think it’s clear in the way that results are presented whether the papers that are discussed showed temporal change as well as associations between malaria and climate indicators.\n\nAlso related to change over time, studies that cover a long time period (e.g. reference 30 covers 1982 – 2018) are going to be more informative than studies that only cover a few years (e.g reference 18 that covers 2011-2013). The authors could consider highlighting the papers with long study periods in some way, for example by presenting them first or going into a bit more detail into their results.\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", "responses": [ { "c_id": "9930", "date": "29 Nov 2023", "name": "Dewi Susanna", "role": "Author Response", "response": "Dear Eleanore Sternberg Tropical Health, London, England, UK) Thank you very much for your valuable review reports for our article. Here are our responses in accordance with your comments: 1. I would simplify the writing and refocus the introduction on malaria. A brief history of the world’s climate is less relevant than covering some of the current literature on climate and malaria (and other vector-borne diseases). There is a substantial body of literature focused on climate change and malaria in Africa that would be relevant, plus modelling results on climate change and infectious disease. We appreciate the considerable input on simplification of the writing to ensure relevance as well as inclusion of modelling literatures out of Africa. We’ve opted to address this comment by adding a line on an existing study out of Africa in the introduction section (Para. 4, Line 4) as well as specifying why particular attention is made to Southeast Asia as a region ( Para. 5, Line 2.) Our reason on the climate focus is specifically because we find that there is a mismatch between understanding of “climate” as a concept across the body of literature in our review identification within the discipline of public health and environmental health. This is also the particular reason why out of the 39 records in full-text assessment (after stages of exclusions), only 19 ended up being included—as the use of climate terminology was most appropriate, i.e., long-term patterns as opposed to weather or seasons. We argue that the emphasis on conceptual introduction is a contribution to the otherwise specialised field. 2. “This implies that as temperatures become warmer within the optimum range, the duration of incubation is shortened, and mosquitoes become infective much sooner” in the discussion is an important point. Once the temperature exceeds the optimal temperature (as it will undoubtedly in some places), that will slow or stop plasmodium development. This could potentially explain why increasing temperature is associated with more malaria in some instances and not in others. We find no particular comment in this section of the review that needs addressing. 3. The results and discussion focuses on significant associations between malaria and climate variables, but the key result would be change over time. Change over time is mentioned in the conclusion, but I don’t think it’s clear in the way that results are presented whether the papers that are discussed showed temporal change as well as associations between malaria and climate indicators. Our emphasis on the results paid particular attention to the regression coefficients or correlation indices given by the reviewed studies. As this is a systematic review of evidence for the relationship between the climatic variables and malaria, said emphasis fits within the scope of this type of study. Moreover, the omission of temporal change discussion is reflective of the fact that key results from the reviewed studies come from a diverse array of methodologies and dataset types that would imply variations in how temporal change could be presented. We leave this room for other research to further specific explorations. 4. Also related to change over time, studies that cover a long time period (e.g. reference 30 covers 1982 – 2018) are going to be more informative than studies that only cover a few years (e.g reference 18 that covers 2011-2013). The authors could consider highlighting the papers with long study periods in some way, for example by presenting them first or going into a bit more detail into their results. Our systematic review of evidence is inclusive of multi-year period studies as identified in our inclusion and exclusion criteria. The basis for this explained by our understanding of climate and emphasis on tracing long-term variations, as opposed to short-term (which are more appropriately termed as weather). That said, our replicable search strategy and review process landed us with the final 19 studies in this paper. Although we would have appreciated more multi-year studies, especially decadal ones such as Noppradit et al. (2021), the only existing studies are as highlighted. Moreover, the only multi-decade study, Noppradit et al. (2021) covered a range of diseases, with malaria being on the side lines. Adding to the fact that their findings showed that malaria and climatic variables revealed no statistical significance, no further detailed explanations that has not otherwise been presented were relevant. Thank you. With warm regards." } ] }, { "id": "181886", "date": "14 Jul 2023", "name": "Imbahale S. Susan", "expertise": [ "Reviewer Expertise Medical entomologist interested in malaria vector ecology", "control and public health in general" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe relationship between climate change and malaria in South-East Asia: A systematic review of the evidence\n\nCongratulations to the authors for taking time to compile existing evidence on climate variability and malaria transmission in South East Asia (SEA) region. The authors need to consider providing enough background information to inform the reader on how similar or different the countries are in relation to climatic variables and malaria i.e. trends over time, so that its clear to the reader that all countries are similar. The changes in weather conditions do not operate in isolation, therefore this being a review, I suggest you consider including all other variables that might have contributed to the changes in malaria transmission in the region, so that you provide an overall picture of what exactly is going on.\nHere are some comments and questions for your consideration.\n\nThe authors need to define what the term “climate” really refers to in their study.\nI would suggest the term “climate variability” rather than climate change in the title. I realize it’s the variations in the climatic variables that is leading to the changes in malaria transmission.\n\nSEA region comprises of 10 countries, but the review focuses on 19 studies that only cover 3 countries on the SEA region. My concern is are the 3 countries a good representation of the whole region? If yes, where is the evidence suggesting that indeed the 3 represents the whole region with respect to the subject matter i.e. climate?\n\nIn view of the same concerns raised above. Malaria transmission and mosquito vectors are highly dependent on the local conditions, which in turn lead to modifications of the local weather conditions that ultimately translate to variations in climatic variables,\na) There is no mention on the specific vectors responsible for malaria transmission in the 10 countries\nb) What are their climatic requirements in in terms of malaria transmission?\nc) Are the conditions for malaria transmission similar in all the 10 countries?\nd) Even within the same country, transmission is never uniform e.g. northern part of Indonesia might be different from southern part with respect to malaria. Local conditions, human activities are the other main drivers. This information is missing, and yet its what makes malaria transmission completely heterogenous.\n\nThe reader needs to be informed of any assumptions that the authors might have put into consideration.\n\nThe concerns raised should also inform you on the recommendations for future studies that are looking at climate variability and its effects on vector borne disease transmission.\n\nConsider revisiting the conclusion of the study and state clearly, how helpful climate data would benefit the environment and health ministries? And what are the specific recommendations to the SEA countries in terms of climate adaptation and malaria elimination?\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", "responses": [ { "c_id": "9929", "date": "29 Nov 2023", "name": "Dewi Susanna", "role": "Author Response", "response": "Dear Imbahale S. Susan Technical University of Kenya, Nairobi, Nairobi County, Kenya. Thank you very much for your valuable review reports to make our article more understandable for the readers. Here are our responses in accordance with your comments: 1. The authors need to define what the term “climate” really refers to in their study. I would suggest the term “climate variability” rather than climate change in the title. I realize it’s the variations in the climatic variables that is leading to the changes in malaria transmission. The definition of climate that this paper adheres to have been stated in the introduction section (Para. 1, Line 2). The use of climate change is warranted to contrast with weather (short and local event) as well as seasonal (medium and monthly event). In a paper by Malpeli et al. (2020), variability and change are used concurrently, denoting no stark difference. Similarly, in other systematic review studies referred in this paper, such as Babaie et al. (2018) and Fischer et al. (2020), researchers opted to use the term climate change to trace the long-term multi-year phenomenon. 2. SEA region comprises of 10 countries, but the review focuses on 19 studies that only cover 3 countries on the SEA region. My concern is are the 3 countries a good representation of the whole region? If yes, where is the evidence suggesting that indeed the 3 represents the whole region with respect to the subject matter i.e. climate? Out of all the 19 studies included in this review, a total of 5 countries were covered. These countries are mentioned across Tables 1-4, they include: Indonesia (Jubaidi, 2015; Mau et al., 2020; Nurmala, 2017; Rejeki et al., 2018, 2019), Vietnam (Bui et al., 2011; Phung et al., 2018; Servadio et al., 2018; Wangdi et al., 2016), Thailand (Jeefoo et al., 2009; Kiang, 2021; Kotepui & Kotepui, 2018; Mercado et al., 2019; Ninphanomchai et al., 2014; Noppradit et al., 2021), Myanmar (Gallalee Sarah et al., 2021; Kaewpitoon et al., 2015; Servadio et al., 2018) Cambodia (Kaewpitoon et al., 2015; Servadio et al., 2018) The multiple studies that cover Indonesia, Vietnam, and Thailand also extend beyond a single region, but in various locations throughout said countries. Not all of the studies were inclusive of all the selected climatic variables which would warrant their absence in descriptive analysis of the studies within the discussion sections. That said, we recognize the indications of locations in describing the studies within the discussion section are not always present. We appreciate the feedback by the reviewer and have further indicated the countries of studies across all discussion sections where appropriate. For example, we’ve now highlighted Gallalee Sarah et al. (2021)’s study location in subsection Precipitation and Malaria (Para. 2, Line 2). 3. In view of the same concerns raised above. Malaria transmission and mosquito vectors are highly dependent on the local conditions, which in turn lead to modifications of the local weather conditions that ultimately translate to variations in climatic variables:. a. There is no mention on the specific vectors responsible for malaria transmission in the 10 countries: The vector identification is only stated in the study by Bui et al. (2011) and Wangdi et al. (2016) and have been indicated appropriately within Tables 1-4. Otherwise, the absence of them being specified in the other reviewed studies did not warrant further mention. b. What are their climatic requirements in in terms of malaria transmission? These are described specific to the studies that mention them. An example of this is in the subsection Temperature and Malaria (Para. 1, Line 3) which indicate the range of temperature requirements for malaria cycle thereby leading to infectivity as well as subsection Humidity and Malaria (Para. 2, Line 5) which indicate the minimum required humidity levels for mosquito activity. c. Are the conditions for malaria transmission similar in all the 10 countries? Though specific conditions are not mentioned, the underlying reasoning for the particular attention to Southeast Asia as a grouping for this review have now been stressed further in the introduction section (Para. 5, Line 2). d. Even within the same country, transmission is never uniform e.g. northern part of Indonesia might be different from southern part with respect to malaria. Local conditions, human activities are the other main drivers. This information is missing, and yet its what makes malaria transmission completely heterogenous. The inclusion of multiple location studies within country addresses the potential variations in malaria response towards climate. Mentions of non-climate variables are also stated where appropriate and if explanations are made by the reviewed studies. For example, studies that mention topographic factors are described in the subsection Temperature and Malaria (Para. 5, Line 2) 4. The reader needs to be informed of any assumptions that the authors might have put into consideration. Our assumptions for the review is reflected in the methods subsection in detail. Therefore, specific assumptions could be found in our search strategy choices as well as defined exclusion and inclusion criteria. 5. The concerns raised should also inform you on the recommendations for future studies that are looking at climate variability and its effects on vector borne disease transmission. Our recommendations for future research, formed on the results of the current available studies and the existing research gap thereof, are stated in the conclusion section (Para. 2, Line 2)—where we argue that future research take into consideration spatial and other non-climatic confounders. 6. Consider revisiting the conclusion of the study and state clearly, how helpful climate data would benefit the environment and health ministries? And what are the specific recommendations to the SEA countries in terms of climate adaptation and malaria elimination? Specific recommendations were omitted from this research as they go beyond the scope of this systematic review of evidence. Overall specific recommendations were not indicated in the reviewed studies either, and the inconclusive evidence in select countries could warrant different policy responses catered to each locations where appropriate. Our conclusion and the recommendation it includes remains concise and brief, leaving room for other research to further specific explorations. Thank you Best regards." } ] } ]	1	https://f1000research.com/articles/11-1555
https://f1000research.com/articles/10-45/v1	23 Jan 21	{ "type": "Research Article", "title": "Attitudes and habits regarding brain training applications and games among Japanese consumers: a cross-sectional study", "authors": [ "Nigel Robb" ], "abstract": "Background: While there is now a large amount of research investigating whether brain training applications and games are effective or not, there is less research on the expectations, attitudes, and habits of potential users of brain training programs. Previous research suggests that people generally have positive beliefs about the effectiveness of brain training which are not dependent on their level of experience of brain training. However, this research has primarily focused on western participants. Methods: In the present study, a questionnaire was used to investigate the attitudes and habits of Japanese consumers towards brain training. The final sample contained responses from 818 people. In addition to descriptive statistics, correlation coefficients were calculated to determine if there were relationships between variables relating to participants' beliefs about brain training and experience of using brain training. Results: Participants had positive beliefs about the effectiveness of brain training. However, these beliefs were only weakly correlated with their level of experience of using brain training, both in terms of the number programs used (Pearson's r = 0.163) and duration of use (Pearson's r = 0.237). The most widely used brain training program (used by 52.93% of participants) was made by Nintendo for the handheld Nintendo DS games console. Conclusions: The research presented here supports previous findings which suggest that people's beliefs about the effectiveness of brain training software are not strongly related to their experience of using such software.", "keywords": [ "brain training", "cognitive training", "cognitive enhancement" ], "content": "Introduction\n\nRecently, there has been much interest in so-called “brain training” (BT) applications and games (the terms “brain training” and “cognitive training” are treated as synonyms in this paper). These programs are typically marketed to consumers as enjoyable, interactive experiences that, if used regularly, are claimed to improve a range of cognitive skills, such as attention, memory, and multitasking ability (Simons et al., 2016). The potential benefits of such training, if effective, are numerous. For example, training executive function skills such as working memory and task switching could potentially lead to improved outcomes in education, quality of life, and employment for the general population (Diamond, 2013). In addition, people with cognitive deficits, such as those with intellectual disabilities or age-related cognitive decline, could also benefit from effective cognitive training software (Robb et al., 2018; Buitenweg et al., 2012).\n\nResearch on the effectiveness of various types of cognitive training has found evidence that it can lead to improvements in tasks that bear some resemblance to the training (“near transfer”), but little or no evidence that these improvements transfer to distantly related tasks (“far transfer”) or indeed to everyday life (Simons et al., 2016; Sala et al., 2019; Aksayli et al., 2019). These findings suggest that theories of transfer that emphasize the importance of overlap between the training and the target skills (e.g., Gobet, 2016; Taatgen, 2013; Oei and Patterson, 2014) may provide the best account of the mechanisms by which cognitive training is effective. Therefore, a detailed theoretical understanding of the overlap between the training and the desired outcome may be an important factor in the design of effective, tailored cognitive training programs in the future (see Smid et al., 2020, for this and other recommendations).\n\nAs part of a more comprehensive science of cognitive training, it is also important to investigate the attitudes and habits of the people who will potentially use the training. Individual differences in personality, motivation, expectations etc., are likely to play a role in determining a user’s engagement with a training program (Smid et al., 2020). Regular engagement is obviously an important factor in any kind of training; however, attrition is a commonly reported problem in trials of cognitive training software (Corbett et al., 2015; Robb et al., 2019), and at least one commercial BT program (Cogmed) assigns users a coach to ensure that they regularly engage with the software. Understanding how and why people use cognitive training programs may therefore be an important additional factor in determining their effectiveness.\n\nPrevious research has found that participants typically have positive beliefs about the effectiveness of BT. Torous et al. (2016) found positive beliefs about the effectiveness of BT mobile applications in young American consumers, both in participants who had used BT programs and those who had not. Other research found similar results in parents of children with intellectual disabilities (who may benefit from cognitive training): parents believed that BT could benefit their children and expressed positive attitudes towards supporting such training. Again, these attitudes were not related to how much experience the parents had with BT apps or games (Robb et al., 2018). It has also been shown that people’s expectations about the effectiveness of BT can be influenced by the information they receive about such programs. Rabipour & Davidson (2015) and Rabipour et al. (2018) found that participants’ expectations about the effectiveness of BT at baseline could be subsequently raised or lowered by presenting them with positive or negative messages about BT. Finally, Ng et al. (2020) found that frequency of engagement was only weakly correlated with perceived cognitive benefit for a range of activities, including BT. However, while this research reveals important information about the attitudes, habits, and expectations of a range of potential consumers of BT, it is primarily focused on Western users. It is widely recognized that much research involving human subjects may be biased towards certain demographics (Henrich et al., 2010). In the case of understanding attitudes and habits regarding BT, the largest previous study was conducted in the United States (Torous et al., 2016). To fully understand the attitudes of BT users, it is vital that a global perspective is considered.\n\nJapan represents a large group of potential consumers of cognitive training who may have different habits or attitudes than, for example, those in the US. Japan also has a developed BT market, with popular BT games having been released in the country for several years (Fuyuno, 2007; Chancellor & Chatterjee, 2011). Therefore, the main purpose of this paper is to understand the habits and attitudes of Japanese people regarding cognitive training, thus expanding our knowledge of how and why such programs are used around the world.\n\n\nMethods\n\nTo facilitate a direct comparison between Japanese consumers and their American counterparts, this cross-sectional study used a Japanese translation of the questionnaire used by Torous et al. (2016) with minor adaptations. Before translation, the original questionnaire was adapted in two ways. Firstly, while Torous et al.’s (2016) questionnaire specifically focused on using smartphone apps, the present study also included questions (and adapted the wording of questions) to refer to games consoles. This was because it was expected that Japanese-produced BT programs would be popular among Japanese people, and some such software is only available on games consoles. Secondly, when asking participants which cognitive training programs they had used, the list of options was updated to reflect apps and games available in Japan.\n\nThis questionnaire was then translated into Japanese by two professional translators, who both independently produced separate translations. Professional translators were contracted through Gengo, a web-based human translation platform. A native Japanese speaker familiar with the research project merged these translations; differences in the two translations were resolved through discussion between this person and the author of the paper. This resulted in a final Japanese version of the questionnaire. Before being used, this version was translated back into English by a third professional translator, and this version was compared with Torous et al.’s (2016) original questionnaire. There were some minor differences in the wording of the original questionnaire and the back-translation. For example, “duration” (original) became “period of time” (back-translation); the phrase “For the purpose of this survey, we will call these ‘brain training apps/games’” (original) became “In this survey, we will refer to these as ‘brain training apps/games’” (back-translation); and the question “Do you own a smartphone?” (original) became “Do you have a smartphone?” (back-translation). It was judged that none of these minor differences would affect the meaning of any of the questions. The questionnaire can be viewed in full in both English and Japanese as extended data on the Open Science Framework (Robb, 2021).\n\nParticipants were recruited using CrowdWorks, a Japanese crowdsourcing website. All registered CrowdWorks users were deemed eligible to participate; there were no additional inclusion or exclusion criteria. Crowdsourcing websites have been shown to be viable methods for recruiting participants for questionnaire research (Behrend et al., 2011; Peer et al., 2017). Previously, Majima et al., (2017) compared participants recruited via CrowdWorks with Japanese student samples and found that there were relatively small differences in some personality traits, and that the CrowdWorks participants were (as would be expected) more diverse in terms of age and employment history. The translated questionnaire was uploaded to CrowdWorks and responses collected during December 2017. At the start of the questionnaire, the purpose of the research was explained, and participants were informed that they were not obliged to take part, that their responses would be used for research purposes, and that by continuing with the questionnaire they would indicating their consent to participate. No identifying information about the participants was collected. All participants were paid 30 JPY (approximately 0.27 USD in December 2017) to complete the questionnaire, whether their response was used in the final analyses or not. The research was conducted according to the recommendations of the Human Research Ethics Committee (Sciences) at University College Dublin, where the lead author of the paper was employed at the time of the research. The protocol was deemed to be exempt from full ethical review as the data were collected anonymously, the participants were not from a vulnerable group, and they were not placed at any risk during the research.\n\nAssuming that the number of people aged 16 and over in Japan is approximately 110,000,000 (Statistics Bureau of Japan, n.d.), and that 50% have used BT (based on results from Torous et al., 2016), with a margin of error of 5% and a confidence level of 99%, the ideal sample size was calculated to be 664. Given that previous research has highlighted concerns with unreliable responses and high attrition rates in crowdsourced samples (Keith et al., 2017), 1000 responses were collected.\n\nAfter collection, the data were inspected, and potentially unreliable responses were removed. Unreliable responses included those with inconsistent answers to similar questions, or the wrong answer to the simple sum of nine plus four (included to check that participants were diligently reading and responding to the questions). There were no missing data in the final dataset used for analysis.\n\nDescriptive statistics were used to investigate smartphone and games console ownership of participants; usage of health and fitness apps; concerns about BT; BT apps/games used by participants; and participants' beliefs about the effectiveness of BT. Spearman's correlation coefficients were calculated to determine if there were associations between participants' beliefs about whether BT could lead to cognitive/emotional improvements (specifically in thinking ability, attention, memory, and mood), whether they had used BT, and if they thought BT apps/games had negative side effects. Following Torous et al. (2016) a score was calculated for each participant measuring how positively they felt about BT. The difference in this score between participants who had used BT and those who had not was investigated using a Mann-Whitney U-test. Finally, Pearson correlation coefficients were calculated between this score, the number of BT apps/games participants had used, and the longest period of time participants had used BT. These analyses were performed using JASP version 0.11.1.\n\n\nResults\n\nA total of 1000 responses were received. Of these, one response was excluded as the age in years was entered as 336, while six responses were removed as they provided an incorrect answer to the sum of nine and four. A further 175 participants’ responses were removed as they gave inconsistent answers about their history of using BT apps or games. There were four kinds of inconsistency. Firstly, 13 participants answered “yes” to item 8 (“Have you ever used an app or game that claims to increase memory, concentration, attentiveness, or other cognitive abilities? In this survey, we will refer to these as ‘brain training apps/games.’”) but answered “I have never used one” to item 16 (“What is the longest period of time you have used a brain training app/game? If you have never used one, please select ‘I have never used one.’”). Secondly, 11 participants answered “yes” to item 8 but did not enter any brain training apps or games that they had used when asked to do so in item 15. Thirdly, 111 participants answered “no” to item 8, but indicated they had used BT apps or games in item 16 (i.e., they entered a period of time they had used apps or games). Fourthly, 152 participants answered “no” to item 8, but entered apps or games they had used when asked to do so in item 15. Note that some participants' responses were inconsistent in more than one of these ways. With these responses removed, the final sample used for analyses contained responses from 818 participants (524 female, 294 male; mean age 36.1 years; standard deviation 9.5 years). The underlying data can be accessed on the Open Science Framework (Robb, 2021).\n\nFigure 1 shows the devices and kind of apps owned by participants, divided into four age categories. In all age groups, over 70% of participants owned a smartphone, with the highest rate of smartphone ownership (94.12%) in participants aged 30 years and under. Games console ownership was approximately 40% in the 0-30 years and 31-45 years categories. Almost 45% of participants over 60 years owned a games console, although there were only nine participants in this age group.\n\nThe most common concerns participants had about BT apps and games were the cost of the product, the time required to use them, and a lack of certainty regarding their effectiveness. Participants were not generally concerned about the safety of their health data or whether the apps or games have medical recommendation (Figure 2).\n\nThe most-used training programs were produced by Nintendo and released on the Nintendo DS handheld games console. Over half the participants reported having used 脳を鍛える大人のＤＳトレーニング (released in the US as Brain Age: Train Your Brain in Minutes a Day! and in Europe as Dr. Kawashima’s Brain Training: How Old Is Your Brain?) and just under a quarter of participants reported using the follow-up game (もっと脳を鍛える大人のＤＳトレーニング; US: Brain Age 2: More Training in Minutes a Day! Europe: More Brain Training from Dr. Kawashima: How Old Is Your Brain?). Of the remaining programs, all but one were used by fewer than 10% of participants. Only 19 participants (2.32%) reported having used Lumosity (Figure 3).\n\nParticipants indicated positive perceptions of BT apps and games, believing that they could improve thinking ability (79.58%), attention (66.26%), memory (78.61%), and mood (73.35%). Spearman’s correlation coefficients were calculated for all combinations of the binary variables (i.e., yes/no questions) regarding participants’ views about whether BT could improve thinking ability, attention, memory, and mood, as well as the binary variables regarding whether they had used BT, and if they thought BT had negative side effects. There were weak to moderate positive correlations between (1) thinking ability and attention (Spearman’s rho = 0.376, p < 0.001), (2) thinking ability and memory (Spearman’s rho = 0.453, p < 0.001), and (3) attention and memory (Spearman’s rho = 0.378, p < 0.001) (Table 1).\n\nSignificant at p = 0.01 level marked with .\n\nFollowing Torous et al. (2016), a score was calculated for each participant measuring how positively they felt about BT. Participants were given one point for each positive answer to the four questions about whether they thought BT improved thinking ability, attention, memory, and mood, and one point for a negative answer to the question about whether they thought BT apps and games have negative side effects. The maximum score of five indicated a participant thought BT improved all four factors and had no side effects, while the minimum score of zero indicated a participant thought BT did not improve any of the four factors and had negative side effects. This score was significantly higher among respondents who indicated that they had used BT apps or games (Mann-Whitney U test, U = 37757, p < 0.001); the rank biserial correlation was -0.213, indicating a weak effect size. This score was weakly positively correlated (Pearson correlation) with both the total number of apps/games a participant had used (Pearson’s r = 0.163, p < 0.001) and the duration they had used BT apps/games (Pearson’s r = 0.237, p < 0.001) (Table 2).\n\nSignificant at p = 0.01 level marked with .\n\n\nDiscussion\n\nThe results of the present study suggest that a high rate of Japanese consumers have positive perceptions of the potential benefits of BT apps and games, comparable to or (in the case of positive effects on mood) higher than the rate in US consumers (Torous et al., 2016). While there were correlations between positive perceptions about the effects of BT on specific cognitive factors (thinking ability and attention, thinking ability and memory, and attention and memory), these were weaker than those found in US consumers (Torous et al., 2016). Similarly to Torous et al.’s (2016) findings in US consumers, the present study indicates that Japanese consumers are not generally concerned about clinical recommendations, privacy of health data, or negative side effects, when considering BT games. Rather, the cost of apps/games, the time involved, and uncertainty about their effectiveness are the main barriers to BT use in Japan. These results suggest that Japanese consumers and US consumers have broadly similar attitudes and expectations regarding BT apps and games. Previously, it was shown that there were only minor demographic differences (in terms of gender and level of education) in beliefs about benefits of BT (Ng et al., 2020). The present study suggests that, at least in terms of attitudes to BT, variation between people from different socio-cultural backgrounds may also be minor.\n\nThe present research revealed large differences in the kinds of BT used by Japanese and US consumers. Perhaps most strikingly, Lumosity, which was used by 70% of US consumers in the previous study by Torous et al. (2016) was only used by 2.3% of the Japanese participants. The most popular BT programs were both made by Nintendo and played on the Nintendo DS handheld games console. While the large difference in number of participants using Lumosity may be partly explained by the fact that the app was only released in Japanese in December 2014, these results could also indicate that there are major differences in BT markets in the US and Japan, which would be an important finding. However, since the previous study (Torous et al., 2016) only focused on smartphone apps, it does not provide any information about how widely used Nintendo BT games are in US consumers. Nintendo BT games are popular globally, however: Brain Age: Train Your Brain in Minutes a Day! (the most used game among Japanese participants in the present study) was among the 10 best-selling video games of 2006 in the US. It is therefore likely that many of the participants in Torous et al.’s (2016) study also had experience of using this BT game.\n\nThe results presented here also support previous findings that people’s perceptions of the positive effects of BT are not strongly related to their experience of using BT. Torous et al. (2016) found that US consumers’ positive beliefs about BT were only weakly correlated with the number of BT apps they had used. Similarly, Rabipour et al. (2018) found that people with experience of BT had similar expectations about its effectiveness to people with no experience. In other research, Robb et al. (2018) found that parents of children with intellectual disabilities had positive beliefs and attitudes regarding BT and had high intentions to support the use of BT by their children, despite the fact that the sample had very little experience with BT programs. Taken together, these results present mounting evidence that experience of using BT is not strongly associated with positive beliefs about the effectiveness of BT. The fact that participants in both the present and previous studies (Rabipour & Davidson, 2015; Torous et al., 2016, Rabipour et al., 2018, Robb et al., 2018) have very positive beliefs about the effectiveness of brain training (whether or not they have actual experience of using BT), combined with the lack of evidence that BT is actually effective (Simons et al., 2016; Sala et al., 2019; Aksayli et al., 2019), illustrates the importance of investigating the role of psychological factors such as motivation, effects of being observed during training and testing, and placebo effects in BT research. It has been shown that users' perceptions about BT can be relatively easily influenced by biased messages regarding their effectiveness (Rabipour and Davidson, 2015; Rabipour et al., 2018), and placebo effects have been found in previous BT research (Boot et al., 2013; Foroughi et al., 2016). Future trials of BT programs would benefit from accounting for such potential confounding factors.\n\n\nLimitations\n\nTo facilitate a direct comparison between Japanese and American users of BT, this study used a direct translation of the questionnaire developed by Torous et al. (2016). In this questionnaire, the items referring to participants’ positive and negative beliefs about BT (e.g., “Do you think brain training apps and games can improve memory?”) were phrased as questions requiring yes/no answers. However, in retrospect, it may have been more informative to adapt the questionnaire to have Likert-style responses. This would still have allowed some comparison with previous research but could have also facilitated more nuanced analysis of the results.\n\nWhile the use of crowdsourcing platforms such as CrowdWorks to recruit participants is becoming more common in recent research, there remain some potential limitations associated with this approach. Firstly, it is recognized that crowdsourced participants may not always be representative of the population of interest (Stewart et al., 2017). In the present study, this issue is most obvious when considering the ages of the participants: in 2015, 26.6% of the Japanese population were over 65 (Statistics Bureau of Japan, n.d.), whereas in the sample analyzed here, only 9 of 818 participants were over 60. Given that BT is often considered as a potential intervention for people with age-related cognitive decline (Buitenweg et al., 2012), the habits and attitudes of this demographic are clearly important. Secondly, it may be suggested that data collected from crowdsourcing platforms is of low quality (e.g., due to participants answering questions without fully reading or considering them). However, previous research has found data collected via the crowdsourcing platform Amazon Mechanical Turk is of comparable quality to other methods (Kees et al., 2017). In the present study, several indicators were used to identify potentially automated or low effort responses (see section Participants and Procedure). A total of 182 responses (18.2%) were removed before analysis, which is comparable to the rate of 14% automated and low effort responses found in a study of Amazon Mechanical Turk workers by Buchanan & Scofield (2018).\n\n\nFuture work\n\nDue to the low number of participants over 60 years old, the present study cannot provide any reliable information on the attitudes and habits regarding BT in the elderly population in Japan. Future research investigating this topic would be important. Future research could also benefit from using Likert-style items, as discussed in the section Limitations. Further research will also be required to understand more completely the factors that influence people’s attitudes towards BT, and the role of psychological confounders such as placebo effects in BT research. Finally, one important finding of the present study is the popularity of BT games produced by Nintendo, emphasizing the importance of games consoles in the BT market, at least in Japan. Since the previous major study of BT habits in western users only focused on smartphone applications (Torous et al., 2016), future research should investigate if BT programs on games consoles, such those produced by Nintendo, are as widely used in countries other than Japan.\n\n\nConclusion\n\nThe present study contributes to a growing literature investigating the expectations, attitudes, and habits of potential users of brain training applications and games. There are two main findings. Firstly, similarly to previous research conducted in the US, Japanese consumers have positive beliefs about brain training which do not seem to be strongly associated with the amount of experience they have using such programs. Secondly, the most widely used brain training software among Japanese participants are two games made by Nintendo and played on the handheld Nintendo DS console.\n\n\nData availability\n\nOpen Science Framework: Attitudes and habits regarding brain training games and apps in Japan, https://doi.org/10.17605/OSF.IO/CW5AG (Robb, 2021)\n\nThis project contains the following underlying data:\n\n- raw-data-retrieved-4-24-2020.csv (File exported from CrowdWorks)\n\n- raw-data-jp (Spreadsheet of questionnaire responses in Japanese)\n\n- raw-data-en (Spreadsheet of questionnaire responses in English)\n\nOpen Science Framework: Attitudes and habits regarding brain training games and apps in Japan, https://doi.org/10.17605/OSF.IO/CW5AG (Robb, 2021)\n\nThis project contains the following extended data:\n\n- questionnaire-v3-final_jp.pdf (Questionnaire in Japanese)\n\n- questionnaire-v3_en-back-translation.docx (Questionnaire back-translated to English)\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\nCompeting interests\n\nNo competing interests were disclosed.", "appendix": "Grant information\n\nThis work was supported by (1) KAKEN grant no. 18H05804 from the Japan Society for the Promotion of Science and (2) funding from the charity RESPECT and the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013; REA grant agreement no. PCOFUND-GA-2013-608728), both to Nigel Robb.\n\n\nAcknowledgements\n\nTomonori Hasegawa assisted with the translation of the questionnaire into Japanese.\n\n\nReferences\n\nAksayli ND, Sala G, Gobet F: The cognitive and academic benefits of Cogmed: A meta-analysis. Edu Res Rev 2019; 27: 229–243. Publisher Full Text\n\nBehrend TS, Sharek DJ, Meade AW, et al.: The viability of crowdsourcing for survey research. Behav Res Methods 2011; 43(3): 800. PubMed Abstract \| Publisher Full Text\n\nBoot WR, Simons DJ, Stothart C, et al.: The pervasive problem with placebos in psychology: Why active control groups are not sufficient to rule out placebo effects. Perspect Psychol Sci 2013; 8(4): 445–454. PubMed Abstract \| Publisher Full Text\n\nBuchanan EM, Scofield JE: Methods to detect low quality data and its implication for psychological research. Behav Res Methods 2018; 50(6): 2586–2596. 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "77997", "date": "05 Feb 2021", "name": "Yuka Kotozaki", "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\nYou are using the Japanese translation of the questionnaire used by Torous et al. (2016). Before conducting this survey, did you verify that the results obtained from the Japanese translated version of the questionnaire are equivalent to the original questionnaire?\n\nIn the case of a manuscript, even if the product name is in Japanese, I think it would be better to describe it in English (or in romaji, etc.).\n\nAs for the correlation, if it is around 0.2, it is almost uncorrelated rather than weakly correlated, isn't it? Generally speaking, 0 to less than 0.3: almost no correlation, 0.3 to less than 0.5: very weak correlation, 0.5 to less than 0.7: correlation, 0.7 to less than 0.9: strong correlation, and 0.9 or more: very strong correlation.\n\nShould the impact of gender differences not be considered? If the difference between men and women was not examined because there was no significant difference, I think an explanation to that effect and presentation of the results would be necessary.\nI think it is an interesting study, but I think it needs to be carefully examined again for more detailed results and correlations.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "7144", "date": "25 Oct 2021", "name": "Nigel Robb", "role": "Author Response", "response": "Thank you very much for taking the time to review the article, and I apologize for taking so long to respond to your comments. I've updated the manuscript now to address your concerns as follows: Apart from the rigorous translation/back-translation process, there were no further checks to verify that the results obtained are equivalent to the original English questionnaire. Given that (1) the questionnaire does not really have multiple items measuring the same construct and (2) it is possible that there are differences between Japanese and American respondents, it may not be feasible to do this kind of verification. I have added some text to the limitations to make this clear. I've changed all the product names to either romaji or English. I have altered the interpretation of the correlation coefficients slightly and added citations to justify the interpretations used here. I agree that several of the correlations found here are negligible, so I have used this word to clarify that. I do think that it is reasonable in this context to interpret a correlation of >0.4 as weak to moderate (Akoglu, 2018). I analysed the impact of gender differences and added these results into the manuscript. Thank you again for your helpful comments, I really appreciate the feedback. References Akoglu H. User's guide to correlation coefficients. Turkish journal of emergency medicine. 2018 Sep 1;18(3):91-3." } ] }, { "id": "77995", "date": "15 Feb 2021", "name": "Kelsey Prena", "expertise": [ "Reviewer Expertise Communication neuroscience", "video games", "learning", "memory" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article summarizes 818 participants’ opinions about brain training games, arguing a Japanese sample makes the paper unique. I compliment the comprehensive review of current research in the beginning of the paper and detailed but clear and concise results section. My comments are listed below.\nMajor comments:\nThe author gives no theoretical support for why they chose Japan (though it does look like grant money may have been involved). A sound theoretical foundation would have provided a framework for anticipating differences across cultures (as the author tries to make claims about in the discussion section). Lack of this foundation, and lack of hypotheses in consideration of this framework, indicates that this study is going to primarily summarize the market rather than make greater contributions to the discipline’s landscape. Furthermore, without this theoretical support, the paper’s method, results, and discussion become more of a free-for-all for the author to pick and choose. Other concerns related to this major comment include:\n- Why did the author select the particular age groups listed in Figure 1? They seem extraordinarily broad and hide important detail from the reader.\n\nThe author indicates that it can be concluded that Japanese consumers aren’t concerned about clinical recommendations, privacy of health, or negative side effects when considering brain training games. I do not think they can draw this conclusion based on the method. This was not analyzed in the results section, or discussed in the method section, and the conclusion feels very random. I have reviewed the survey items, and do not believe this can actually be concluded based on the questions provided. Lack of answer does not equate to lack of concern. Similar arguments can be made for other conclusions listed here:\n- The author includes the following comment in the conclusion: \"the present study suggests that, at least in terms of attitudes to BT, variation between people from different socio-cultural backgrounds may also be minor.\" This cannot be concluded by the current method. There were no questions asked or analyzed to draw this conclusion.\n-The author indicates major differences between the Western and Japanese BT markets as a core conclusion to the article. However, they later consider in the discussion that these differences might be because of differences in software availability. I’m not sure that this conclusion really contributes to the paper, and I don’t believe it can be concluded accurately without further research.\n\nThe author uses single-item variables for all measures, most of them with answer options of simply “yes” or “no.” I know this is in replication of a heavily cited other study (Torous et al., 20161), but there are many problems with this methodology and question the integrity of the validity of the measure. The author, appropriately, includes this as a limitation but it’s a major one. I have a hard time trusting that these questions get at the true answers, and yields this study’s conclusions as preliminary rather than substantial.\nMinor comments:\nIs brain training actually synonymous with cognitive training? In some cases it can be, but the author makes this claim and then presents a slightly different definition of brain training in the third paragraph.\n\nIt’s my understanding that Spearman’s Rho should only be used with rank-order variables, and we have dichotomous variables here, not rank-order variables.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "7145", "date": "25 Oct 2021", "name": "Nigel Robb", "role": "Author Response", "response": "Thank you for your review. My apologies for the delay in my response. I've updated the manuscript now to address your comments. I've made the following changes: Major comments 1. I've added more detail to the introduction about the justification for using a Japanese sample. Specifically, I have shown that there is evidence from previous research that, when it comes to mobile app use behaviors and attitudes, it is reasonable to anticipate differences between users from Japan and from the US. So, since the previous study focused on American users and Japan is a highly-developed brain training market, I think it is justified to study Japanese consumers. To clarify, the funding from the Japanese funder (Kaken grant) was awarded after the data collection in the present study was completed, so grant money in no way influenced the decision to choose Japan. I have changed the age groups in Figure 1, now using seven categories. 2. I've reworded the interpretation of the results to soften my claims about Japanese consumers' concerns regarding BT. I have reworded the interpretation of the results regarding socio-cultural differences and changed the language to emphasize that this is a preliminary study with limited findings I have removed the claim that there are major differences between the Japanese and US BT markets and instead just pointed out the differences between this and the previous study in this respsect. 3. I agree this is the major limitation of the study, and I've made that more explicit in the limitations section. I have also changed the language throughout the paper to emphasize that these results are preliminary and that hypothesis-testing in future research would be required. Minor comments 1. I removed the point about BT being synonymous with cognitive training. 2. In this case, Spearman's Rho, Pearson's r, and the phi-coefficient are all equivalent. However, I agree that it would be better to report the statistic in a way that is more recognized as appropriate for binary variables, so I have changed these results to report the phi-coefficient (although the values remain the same). Again, thank you for your help in improving the manuscript. Your feedback is greatly appreciated." } ] } ]	1	https://f1000research.com/articles/10-45
https://f1000research.com/articles/12-862/v1	20 Jul 23	{ "type": "Research Article", "title": "Amanita thiersii and Amanita foetens are closely related but genetically and geographically distinct species, leaving the origins of A. thiersii and its range expansion enigmatic", "authors": [ "Nora Dunkirk", "Yen-Wen Wang", "Milton T. Drott", "Holly Elmore", "Gerardo Robledo", "Rodham E. Tulloss", "Anne Pringle", "Yen-Wen Wang", "Milton T. Drott", "Holly Elmore", "Gerardo Robledo", "Rodham E. Tulloss" ], "abstract": "Background: The decomposer Amanita thiersii was originally described from a Texas lawn. Over time the species appears to have spread its range, but whether A. thiersii is an introduced and invading fungus or a native expanding its range remains an open question. A striking morphological similarity between A. thiersii and the Argentinian A. foetens led us to question whether the two species are the same. We hypothesized A. thiersii was simply an A. foetens introduced from Argentina. Methods: We first compared the original species descriptions of both taxa. Next, we used databases associated with iNaturalist and Mushroom Observer to plot the global ranges of A. thiersii and A. foetens, revealing new reports of A. thiersii in Mexico and an expanded range in the United States of America. Next, we sequenced three genomes: an A. thiersii specimen from the U.S.A., an isotype of A. foetens, and an Argentinian specimen tentatively identified as A. thiersii. We reconstructed phylogenies using our own and publicly available data of other Amanita species. Because the genetic diversity of A. thiersii in the U.S.A appears to be very low, we also searched for mating type loci. Results: Macroscopic descriptions suggest the two taxa are distinguishable by mushroom stature and the decoration of the stipe. The geographic ranges of the two taxa seem distinct and not overlapping, although the inconsistent names used by database users causes confusion. Phylogenies suggest the genomes of mushrooms collected in U.S.A. are different from Argentinian genomes. We discovered an individual which appears to have a mating type locus present in one nucleus of the dikaryon and absent from the second nucleus. Conclusions: While A. thiersii and A. foetens appear strikingly similar, each is morphologically, geographically and genetically distinct, leaving the question of whether A. thiersii is native or introduced to the U.S.A. unanswered.", "keywords": [ "Biogeography", "decomposer fungi", "invasive fungi", "invasion biology", "fungi", "geographic distribution", "taxonomy", "introduced species", "integrative species" ], "content": "Introduction\n\nHumans often move organisms across continents, either deliberately or inadvertently, and by doing so facilitate long distance dispersal. Introductions may lead to invasions, and invasive species are one of the top five threats to Earth’s biodiversity (Butchart et al., 2010; Pyšek et al., 2020). We define an invasive species as a species outside its natural range which becomes established in local habitats and threatens native biodiversity (Desprez-Loustau et al., 2007). Invasive species can cause severe, often unpredictable problems. For example, the chestnut blight fungal pathogen, Cryphonectria parasitica, caused devastation to Chestnut tree populations in North America, which in turn had cascading, ecosystem-wide effects (Desprez-Loustau & Rizzo, 2011). Invasive nonpathogenic fungi have not received as much attention as invasive vertebrates and plants, but because decomposer and symbiotic fungi shape biodiversity (because they themselves are diverse, and through interactions with animals and plants) and because decomposer fungi drive biogeochemical cycles, their potential impacts on native species and ecosystem services are tremendous (DAISIE, 2012).\n\nFungi are ubiquitous, but only a fraction of Earth’s total species have been described (Blackwell, 2011). Moreover, the past and present ranges of most fungal species remain unmapped, in part because the native habitats of many fungi are not documented: often, species are only known from the one or two specimens used to describe them (Pringle & Vellinga, 2006). In fact many fungi are described from places where they are introduced, for example, botanical gardens (Pringle & Vellinga, 2006). Finding a fungus somewhere does not necessarily mean it is native there (Golan & Pringle, 2017). Often, invasive fungi are identified as invasive only because they are charismatic or dramatically affect humans, for example the invasive Death Cap, which is deadly poisonous (Wang et al., 2023). Unsurprisingly, invasions by plant pathogens like C. parasitica are more studied than invasions by decomposers or symbionts (Fisher et al., 2012; Pringle & Vellinga, 2006). For example, while the story of the saprotrophic Clathrus archeri’s spread throughout Europe is more than a century old, its potential impacts on native fungal communities remain unknown (Brännhage et al., 2021; Desprez-Loustau et al., 2007). Nonetheless, the scarce data available confirm invasive nonpathogenic fungi matter: for example, the beetle symbiont Flavodon subulatus, which was introduced alongside its invasive beetle, suppresses native fungal species in the invasive range (Hulcr et al., 2021; Jusino et al., 2020).\n\nThe striking lawn mushroom Amanita thiersii is a saprotroph within the asymbiotic clade of the genus Amanita (Cui et al., 2018; Tulloss et al., 2016; Wolfe, Tulloss et al., 2012). Originally described from College Station, Texas, U.S.A. in 1957 (Thiers, 1957), herbarium records from the 1960’s onward document the dramatic spread of A. thiersii out of Texas and across the southern and midwestern United States (Wolfe, Kuo et al., 2012). An expanding range is a hallmark of an invasive species and has been documented for other symbiotic species in the genus, not only for the Death Cap Amanita phalloides (Pringle et al., 2009), but also the Fly Agaric A. muscaria (Vargas et al., 2019). North American populations of A. thiersii appear to be genetically homogeneous (Wolfe, Kuo et al., 2012). The lack of genetic diversity across its entire known distribution suggests an introduction associated with a genetic bottleneck. Although A. thiersii possesses characteristics of an invasive species, if it is native to Texas, then by definition it is not invasive. It may still be undergoing a range expansion, perhaps in response to climate change (Hobbie et al., 2017).\n\nBut is A. thiersii truly native to North America? Morphological similarities between A. thiersii and another white decomposer, the Argentinian A. foetens (Singer, 1953), raise two questions: are the two species the same species? Was the species introduced to North America from Argentina? If A. thiersii was introduced to the U.S.A. from South America, its rapid geographic spread and the dramatic increase in its population size over recent decades would define it as an invasive species. As conservation biology slowly begins to focus on fungi, as well as animals and plants (Gonçalves et al., 2021; May et al., 2018), efforts to record and stop the spread of introduced and invasive nonpathogenic fungi are ramping up (Dickie et al., 2016; Pyšek et al., 2020). An essential prerequisite is the ability to differentiate between native and invasive fungi.\n\nUsing an integrative species concept (Barrett & Freudenstein, 2011; Wiens, 2007), we hypothesized the two species are the same; A. thiersii is simply an A. foetens introduced from Argentina. To test our hypothesis, we first revisited and compared the original species descriptions of A. thiersii and A. foetens, focusing on morphological similarities and differences. Next, we investigated their current global ranges using the biodiversity databases iNaturalist and Mushroom Observer. Finally, we sequenced three genomes and compared the sequence data of a U.S.A. A. thiersii, an isotype of A. foetens, and a recently collected Argentinian mushroom initially identified as A. thiersii. Our data provide a unique opportunity to document the history of an Amanita species currently spreading in North America.\n\n\nMethods\n\nThe species Amanita thiersii was first described by Harry D. Thiers from College Station, Brazos County, Texas, U.S.A. in 1957 (using the invalid name A. alba Thiers; Thiers, 1957), and it was later validly named for Thiers (Bas, 1969). The 1969 text is the protologue of A. thiersii. The specimens used to describe the species were collected in September 1952 from a lawn. The species Amanita foetens was first described from Pié del Periquillo in Tucumán Province, Argentina by Rolf Singer (Singer, 1953). The specimens used to describe A. foetens were collected in December 1951 from a semiarid pasture. Amanita foetens was revised again at length by Bas (Bas, 1969). We used all descriptions in our comparisons.\n\nWe used two public databases to establish the current known distributions of A. thiersii and A. foetens: iNaturalist (iNat) and Mushroom Observer (MO). While MO uses the name Amanita thiersii, iNat uses the name “Saproamanita thiersii.” The generic name “Saproamanita” Redhead, Vizzini, Drehmel & Contu was proposed in 2016 for use with asymbiotic Amanita species (Redhead et al., 2016), but it is controversial (Hawksworth, 2016; Tulloss et al., 2016). Confusingly, iNat uses the generic name “Amanita” for A. foetens, even though it is also asymbiotic. Both iNat and MO are populated with observations of mushrooms submitted by the public. Names for observations are determined by popular vote on iNat and by a different, more complex community voting system on MO. To search in each database, we used the search terms “Amanita thiersii” and “Amanita foetens”. Searching for “Amanita thiersii” in iNat leads to the page for “Saproamanita thiersii,” and using “Amanita foetens” leads to the page for “Amanita foetens”. Data from iNat were downloaded between June 14 and 15, 2022, and MO data were downloaded on June 7, 2022. We used iNat data with a data quality assessment of “research grade” and additional observations with photos clearly resembling white Amanita. Next, we manually checked each individual observation in both datasets to confirm species identifications using the gross morphology visible in pictures, authors’ descriptions, and/or DNA sequence data, as available. Observations without latitude and longitude were almost always excluded, as were observations not strongly resembling one of our target species. However, observations from South America were relatively rare (as compared to observations in North America), and in a few instances we estimated exact latitude and longitude coordinates from observer’s location descriptions, especially for MO observations from South America. In these cases, coordinates are not exact. Eventually, all observations made outside of North and South America were removed because none matched the descriptions for either A. thiersii or A. foetens. Data from each of the databases were compiled into a single dataset (dataset on Dryad) and mapped. The locations of specimens used in genome sequencing were manually added to the dataset.\n\nWe sequenced the genomes of three mushrooms: AmanitaBASE 10801, 10802 and 10175. AmanitaBASE 10801 (Elmore, 2020) is an isotype of A. foetens sent from the University of Michigan herbarium (voucher: MICH4948) originally collected in Pié del Periquillo, Tucumán Province, Argentina by R. Singer and H. Helberger in December 1951 (Singer original voucher: T1672). AmanitaBASE 10802 is an A. thiersii mushroom collected by S. Kay from a lawn in Baldwin City, Kansas, U.S.A. in 2009 (Kay voucher: SKay4041). A single spore of mushroom SKay4041 was cultured and its haploid genome previously sequenced by Wolfe et al. (Wolfe, Kuo et al., 2012; more fully described in Hess & Pringle, 2014). We re-sequenced the same single spore cultivar to take advantage of improved sequencing technologies. AmanitaBASE 10175 was collected in Córdoba, Argentina in 2014 and it was originally identified as A. thiersii by G. Robledo (Robledo voucher: G201); from this point forward, we refer to 10175 as an Amanita sp. We also refer to the genomes generated from each mushroom specimen by their AmanitaBASE numbers. DNA extraction for genome sequencing and library preparation followed protocols described by Wang (Wang et al., 2023). Genomes were sequenced on the Illumina HiSeq 2500 short reads platform with 251 bp paired-end reads (Wang et al., 2023).\n\nTo assemble the genomes of A. thiersii 10802, A. foetens 10801, and Amanita sp. 10175, the raw reads were first trimmed using bbduk from the BBMap suite ver. 38.32 (kmer length 23; Bushnell, 2016). The genomes were then assembled using SPAdes ver. 3.5.0 with default parameters using two libraries (Prjibelski et al., 2020).\n\nSaprotrophic Amanita species are closely related to each other and basal to ectomycorrhizal Amanita (Wolfe, Tulloss et al., 2012). To clarify the phylogenetic relationship among specimens collected as either A. thiersii or A. foetens, we obtained DNA sequences of the nuclear regions ITS, NucLSU (28S), and NucSSU (18S), and of the mitochondrial regions MitLSU, and MitSSU loci, from all saprotrophic or asymbiotic Amanita available from NCBI as of March 11, 2022. We included all sequences meeting the following criteria: 1) the sequence was from a specimen (Collector’s ID) associated with at least two of the five loci of interest, and 2) the mushroom corresponding to the sequence was not identical to any represented by our own genomes. We included NCBI data from two A. thiersii specimens; one of them (Collector’s ID SKay4041_het) is directly related to our sequenced single spore cultivar. It is the dikaryotic parent of our genome A. thiersii 10802, in other words, A. thiersii 10802 is the monokaryotic offspring of SKay4041_het. Because the diploid SKay4041_het data captures all of the genetic information of the original specimen, we omitted the haploid genome of A. thiersii 10802 from the 5-locus analysis. In total, we included data from eight asymbiotic Amanita species, each species represented by between one and three specimens, and from two specimens of an outgroup species (Pluteus cervinus) which also met our criteria (Table 1). We also identified and extracted the five loci from our remaining genomes (10801 and 10175) by querying the genomes with known sequences of closely related species using blastn from the BLAST+ suite (Altschul et al., 1990). Sequences corresponding to the best BLAST hit were obtained using seqinr in R (Charif & Lobry, 2007; Team, 2016).\n\nTable includes species name, the identifier given by the mushroom collector “Collector’s ID”, and all the NCBI accession numbers associated with that mushroom used in this analysis for the five loci.\n\nWe aligned each sequence set using MAFFT ver. 7.490 (code and tags can be found on GitHub; Katoh et al., 2002). Resulting alignments were used to construct maximum-likelihood phylogenies with IQtree ver. 1.6.12. Our pipeline first used the ModelFinder tool to find the best nuclear or mitochondrial substitution model for each alignment (Kalyaanamoorthy et al., 2017), and then ran 1000 bootstraps using the ultrafast bootstrap approximation method (Nguyen et al., 2015). To construct a single phylogeny using the data of all five single-locus phylogenies, we concatenated alignments. The concatenated sequence was used to reconstruct a maximum-likelihood phylogeny to create the best tree to fit the data, with informative branch lengths corresponding to genetic distances. The five-locus phylogeny was created using IQtree run with partition models to distinguish the loci based on the ModelFinder tool, and bootstrapped 1000 times using the ultrafast bootstrap approximation (tags found on GitHub; Dunkirk, 2023). We verified the results of this method by also creating a consensus tree using ASTRAL (Zhang et al., 2018). The trees were rooted with P. cervinus as outgroup.\n\nAs a final analysis and to contextualize the close relationship between A. thiersii and A. foetens, we downloaded all 2,237 Agaricales ITS sequences available from NCBI on October 1, 2022, and we included these with the ITS sequences we used to generate the five-locus phylogeny. Sequences were aligned with MAFFT using the ‘-auto’ parameter and trimmed with trimAL using the ‘-automated1’ parameter (Capella-Gutiérrez et al., 2009). The resulting trimmed alignment of 279 bp was used in IQtree to construct a maximum likelihood phylogeny using the ‘test’ parameter to find the best model as constrained within ‘raxml’ options. All identical sequences were removed by default. All pairwise distances in the resulting tree were obtained from the ‘mldist’ file and filtered to only include comparisons within the same genus. Only the lowest distance comparison within and between species was kept for a given sequence. We visualized the data as a histogram to compare pairwise distances between intraspecific and interspecific species, as named in the database.\n\nTo contextualize the genomes of A. thiersii 10802, A. foetens 10801 and Amanita sp. 10175 within the genus Amanita, we downloaded all publicly available Amanita genomes, both asymbiotic and mycorrhizal, in addition to those of Volvariella volvacea and Pluteus cervinus, both used as outgroups (genomes downloaded from NCBI between March 29 and 31, 2022; Table 2). We identified a set of fungal Benchmarking Universal Single-Copy Orthologs (BUSCOs) from each of 15 genomes using the program BUSCO (ver 3.0.2 run with Laccaria bicolor as reference; Simão et al., 2015). We subset this dataset to include only those BUSCOs present as single copies in all 15 taxa (n = 55 BUSCOs). We aligned the sequences of each BUSCO with MAFFT and constructed single-BUSCO maximum-likelihood phylogenies for each resulting alignment with IQtree.\n\nTable includes data downloaded from NCBI detailing the species name, genome assembly accession number, and genome ID associated with the genome.\n\nWe took two approaches to generate subsequent multi-gene species-trees: first, we concatenated the alignments and made a single tree, and second, we used a consensus tree method to generate a consensus tree. First, concatenated sequence data were used to generate a maximum-likelihood phylogeny using IQtree run with a partition model, using methods parallel to the methods used to generate the five-locus tree (described above). Second, ASTRAL ver. 5.7.8 was used to reconstruct a consensus tree (Zhang et al., 2018) based on the phylogenies constructed for each individual BUSCO. Essentially, using ASTRAL, the BUSCO species tree was created by using single-gene-BUSCO trees as inference and by considering discordance among the single-gene trees. As an extra check to verify the topology of the BUSCO species trees, we used additional methods. To determine the number of informative gene-trees which showed topology in concordance with the consensus phylogeny, we re-ran ASTRAL and measured quartet support (Zhang et al., 2020), and we calculated gene concordance with IQtree ver. 2.1.2 (Minh et al., 2020) using the single-gene BUSCO trees and the maximum-likelihood phylogeny previously generated using IQtree. The quartet support option in ASTRAL indicates, at each branch, how much conflict there was between gene-trees in the resulting consensus tree (Zhang et al., 2018). The concordance factor option in IQ-tree indicates the percentage of locus-trees which support that branch (Minh et al., 2020). The tree was rooted with P. cervinus and V. volvacea as outgroup taxa.\n\nU.S.A. populations of A. thiersii are characterized by a lack of genetic diversity, suggesting sexual reproduction is absent or involves genetically similar pairs (Wolfe, Kuo et al., 2012). In fungi, successful sexual reproduction typically requires the interaction of compatible mating type genes, named as Homeodomains 1 and 2 (HD1 and HD2). To determine if our three genomes include the mating type loci required for sexual reproduction, we used the methods described above to extract the genes HD1 and HD2. To identify HD2, we queried genomes 10175, 10801, and 10802 using the tblastn function of BLAST with the amino acid (AA) sequences of the HD2 gene identified from an earlier annotated genome of A. thiersii (Hess et al., 2014), from the genome of another closely related asymbiotic Amanita, A. inopinata (Hess et al., 2014), and from Coprinopsis cinerea (Stajich et al., 2010). To identify HD1, we queried the same genomes using tblastn with the AA sequences of HD1 from A. inopinata, and C. cinerea.\n\nThe published, annotated genome of A. thiersii (Hess et al., 2014) does not appear to include the HD1 gene region and so we could not use it as a query. To explore this dynamic further, we searched for HD1 in a publicly available transcriptome (NCBI ID: SRX037158; Wolfe, Kuo et al., 2012) sequenced from a culture of the dikaryotic parent mushroom of the single spore used to generate genome 10802. We first used the HD1 nucleotide sequence from Amanita sp. 10175 as query in an SRA BLAST (Sequence Read Archive Basic Local Alignment Search Tool) of the transcriptome. Next, we downloaded all output sequences and used the program EGassembler to merge sequence fragments into a single consensus sequence (Masoudi-Nejad et al., 2006). We used the resulting consensus sequence as the next query to SRA BLAST, once again searching in the transcriptome, and repeated our searches until no new transcriptomic reads could be incorporated into the consensus.\n\nBecause the HD2 gene includes introns, we used the annotated genome of A. thiersii to locate and remove them (Hess et al., 2014). After removing introns, we used the tool Expasy to translate the DNA sequences of both HD1 and HD2 into AA sequences (Duvaud et al., 2021). Homeodomain proteins are typically identifiable by three helices (Hull et al., 2002). To confirm the presence of the three helix motif, we used a position-specific iterative predictor, PSIPRED, to predict and confirm secondary structural motifs (McGuffin et al., 2000). We checked the PSIPRED predictions using blastp (Altschul et al., 1990). Next we searched for HD1 and HD2 in other Amanita and V. volvacea (Hess et al., 2018). To compare HD1 and HD2 among species, we aligned only the conserved three-helix homeodomain AA sequences using MAFFT (default settings; Katoh et al., 2002).\n\nTo confirm the absence of mating-type genes in assemblies as the result of true deletions and not error related to genome assembly, we aligned raw reads from 10802 to the genome of 10801 that contained both mating type genes using BWA mem (Li, 2013). Resulting alignments were visualized in Integrative Genomics Viewer (Thorvaldsdóttir et al., 2012) to confirm the absence of reads aligning at mating type loci.\n\n\nResults\n\nAmanita thiersii and A. foetens are morphologically very similar, but key differences are apparent in the original species’ descriptions. Features which appear identical include gill characteristics, ring location, and basidiospore shape (Figure 1). Features which appear similar include the general appearance of mushrooms, more specifically their color, height, cap size and wart characteristics; the integrity of the ring on developing mushrooms; and basidiospore size. Conflicting or ambiguous descriptions relate to the structure of the volva, details of stipe and ring morphology, and, notably, mushroom scent.\n\nMorphology summarized from the original descriptions by Singer (1953) and Thiers (1957) and secondary descriptions by Bas (1969) for notable characteristics. Photos under creative commons license (Cc-by-sa-3.0) or reproduced with permission from Bas (1969).\n\nBoth species are described as entirely white in color (A. foetens may also be pink or yellowish), with medium to large mushrooms and convex caps (Bas, 1969). Caps possess abundant floccose or fleshy warts with crowded and freely attached gills. The caps of A. thiersii appear to be slightly smaller than caps of A. foetens but ranges are not disjunct. The mushrooms are described as either “rather thick-fleshed” (A. thiersii; Bas, 1969) or with a “rather sturdy fruit body” (A. foetens; Bas, 1969). Stipes are reported as textured as opposed to smooth (Bas, 1969). The stipe of A. thiersii is described as being equally wide across its height, but with a slight bulb at its base (Thiers, 1957). The stipe of A. foetens is described as “white, firm, broad” with a strongly bulbous base (Singer, 1953). Stipe height for both species is reported similarly at between 80-200 (A. thiersii) or 80-210 (A. foetens) mm (Bas, 1969; Thiers, 1957). Basidiospores appear to have the same shape: globose to subglobose, and mushrooms drop a white spore print (Singer, 1953; Thiers, 1957). Basidiospores are amyloid and less than 10 × 10 μm (Bas, 1969). Basidia lack clamps, a feature typical for stirps Thiersii, the subset of the genus Amanita housing both A. thiersii and A. foetens (Bas, 1969).\n\nOther characters in the two species’ descriptions are either difficult to compare or are ambiguous. Within the genus Amanita, the volva is a key distinguishing feature. If A. thiersii and A. foetens are the same species, we would expect to find similar or identical volval descriptions. The volva of A. thiersii is described as usually evanescent “or present as a series of irregular rows of easily detached, fibrillose warts along the base of the stipe” (Thiers, 1957). The volva of A. foetens is described as strongly reduced or absent “or represented by some girdles” (Singer, 1953). Although these descriptions use different words, fibrillose warts versus girdles, they both allude to a volva made up of evanescent pieces of mushroom tissue around the stipe; a contrast to the obvious, persistent, and cup-shaped volva of many Amanita. Both descriptions point to the lack of a volva, or a volva present as remnants only, but because it is difficult to interpret the original descriptions further, how the volva might compare to each other remains ambiguous.\n\nLess ambiguous are other differences, including differences in the internal morphology of the stipe; the stipe of A. thiersii is described as “stuffed to hollow” (Thiers, 1957) while the stipe of A. foetens is described as “solid, firm” (Bas, 1969; Singer, 1953). After revisiting Bas’s (1969) species descriptions one of us (Tulloss) a taxonomic expert and specialist of the genus, concluded fresh specimens of the species can be distinguished based on stature. The stature of A. thiersii is significantly more “gracile” than the stature of A. foetens (Bas, 1969: Fig. 85 vs. Fig. 88). The word gracile is used to mean slender, and a comparison of the ratios of stipe length to stipe width can stand in for the qualitative term “gracile.” In A. thiersii the ratio ranges from 6.9 to 7.3 (based on data of Bas, 1969) while in A. foetens the ratio ranges from 10 to 20 (also using data from Bas, 1969).\n\nDescriptions of the ring also emerge as distinct. While both species’ rings are described as white, membranous, and located apically on the stipe (Bas, 1969), A. thiersii’s ring is described as thin and “easily torn, sometimes disappearing” (Bas, 1969) while A. foetens’ ring is described as “rather thick”, “frequently fragmentary” (Singer, 1953), and as “falling to pieces” (Bas, 1969). While both rings appear fragile, the distinction of thin versus thick cannot be ignored.\n\nFinally, the scent of A. thiersii is reported as indistinct (and we ourselves have never found a strong-smelling A. thiersii), whereas the smell of A. foetens is “resolutely stinking” and in mature specimens, like urine (Singer, 1953). In the aggregate, the morphological differences recorded for A. thiersii and A. foetens suggest they are different species. Later we discuss the usefulness of these diagnostic characters to the field biologist.\n\nThe two species were not equally represented across iNat and MO. There were a total of 24 observations of A. foetens in iNat, of which we used 15 (we removed nine observations with low quality data grades), and no observations in MO. We manually added the locations of the isotype of A. foetens collected from Tucumán, Argentina (AmanitaBASE 10801/MICH4948) and the mushroom collected as Amanita sp. from Córdoba, Argentina (AmanitaBASE 10175) to our dataset (total observations included in subsequent analyses: 17). There were a total of 286 observations of A. thiersii in iNat, of which we used 155 (we removed 131 observations with aberrant morphologies or low-quality data grades), and 15 observations in MO. We manually added the location of our genome-sequenced sample from Kansas, U.S.A. (AmanitaBASE 10802) to our dataset (total observations included in subsequent analysis: 171). Because the nomenclature within iNat and between iNat and MO is inconsistent (iNat uses the pseudonym Saproamanita thiersii, while A. foetens remains as Amanita foetens (Hawksworth, 2016; Redhead et al., 2016; Tulloss et al., 2016; at the date of download, MO did not use the generic name Saproamanita), we use the names Amanita thiersii and Amanita foetens to describe records from both iNat and MO (except on Figure 2, where for clarity we use the names used in the databases themselves).\n\nA. Map of U.S.A. and Mexico plotted with observations of A. thiersii (as blue squares from MO, and blue circles named as Saproamanita thiersii from iNat). Mushroom A. thiersii 10802, the source of a sequenced genome, plotted as a black X. Geographic distribution of A. thiersii as published in Wolfe, Kuo et al. (2012) shown as small red dots. B. Map of Argentina and Uruguay plotted with observations of A. foetens (iNat) as orange circles, A. thiersii (MO) as blue squares, and Saproamanita thiersii (iNat) as blue circles. Mushrooms Amanita sp. 10175 and A. foetens 10801, sources of sequenced genomes, plotted as black X and +, respectively. Axes of A. and B. reference latitude and longitude.\n\nBoth species are observed within North and South America and not on other continents. While two observations were made from Taiwan and South Africa (iNat observations 118324696 and 117233579, respectively), neither observation matched either species’ morphology. Amanita foetens was observed predominantly in Argentina (n=15), as far south and east as Buenos Aires and as far north and west as Tucumán. It was also found in Uruguay (n=2). The fungus was most frequently observed in the Argentinian province of Buenos Aires (n=13). Amanita thiersii was found overwhelmingly in the U.S.A. (n=160), but its range appears to be expanding. Wolfe et al. (2012) reported it as far north as Illinois and east to Kentucky (red dots on Figure 2A), but the fungus now appears as far north as Wisconsin, and as far east as Pennsylvania and Maryland (Figure 2A). It has also been reported from Florida. Amanita thiersii appears to be newly common in Illinois, with 16 observations recorded from the state since 2012. But in the U.S.A., A. thiersii was most frequently observed in Kansas (n=38), Maryland (n=31), and Texas (n=28). Although MO records observations of A. thiersii in Argentina (n=1) and Uruguay (n=1), the records likely reflect a bias towards recording this well-known species. Moreover, within MO, all Argentinian A. thiersii observations have comments urging observers to name the observations as A. thiersii or “Amanita stirps Thiersii,” and not A. foetens. MO users do not appear to use the name A. foetens. The iNat records of A. thiersii from Mexico (n=4) are among the first observations of the fungus in that country (see below). One of us (Tulloss) keyed out one of the Mexican mushrooms and confirms it is A. thiersii (Tulloss, 2020). Mexican A. thiersii appear to be collected from lawns; images of the observations show mushrooms growing with lawn grasses and in one case, mulch (see iNat observation 53329070). Lawns are also where U.S.A. A. thiersii are found. There are also four iNat records of “A. thiersii” in Argentina, one from Mar del Plata, Argentina, and the others from Buenos Aires. The record from Mar del Plata is the southernmost record in South America. We are skeptical the Argentinian A. thiersii records are real, and later we discuss the issue.\n\nMost mushrooms in both databases were observed around urban centers. By contrast, the two Argentinian specimens used for genome sequencing were collected far from any city; the isotype of A. foetens (AmanitaBASE 10801/MICH4948) was collected in a grass pasture in the Tucumán region (+ on map, Figure 2B) and the specimen originally described as A. thiersii (AmanitaBASE 10175), which helped spark our study, was collected from a grassy paddock outside of Córdoba, between Tucumán and Buenos Aires, Argentina (X on map, Figure 2B). The A. foetens observations in Argentina and Uruguay are typically pictured in grass lawns, although some are featured in a mulch or heavily wooded environment (see iNat observation 12341687).\n\nWe used sequences of the ITS, NucLSU, NucSSU, MitLSU, and MitSSU loci to clarify the phylogenetic relationships of our specimens and other saprotrophic, asymbiotic Amanita. We downloaded between two and five gene sequences from a total of 17 mushrooms representing ten different species from NCBI (Table 1), and also used our data from AmanitaBASE specimens 10801 and 10175. (Because publicly available sequences from the dikaryon A. thiersii Skay4041_het represent the parent genome of our haploid (monokaryotic) genome A. thiersii 10802, we omitted our genome 10802 from this analysis.)\n\nThe topology of the concatenated five-locus species tree (Figure 3) is congruent with the topologies of each of the single-locus trees and the consensus tree (not shown). Specimen Amanita sp. 10175 is nearly identical to A. foetens 10801, evidence it is A. foetens and is not A. thiersii. Notably, mushrooms of A. thiersii and both A. foetens 10801 and Amanita sp. 10175 are more closely related to each other than they are to any other saprotrophic Amanita, a clustering strongly supported by bootstrapping. However, A. thiersii specimens from North America form a separate monophyletic clade from A. foetens 10801 and Amanita sp. 10175, and bootstrap support is moderately strong. While the samples from North and South America appear to be in two distinct monophyletic groups, the genetic distance between A. thiersii 10802 and A. foetens 10801 in our distance matrix is only 0.000001: the two species appear very closely related to each other (Figure 4). However, in this analysis of the ITS locus, interspecific measures of genetic distance are frequently very low (Figure 4). The overlap between intraspecific and interspecific genetic distances is striking.\n\nSingle phylogeny generated from five concatenated loci of saprotrophic Amanita, with Pluteus cervinus used as outgroup. Branch lengths correspond to genetic distances.\n\nHistogram of all pairwise genetic distances inferred between all non-identical publicly available Agaricales ITS sequences on NCBI. Comparisons of species from different genera are not reported.\n\nThe BUSCO analysis resulted in a different number of single-copy BUSCOs from each of the genomes, ranging from 197 in A. pseudoporphyria to 279 from A. inopinata. The BUSCO completeness values for our own genomes were good for genomes 10175 (94.8%) and 10802 (95.1%) and moderate for genome 10801 (81.7%). We used the sequences of 55 BUSCO genes which were found as single-copy genes from each of 15 Amanita genomes (including our genomes of AmanitaBASE specimens 10801, 10175 and 10802) to elucidate phylogenetic relationships between the three Amanita spp. specimens and other symbiotic and asymbiotic Amanita from across the genus (Table 2). Both methods (concatenation and consensus) used to construct a BUSCO species tree resulted in identical topologies for A. thiersii and A. foetens (Figure 5; concatenated sequence tree not shown).\n\nA 55-BUSCO-gene phylogeny of Amanita based on all available Amanita genomes from NCBI with P. cervinus and Volvariella volvacea used as outgroups. The phylogeny was generated with IQtree (with concatenated sequences), and a phylogeny reconstructed with ASTRAL has the same topology. Branch supports indicate ASTRAL’s quartet support test and IQtree’s concordance factor (shown before and after slashes, respectively).\n\nIn the BUSCO-species tree, our three specimens form a monophyletic group distinct from all other Amanita, and the clustering is supported by high levels of ASTRAL quartet support and IQtree concordance factor support (Figure 5). Consistent with the first analysis (Figure 3), the topology of the BUSCO phylogeny shows the Argentinian samples 10801 and 10175 as clustering together to form a monophyletic clade, additional evidence Amanita sp. 10175 is the same species as A. foetens 10801. These two are consistently separate from A. thiersii 10802, additional evidence A. foetens and A. thiersii are distinct species.\n\nThe presence of the mating type genes HD1 and HD2 in a genome would signal the potential for sexual reproduction by an individual. Using AA sequences as queries, we were unable to find the HD1 gene in the A. thiersii 10802 genome assembly (a finding we confirmed using genome alignment methods), but we could isolate partial sequences in both Amanita sp. 10175 (AA length=222) and A. foetens 10801 (AA length=103). We also isolated a sequence of HD1 from the transcriptome of A. thiersii SKay4041_het (AA length=533), a transcriptome sequenced from a dikaryotic mushroom, the parent of the germinated basidiospore used to generate the genome sequence A. thiersii 10802. In other words, while the transcriptome of the dikaryotic parent does have HD1, the genome of one of its nuclei does not: the second nucleus of the parent must be the source of the transcriptome’s HD1. The HD1 sequence found in the genome of Amanita sp. 10175 possesses a single AA substitution distinguishing it from the HD1 sequence found in the genome A. foetens 10801 and in the transcriptome of A. thiersii SKay4041_het across the conserved three-helix homeodomain region (AA length=60; Figure 6A, HD1; AA substitutions shown with asterisks). Using AA sequences as queries we were able to identify the complete sequence of HD2 in each of our three genomes and the transcriptome of A. thiersii SKay4041_het (AA lengths=289), and each sequence possessed the typical three-helix structure of the conserved homeodomain motif (AA length=60; Figure 6B, HD2). The HD2 sequences possess only one AA substitution, between Amanita sp. 10175 and A. foetens 10801. This is the first report of mating type loci for these Amanita spp.\n\nAmino acid sequences of mating type loci HD1 (A) and HD2 (B). A. thiersii 10802 is missing the HD1 gene, but a transcriptome generated from the dikaryotic parent of 10802 (A. thiersii Skay4041_het) houses a transcript of HD1, suggesting one of the nuclei of the dikaryotic parent houses HD1 while the other does not. Sequence similarity among A. thiersii and A. foetens is very high, with only one or fewer amino acid differences in the conserved homeodomain region of both mating type genes. Asterisks are near key amino acid differences.\n\n\nDiscussion\n\nSpecies’ descriptions, ranges, and phylogenies contextualized by other taxa in the genus Amanita each suggest A. thiersii and A. foetens as two different species. The morphological differences distinguishing them may enable identification in the field. However, identifying fungi based on morphology alone is often difficult (Houbraken et al., 2020; Looney et al., 2020), and if a specimen is old or weathered, key characters may be absent (a full description of the characters used to identify Amanita species is provided by Tulloss (Tulloss, 2023). While it may be possible to identify fresh material as A. thiersii or A. foetens using features of the stipe and smell; by measuring stipe length and width, and deciding if a specimen smells and, if so, what it smells like, in practice many will find these to be difficult field characters (or not know to measure or record them). For example, the smell of A. thiersii mushrooms is described as indistinct, while mushrooms of A. foetens are supposed to smell like urine (Figure 1). But collectors posting to MO report A. thiersii as having a range of scents, from indistinct and “scentless” to “smells like urine”, “has a fishy, bad odor”, all the way to “the odor was unpleasant, a bit like a sweaty locker room”. Collectors posting to iNat do not include details of A. foetens smell. While morphology emerges as formally useful, it may not serve as a practical guide for choosing whether a particular mushroom is A. thiersii or A. foetens. It is also possible the original species descriptions (especially of A. thiersii) are missing descriptions of intraspecific variability in scent, or variability between e.g. young and old mushrooms.\n\nThe geographic origin of any material is likely to be a more useful diagnostic for most collectors. Both iNat and MO document A. thiersii as growing throughout much of North America. The fungus continues to expand its range and is now found throughout the U.S.A. east of the Rocky Mountains, from Texas and Florida up to Wisconsin, Pennsylvania and Maryland (Figure 2, compare to red dots denoting range of A. thiersii in Wolfe, Kuo et al., 2012). The continuing spread of A. thiersii is remarkable. In the U.S.A., A. thiersii is most often recorded from typical lawn environments, e.g., iNat observations 94653088 from Kansas and 60276048 from Indiana. Notably, some of what are now the eastern-most collections, for example collections in Florida, show the mushroom growing from dead leaves, for example iNat observation 74461419, described at “woodroad’s edge” and pictured without any grass in sight. The fungus is hypothesized to be moving north and east in response to climate change (Hobbie et al., 2017).\n\nWith this hypothesis in mind, the northward and eastward movements of the fungus are perhaps less surprising than the discovery of A. thiersii in Mexico. In Mexico the fungus is found directly north of Mexico City and to the south in Oaxaca. However, we do not know if the Mexican observations reflect the ongoing range expansion or the discovery of the native range. We hypothesize the discovery of A. thiersii in Mexico represents a new range for the fungus, and not the discovery of a native range, basing our hypothesis on the habitats of the Mexican mushrooms. As is true for A. thiersii in the U.S.A., in Mexico A. thiersii appear to grow in lawns, for example iNat observations 86939921 and 86236720 from México, Mexico. Lawns of grasses are habitats grown by humans and the current scarcity of collections from natural habitats suggests a link between human activity and the fungus.\n\nAmanita foetens mushrooms have not been reported in North America. Instead, the observations of A. foetens from iNat suggest it is a South American mushroom of urban and anthropogenic habitats, including lawns, pastures, and gardens. It grows in both Argentina and Uruguay. The preponderance of urban observations may reflect a simple bias; perhaps people in cities are more frequently using the database, as compared to people outside of cities. The fifteen observations are clustered in Buenos Aires Province, Argentina. By contrast, the two Argentinian mushrooms we used in genome sequencing were found far from urban habitats. The isotype and other specimens used in the original species’ description were discovered in a pasture near Tucumán (although the exact coordinates are unknown and the location is given simply as “Pie del Periquillo, Tucumán Province, Argentina”). The specimen which began our debate about A. thiersii and A. foetens, Amanita sp. 10175, was collected similarly in a paddock in the hills near Córdoba, well outside of the city center.\n\nObservations of A. thiersii or “Saproamanita thiersii” (depending on the database) are also reported from Argentina and Uruguay. Because the name A. foetens is not used by MO collectors, it is difficult to know if records of South American “A. thiersii” in MO are actually records of A. foetens; in fact, because of the general confusion, iNat “Saproamanita thiersii” records may also represent misidentifications. The difficulty highlights the complications of using data in public databases. In iNat, Argentinian “Saproamanita thiersii” were sometimes observed from locales very close to iNat observations of A. foetens. In MO, the question of whether A. thiersii and A. foetens are the same species has been debated for nearly a decade, and the community has actively encouraged the naming of Argentinian samples as “A. thiersii” or “Amanita stirps Thiersii” (the latter convention encompasses both A. thiersii and A. foetens). Either A. thiersii is also growing in Argentina alongside A. foetens, or the Argentinian MO and iNat records are misidentifications (the records are A. foetens mislabeled as A. thiersii or S. thiersii). We favor the second hypothesis. Comments within MO offer support for our hypothesis, for example, MO observation 200425 is annotated with “… Of note to me is that this amanita [sic] was not found in its typical lawn habitat, but with trees and shrubs.”.\n\nPhylogenies consistently place mushrooms of A. thiersii and A. foetens apart from each other, although the two species appear to be very closely related. A discussion of intraspecific diversity of the ITS locus is beyond the scope of our current study, but we were struck by the overlap between intraspecific and interspecific comparisons of genetic distances (Figure 4). We considered an hypothesis of the two species as distinct populations of the same species, but using the morphological and geographic data as context, we consider the phylogenies as better supporting the hypothesis of two distinct species. Although they were collected 570 kms away from each other, specimen Amanita sp. 10175 consistently groups with the isotype of A. foetens and is clearly an A. foetens, additional evidence A. thiersii is absent from Argentina.\n\nThe species most closely related to A. thiersii and A. foetens is A. praeclara (A. Pearson) Bas, a species originally described from the Cape Province of South Africa as an “aberrant” Lepiota (Figure 3; Pearson, 1950). It is another “white to whitish” (Reid & Eicker, 1991) decomposer Amanita collected from lawns; the original collections were made in the “grassy ground of paddock” and from “football” [soccer] fields (Pearson, 1950). The fungus was recently reported from India (Kantharaja & Krishnappa, 2022), and the Indian record suggests another potential introduction involving this different asymbiotic Amanita. However, the habitat for the Indian A. praeclara is described as “on soil under in [sic] dry deciduous forest region”. Moreover, while South African A. praeclara are described as white staining yellow (sulfur- or lemon-yellow), the Indian A. praeclara appears to be somewhat different; the description states mushrooms are “white, covered with pale yellow to orange yellow lanose-floccose covering when young … staining pale yellow afterwards” (Kantharaja & Krishnappa, 2022). One of us (Tulloss) does not believe the Indian A. praeclara is the same as the South African A. praeclara. Once again, the question of whether or not a newly discovered species is native or introduced is unanswered. Regardless, Bas (Bas, 1969) grouped A. praeclara in the same stirps as A. thiersii and A. foetens, and his grouping is now confirmed by our DNA sequence data (Figure 3).\n\nInvasive species often reproduce asexually, and clonal propagation can facilitate spread (Gao et al., 2018). In North America, A. thiersii lacks genetic diversity (Wolfe, Kuo et al., 2012). While we identified the mating type locus HD1 in the transcriptome of a dikaryotic strain of A. thiersii, the locus is missing from its monokaryotic offspring (which was cultured from a single basidiospore of the mushroom used to generate the dikaryotic strain, see also Elmore, 2020). The HD1 locus appears to be present in some nuclei and absent from others. Mushrooms are sexual structures and A. thiersii clearly grows mushrooms. But the lack of genetic diversity and existence of a nucleus missing HD1 suggests unusual mating dynamics, an analog to the biology of invasive Death Caps in California (Wang et al., 2023), and to other unusual basidiomycete mating systems (Coelho et al., 2017). We found no evidence for missing mating type loci in either of the A. foetens genomes, however, neither genome involved a monokaryotic culture.\n\nFor the moment, we recommend all mushrooms keyed to A. thiersii and A. foetens observed in North America be named as A. thiersii and all those found in South America be named as A. foetens. Using geography to choose names will simplify identification of morphologically ambiguous mushrooms. However, basing identification on geography will also obscure future introductions. If or when either species is introduced to the other continent, the introduction will be difficult to recognize. There is a great need for simple molecular tools enabling straightforward identification of specimens to species, and tools would be strengthened by greater efforts to sequence types and apparent novelties.\n\n\nConclusions\n\nIn the aggregate, morphological descriptions, data on occurrence and habitat, and phylogenies based on both a few loci and many specimens, as well as many loci of a few specimens, support A. thiersii and A. foetens as closely related but distinct species. The species appear morphologically and genetically distinct, and geographically isolated. We reject the hypothesis of A. thiersii as an A. foetens introduced to Texas from Argentina by humans. While our data do not establish A. thiersii as an introduced and now invasive species, they also do not establish it as native; the native range of A. thiersii remains unknown. It may have been introduced to North America from a country other than Argentina. For the first time, we report A. thiersii in Mexico. The question of why A. thiersii is spreading rapidly throughout North America remains open. In this instance, baseline data on fungal biodiversity have failed us; there are no baseline data for A. thiersii. Thus, we started with an enigma, and end with one as well.", "appendix": "Data availability\n\nDryad: Mushroom Observations of Amanita thiersii and A. foetens, https://doi.org/10.5061/dryad.7h44j1008 (Dunkirk et al., 2023a).\n\nThis project contains the following underlying data:\n\n• Database_Mushroom_Observations.csv\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nNCBI: Are Amanita thiersii and Amanita foetens the same species? Accession numbers SRR23983939, SRR23983940, and SRR23983941, https://identifiers.org/NCBI/bioproject:PRJNA947219 (Dunkirk et al., 2023b).\n\nThis project contains the following underlying data:\n\n• Genome sequences Athiersii 10802, Afoetens 10175, and Afoetens 10801\n\nSource code available from: https://github.com/noramushrooms/Amanita_thiersii.\n\nArchived source code at time of publication: https://doi.org/10.5281/zenodo.7996518 (Dunkirk, 2023).\n\nLicense: Open.\n\n\nAcknowledgements\n\nWe thank Dr. Timothy James and the University of Michigan herbarium for sending us the voucher specimen of A. foetens.\n\n\nReferences\n\nAltschul SF, Gish W, Miller W, et al.: Basic local alignment search tool. J. Mol. Biol. 1990; 215(3): 403–410. Publisher Full Text\n\nBarrett CF, Freudenstein JV: An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid. Mol. Ecol. 2011; 20(13): 2771–2786. 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Revue de Mycologie. 1953; 18(1): 1–17.\n\nStajich JE, Wilke SK, Ahrén D, et al.: Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc. Natl. Acad. Sci. U. S. A. 2010; 107(26): 11889–11894. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTeam, R: R: A language and environment for statistical computing [Computer software manual]. 2016.\n\nThiers HD: The Agaric Flora of Texas. I. New Species of Agarics and Boletes. Mycologia. 1957; 49(5): 707–722. Publisher Full Text\n\nThorvaldsdóttir H, Robinson JT, Mesirov JP: Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 2012; 14(2): 178–192. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTulloss RE: Amanitaceae: Amanita thiersii. Amanitaceae Studies; 2020. Reference Source\n\nTulloss RE: Studying Morphology. Amanitaceae Studies; 2023. Reference Source\n\nTulloss RE, Kuyper TW, Vellinga EC, et al.: The genus Amanita should not be split. Amanitaceae. 2016; 1(July): 1–16. Reference Source\n\nVargas N, Gonçalves SC, Franco-Molano AE, et al.: In Colombia the Eurasian fungus Amanita muscaria is expanding its range into native, tropical Quercus humboldtii forests. Mycologia. 2019; 111(5): 758–771. PubMed Abstract \| Publisher Full Text\n\nWang Y-W, McKeon MC, Elmore H, et al.: Invasive Californian death caps develop mushrooms and sporulate unisexually and bisexually. BioRxiv. 2023. Publisher Full Text\n\nWiens JJ: Species delimitation: New approaches for discovering diversity. Syst. Biol. 2007; 56(6): 875–878. PubMed Abstract \| Publisher Full Text\n\nWolfe BE, Kuo M, Pringle A: Amanita thiersii is a saprotrophic fungus expanding its range in the United States. Mycologia. 2012; 104(1): 22–33. PubMed Abstract \| Publisher Full Text\n\nWolfe BE, Tulloss RE, Pringle A: The irreversible loss of a decomposition pathway marks the single origin of an ectomycorrhizal symbiosis. PLoS One. 2012; 7(7): e39597. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang C, Rabiee M, Sayyari E, et al.: ASTRAL-III: Polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics. 2018; 19(Suppl 6): 15–30. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang C, Scornavacca C, Molloy EK, et al.: ASTRAL-pro: Quartet-based species-tree inference despite paralogy. Mol. Biol. Evol. 2020; 37(11): 3292–3307. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "201477", "date": "28 Sep 2023", "name": "Duur K Aanen", "expertise": [ "Reviewer Expertise mycology", "phylogenetics", "population genetics", "social evolution", "kin selection", "symbiosis" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 generally well-written manuscript. It describes the results of a study to answer the question whether a recently described mushroom species from north America, Amanita thiersii, is a recently introduced invasive species, or a native species that recently has expanded its range. It studies its relationship with a resembling species from Argentina, Amanita foetens, using morphological, geographical and genetic data. The paper finds a close relationship between the two species, although both seem separate species (but see my comments). Overall, the topic is interesting and relevant, and interesting data are presented. I think the paper can be accepted for indexing if my comments are addressed.\nMy main comment is about the interpretation of your results. I think your data point to a very close relationship between the two taxa. None of the data you present provide conclusive evidence to conclude that they are two different species. The only convincing data, which in principle could show reproductive isolation would be genetic data of a larger sample of strains. The four specimens for which sequence data are provided are not enough for any form conclusions. Just randomly rearranging branches will give a large fraction where the two will form monophyletic groups. And even if this is confirmed for a larger sample, you might still argue that genetic differentiation has occurred after migration of an invasive population. I would suggest to discuss the implications of your findings in a more open way, without firm conclusions on species identity. To me your data seem consistent with an introduction of this taxon from south America, or from a related taxon not included in your sample (a possibility you also discuss).\nI have the following more detailed suggestions to improve the manuscript:\nOn page 4, the term “integrative species concept” is used with a reference to the literature. Since the species concept used in this paper seems highly relevant for the conclusions drawn, it is necessary to explain this species concept and perhaps to discuss it in the context of competing species concepts.\n\nOn page 4: “As conservation biology slowly begins to focus on fungi, as well as animals and plants”. This can be misunderstood as that animals and plants slowly begin to focus on fungi, which I guess is not what you mean. Please change to: “As conservation biology slowly begins to focus on fungi, as well as on animals and plants”.\n\nPage 5: “basal to”, please change to “are the sister group of”.\n\nWhy don’t you present all taxa used for the 2-5 gene analysis in Table 1? Now, I was struggling to find the origin of taxa of Figure 3, because two were not included in table 1.\n\nYou searched for the presence of mating-type loci and were able to find HD2 for all three genomes, but for one of the strains HD1 only was present in the (dikaryotic) transcriptome, but not in the genome of one of its nuclei. From this you conclude that HD1 is missing in one of the nuclei of the dikaryon. Since ‘absence of proof is not the proof of absence” you need to be more careful in drawing any conclusions from this. So, for example, in the abstract you should rephrase “We discovered an individual which appears to have a mating type locus present in one nucleus of the dikaryon and absent from the second nucleus.” to “We discovered mating type sequences in some strains, but in one of the dikaryotic strains, we were able to find a mating-type locus in one of its nuclei, but not in the other”.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "246576", "date": "27 Feb 2024", "name": "Julieta Alvarez Manjarrez", "expertise": [ "Reviewer Expertise Mycology", "taxonomy", "fungal ecology", "ectomycorrhiza", "tropical ecology" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript compares two saprotrophic species Amanita thiersii and A. foetens. The authors hypothesized that they could be the same species because they present morphological similarities and nutrition mode. Amanita thiersii was described from Texas and now its consider an invasive species, while A. foetens inhabits in Argentina. After exhaustive methods including public observation databases and fresh specimens, they conclude they are different species but sister clades. The information is well written however for me it is uncomprehensive the justification of using genomics for a simple taxonomic question. A more easy way was to amplify the barcode and/or other DNA regions would be enough. Additionally, subtle but observable features help to distinguish between the two species. With the obtained data they confirmed they were two different species closely related. And because the data did not help to elucidate the potential introduction of A. thiersii, I think the manuscript should be written just about the differences between the two species rather than left an unanswered question about A. thiersii distribution.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "246580", "date": "30 Aug 2024", "name": "Martin P A Coetzee", "expertise": [ "Reviewer Expertise Fungal systematics", "fungal genomics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn their study, Dunkirk and colleagues investigated the taxonomy and biogeography of Amanita thiersii and A. foetus. Amanita thiersii was described from Texas and is present in the eastern United States and Mexico, while Amantita foetense was described from Argentina. The basidiocarps of both species are morphologically very similar. The current question is whether A. theirsii is an introduced and invading fungus, or native and expanding its range. The working hypothesis of this study was that A. thiersii is an A. foetens and that it was introduced into North America. The authors, therefore, investigated whether the two species are conspecific and, if A. thiersii is a different species from A. foetens, whether it is native and spreading. To test this hypothesis, the authors used distribution data from iNaturalists and Mushroom Observer, conducted phylogenetic studies, and compared the phenotypic characteristics of the two species. They also investigated the mating locus of the two species. Based on their results, the authors concluded that A. thiersii and A. foetens are two different species. However, it is still unclear if A. thiersii is native or introduced into the U.S.A. The HD1 and HD2 mating genes are present, but one dikaryotic individual had the HD1 present in one nucleus but not the second nucleus.\nI enjoyed reading the paper and found the results interesting. The manuscript is well written, in my opinion. However, I do have some recommendations for the authors and some questions, which are outlined below.\nI am concerned about the small sampling size to determine if there are one or two species. However, this is not unusual in fungal taxonomy. Firm conclusions can, therefore, not be drawn, but the results set a working hypothesis for future studies. The authors might want to address this in their discussion section.\nThe authors should provide some background information regarding the mating system of Amanita in the Introduction section. The HD1 and HD2 genes are typically associated with the one mating type locus in Basidiomycota, while the second locus has the pheromones and pheromone receptors. Since the authors only searched for the HD1 and HD2 genes, the question is, what about the second locus, or are the pheromone and pheromone receptors linked to the HD1 and HD2 genes at the same mating type locus? Is it tetrapolar or bipolar, is heterothallic or homothallic?\nThe authors could have used the term phylogenomic trees for the BUSCO-gene trees. Or at least add the word phylogenetic. For example, BUSCO-gene phylogenetic tree. Still, I recommend using the term phylogenomic tree as the analysis was based on a phylogenomic approach.\nI do not think trees generated with ASTRAL are consensus trees. These should be referred to as species coalescent trees. A consensus tree is generated from a set of trees, but it only shows the agreement among the trees. This is different from what ASTRAL does.\nPage 5: “Saprotrophic Amanita species are closely related to each other and basal to ectomycorrhizal Amanita (Wolfe et al. 2012)”. This is wrong; in the paper, they are shown as two monophyletic sister groups.\nPage 7: Change “… used the ModelFinder tool to find the best nuclear or mitochondrial substitution model …” You meant the best nucleotide substitution model; there is no model for substituting the nucleus or mitochondria. Similarly, you use an amino acid substation model if amino acid sequences were used.\nPage 7: To get statistical support, 1000 bootstraps using the ultrafast bootstrap approximation method were used. When using an ultrafast bootstrap, a Shimodaira-Hasegawa-like (SHL) approximate likelihood ratio test replicates is recommended in addition to the bootstrap analysis. It may not affect the conclusions, but it is something to consider in the future.\nPage 7: The authors stated that they verified the results of their phylogenetic method using concatenated data by also creating a consensus tree using ASTRAL. I do not think that it would really verify the results, as the supertree is generated from individual five locus trees. I am unsure how they obtained the gene trees, as the data available were very patchy for most of the genes (Table 1). There are 17 strains in Table 1, data only from the nulLSU.28S is complete, while the rest have less than 50% sequences available. What was the effect of this on the Astral analysis? I recommend following a Bayesian approach, which often performs better with missing data, and is an alternative to verify the results. Please state what version of ASTRAL was used.\nPage 7: It is not clear what the authors meant with “To contextualize the genomes of A. thiersii 10802, A. foetens 10801 and Amanita sp. 10175 within the genus Amanita, …” The data was used to construct phylogenomic trees and to determine concordance among the gene trees, which are then related to genealogical concordance (i.e. genealogical concordance phylogenetic species recognition). How did this contextualize the genome?\nOn page 10 the heading reads “A. thiersii continues to expand its range in North America, and collections are clustered around urban centers” My issue here is with the word “continues”. How does one know that it is continuing to expand its range? Also, the fact that it was not reported on iNaturalists or Mushroom Observer does not mean it is not already in an area outside its current range. Perhaps this can be addressed and better discussed in relation to the methods used by Wolf et al. (2012) in which historical collections were used to follow the presence/absence of the fungus over time.\nPage 11: The authors stated, “However, A. thiersii specimens from North America form a separate monophyletic clade from A. foetens 10801 and Amanita sp. 10175.” A clade is, by definition, monophyletic; remove the word “monophyletic” before clade at all instances.\nPage 12: The authors stated that the HD1 locus was not found in the nucleus of some monokaryotic offspring of a dikaryotic strain. While there is precedent for this finding (Wang et al. 2023), do the methods used to find the HD1 gene enable proving that it is not present? How would it have been removed if it was indeed absent, and what would the effect be?\nThe link to Dryad: Mushroom Observations of Amanita thiersii and A foetens, https://doi.org/10.5061/dryad.7h44j1008, gives an error and is not accessible.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-862
https://f1000research.com/articles/12-859/v1	20 Jul 23	{ "type": "Case Report", "title": "Case Report: Abdominal variant of Lemierre’s syndrome", "authors": [ "Ryan Pollard", "Vashistha Patel", "Shreya Patel", "Kenny Murray", "Ryan Pollard", "Shreya Patel", "Kenny Murray" ], "abstract": "Lemierre's syndrome is a rare condition characterized by Fusobacterium bacteremia from an oropharyngeal source with septic emboli causing internal jugular vein (IVJ) thrombophlebitis in an otherwise young and healthy host. Rare variants of this rare disease have been described impacting the gastrointestinal, pulmonary, neurologic, musculoskeletal, soft tissue, and genitourinary systems. We discuss a case of an abdominal variant of Lemierre's syndrome. An otherwise young and healthy male presented with two pyogenic hepatic abscesses, Fusobacterium necrophorum bacteremia, and local hepatic venous thrombosis. The hepatic abscesses were percutaneously drained, he received broad-spectrum antibiotics and therapeutic-level anticoagulation, and he showed marked clinical improvement over a six-day hospital course. He was discharged with four weeks of daily oral and intravenous (IV) antibiotics, six months of direct oral anticoagulation, and close follow up. Clinicians should consider thrombophlebitis in more anatomical locations than the IVJ which is found classically in Lemierre’s syndrome in the setting of Fusobacterium bacteremia.", "keywords": [ "Fusobacterium necrophorum", "Bacteroides thetaiotaomicron", "Lemierre's Syndrome" ], "content": "Background\n\nFusobacterium infections have been described in the gastrointestinal, pulmonary, neurologic, musculoskeletal, soft tissue, and genitourinary systems.1–7 This case highlights a rare variant of a rare disease. However, it highlights a clinically important principle that variants of Lemierre’s syndrome exist and should be considered in the setting of Fusobacterium bacteremia. When Fusobacterium bacteremia is identified, investigation of venous patency local to the primary infection site is warranted. The foundation for the discovery of Lemierre’s syndrome was laid when Fusobacterium, a gram-negative rod-shaped anaerobe, was discovered in 1887 by Friedrich Loeffler.8 Bang and Schmorl further classified the bacteria in animal studies.9,10 Subsequently, Andre Lemierre discovered Fusobacterium in humans as described in his landmark dissertation on anaerobes in 1936.11 This set the stage for the discovery of a rare disease now which carries the eponym Lemierre’s syndrome. Lemierre’s syndrome is characterized by septic thrombophlebitis of the IJV due to an oropharyngeal primary infection with Fusobacterium in an otherwise young and healthy adult.11 Patients with Lemierre’s syndrome also present with fever, sore throat, exudative tonsillitis, and unilateral neck swelling and tenderness.3 Treatment generally includes anaerobic coverage with an antibiotic resistant to beta-lactamase.10 Anticoagulation for IJV thrombosis is controversial. Variants of Lemierre’s syndrome are rare and occur when the primary Fusobacterium infection develops in locations other than the oropharyngeal cavity.12 They are also characterized by septic thrombophlebitis local to the primary infection. Fusobacterium bacteremia is rare with an incidence of 0.99 in 100,000.12 For decades Fusobacteriae have been thought to be part of the normal oropharyngeal and appendiceal flora; however, a recent study published in 2007 suggests it is pathogenic.13 The appendix is the next most common location of a Fusobacterium infection.\n\n\nCase presentation\n\nA 38 year old healthy Hispanic male construction worker presented to the emergency department of Shelby Baptist Medical Center (SBMC) with one week of constant, sharp, right-sided flank pain, three days of fever and chills, and one day of a severe headache. He reported no chronic medical conditions, current medications, or supplements. He endorsed taking an unknown blood thinner for 60 days two years prior to his presentation for an unspecified reason. He had an appendectomy 10 months prior, recent travel to South America six months prior, and worked temporarily in a paper mill for multiple months within the past year. He denied allergies, tobacco use, alcohol use, or illicit drugs. He endorsed a balanced diet and regular exercise. The patient had two recent hospitalizations at other facilities for similar symptoms without resolution. The details of these hospitalizations were not accessible.\n\nWhile at SBMC, the patient was diagnosed with two pyogenic hepatic abscesses, one of which was drained under computed tomography (CT) guidance and the other was not drained but treated with broad-spectrum IV antibiotics due to its proximity to significant anatomical structures. Blood cultures at SBMC grew Fusobacterium necrophorum (pathogenic rod-shaped gram-negative anaerobe), a hepatic abscess aspirate grew an unidentified gram-negative anaerobe, and urine and ascites cultures were negative. The patient was discharged from SBMC on oral amoxicillin-clavulanic acid and oral metronidazole.\n\nHowever, one day later, the recurrence of his symptoms led him to the emergency department (ED) of Grandview Medical Center (GMC). On presentation, his temperature was 100.3° Fahrenheit, his heart rate was 131 beats per minute (bpm), his blood pressure was 131/88 millimeters of mercury, and his respiratory rate of 18 per minute. In the ED an initial history, review of systems, physical exam, labs, and imaging were performed as detailed below.\n\nPhysical examination at the time of admission revealed a well-appearing male in his 30s in no acute distress. His head and neck were normocephalic, atraumatic, and supple without lymphadenopathy. His oropharynx appeared non-erythematous with moist mucous membranes, and his trachea was midline without palpable masses. He was able to phonate in full sentences. He had normal chest wall expansion with clear breath sounds at both lung fields without wheezes, rhonchi, or crackles. Cardiac auscultation and pulses in his bilateral upper and lower extremities were within normal limits. His abdomen had laparoscopic surgical scars, but was soft, non-tender, and non-distended with normal bowel sounds. The neurological exam including cranial nerves, strength, sensation, and reflexes was normal. A complete blood count (CBC) showed an elevated white count of 26.1 with neutrophilic predominance. His hemoglobin, hematocrit, and platelet counts were within normal limits. A comprehensive metabolic panel showed creatinine 1.44, glucose 199, sodium 133, potassium 3.8, calcium 8.1, alkaline phosphatase 164, aspartate aminotransferase (AST) 35, alanine aminotransferase (ALT) 84, and total bilirubin 0.8. Additional labs showed lactic acid 5.2 and lipase 871. One sample of stool ova and parasite studies was negative (guidelines recommend sending stool samples on three consecutive days, and daily stool samples for three days were ordered, but only one day was collected). Stool culture was pan-negative (including Salmonella, Shigella, Campylobacter, E. coli 0157, Aeromonas, Yersinia, and Shiga Toxin 1 or 2). Hepatitis panel was pan-negative (including Hepatitis A Ab IgM, Hepatitis B Core Ab IgM, Hepatitis B Surface Ag, and Hepatitis C Ab), and HIV Ag/Ab was negative. A CT with contrast of his chest, abdomen, and pelvis was obtained that showed a 2.8 cm × 3.3 cm × 2.8 cm hepatic abscess at the junction of segments 7 and 8 of the liver complicated by local hepatic venous thrombosis (Figures 1 and 2). Blood cultures drawn at GMC were negative. Interventional Radiology (IR) was consulted for drainage of hepatic abscess. The sample from hepatic abscess grew Bacteroides thetaiotaomicron (commensal rod-shaped gram-negative anaerobe)–though it is important to note that he had recently received inpatient antibiotic coverage from SBMC with outpatient antibiotic coverage at discharge.\n\nThe patient was admitted to the intensive care unit and his treatment plan involved broad-spectrum coverage with administration of IV vancomycin, cefepime, and metronidazole. Further, he received aggressive IV fluid resuscitation according to sepsis guidelines. Once stabilized, his hepatic abscess was drained under CT guidance by IR. We consulted infectious disease who recommended four weeks of antibiotic coverage with IV ceftriaxone 2 grams daily at an infusion clinic and four weeks of oral metronidazole 500 milligrams (mg) four times daily with close outpatient follow up at an infectious disease clinic. A peripherally inserted center catheter (PICC) was placed at discharge for antibiotic infusions.\n\nFor hepatic venous thrombosis local to the patient's hepatic abscesses, he was started on a therapeutic heparin drip at admission. This was held before the hepatic abscess was drained to avoid bleeding complications. Subsequently, he received therapeutic anticoagulation with apixaban. We planned to keep the patient on a six-month course of anticoagulation (apixaban 10 mg) oral twice daily for seven days followed by apixaban 5 mg oral twice daily for six months with reevaluation of the need for continuing anticoagulation after six months.\n\nThe patient's lactic acidosis, elevated lipase, and acute kidney injury resolved with IV fluids over his six-day hospital course.\n\nThe patient’s follow-ups and outcomes are unknown as he is followed by a primary care provider (PCP) outside of our network.\n\n\nDiscussion\n\nWe propose the most likely source of the patient’s infection was his recent appendectomy. Kanellopoulou, et al. found that appendicitis is the most common cause of pylephlebitis, or infectious suppurative thrombophlebitis of the portal venous system,14 and abdominal surgeries have been shown to lead to new cases of the abdominal variant of Lemierre’s syndrome.2,15\n\nIn 2017, Jayasimhan et al.16 conducted a systematic review finding 48 cases of hepatic abscesses associated with Fusobacterium. Ten of these cases were either confirmed or suspected to be due to a lower gastrointestinal infection. Treatment was highly successful with complete resolution in 47 of 48 cases. Treatment consisted of hepatic abscess drainage plus extended-length medical therapy with beta-lactams in combination with metronidazole, monotherapy with metronidazole, carbapenems, or fluoroquinolones. In the sole case with a poor outcome, the patient’s Fusobacterium bacteremia was not treated because it was not discovered until post-mortem.16 Fusobacterium is a rare cause of pylephlebitis, an inflamed thrombosis of the portal vein. Pylephlebitis is more frequently caused by: Streptococcus viridans, Escherichia coli, and Bacteroides fragilis.17 Historically, death rates of pylephlebitis have ranged from 50 to 80 percent but have improved to 25 percent with earlier detection and more aggressive antibiotic therapy.18 One theory for the significantly better outcomes in Fusobacterium infections is the absence of antibiotic resistance because the infections are so rare. However, due to the difficulty of making the diagnosis of abdominal variant of Lemierre’s syndrome, it is reasonable to assume that multiple cases are likely missed, and selection bias might result in an overly optimistic prognosis.\n\nThere is some controversy about anticoagulation in pylephlebitis. A systematic review found similar mortality rates in the “antibiotic alone” and “antibiotic plus anticoagulation” groups.14 The same review found the mortality rate to be zero for the “anticoagulation alone” group.14 However, the number of cases in this review is too small to make definitive recommendations. Considering these mixed results and due to the historical benefit of anticoagulation in the setting of thrombosis, most authors favor early anticoagulation.19\n\nStrengths of our diagnosis include a rational explanation of the most likely etiology for the patient’s presentation and course considering the specificity of a Fusobacterium infection. A confirmed Fusobacterium bacteremia in the setting of two pyogenic hepatic abscesses with localized hepatic venous thrombophlebitis after a recent appendectomy supports a diagnosis of abdominal variant of Lemierre’s syndrome.\n\nWeaknesses in our case include the lack of Fusobacterium found in the patient’s hepatic abscess aspirates and the possibility of alternative diagnoses (though thought to be highly unlikely). At SBMC we confirmed the presence of Fusobacterium bacteremia and a gram-negative rod from the patient’s hepatic abscess aspirate. This matches the profile of Fusobacterium, but no final microbiological identification was determined. At GMC the hepatic abscess aspirate grew Bacteroides thetaiotaomicron, a commensal gram-negative anaerobe, with a negative blood culture. However, these cultures were drawn after the administration of IV and oral antibiotics from SBMC. Additionally, the timing of the appendectomy to presentation (nine months) could suggest another etiology. Fusobacteria infections may take weeks-to-months to develop into abscesses partly because anaerobic bacteria grow slower than aerobic bacteria. However, nine months is a relatively long course for an abscess to form and become symptomatic. Lastly, only one of the three stool samples ordered was collected. Based on guidelines, parasites like Entamoeba histolytica which often cause liver abscesses in the setting of recent travel can be missed with just one stool sample.\n\n\nConclusion\n\nThis case supports the need for clinicians to consider additional anatomical locations (including the liver and portal veins) for infectious thrombophlebitis in the setting of Fusobacterium bacteremia in addition to Lemierre’s syndrome’s traditional locations affecting the oropharynx and IJV. When Fusobacterium bacteremia is identified, clinicians should evaluate the vasculature local to the primary infection for thrombophlebitis. It is important to recognize and treat Fusobacterium bacteremia early because antibiotic resistance has not developed, and current treatments have shown universal resolution16 while the mortality rate for pylephlebitis is 25%.19\n\n\nEthics and consent\n\nWritten informed consent for publication of clinical details and images was obtained from the patient.", "appendix": "Data availability\n\nData availability is not applicable to this article as no new data were created or analyzed in this study.\n\n\nReferences\n\nMellor TE, Mitchell N, Logan J: Lemierre's syndrome variant of the gut. BMJ Case Rep. 2017; 2017: bcr2017221567. Published 2017 Oct 20. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFuruncuoglu Y, Oven BB, Mert B, et al.: Abdominal Variant of Lemierre's syndrome in a Patient with Pancreatic Adenocarcinoma. Medeni Med. J. 2021; 36(1): 58–62. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHadjinicolaou AV, Philippou Y: Lemierre’s syndrome: A Neglected Disease with Classical Features.Case Rep. Med.2015; 2015: 4. Article ID 846715. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBouziri A, Douira W, Khaldi A, et al.: Neurological variant of Lemierre's syndrome with purulent meningitis: a case report and literature review. Fetal Pediatr. Pathol. 2013; 31(1): 1–6. PubMed Abstract \| Publisher Full Text\n\nHarris J, Kaeding C, et al.: Severe Musculoskeletal Infection Variant in Lemierre’s syndrome. Orthopedics. 2010; 33(10): 774. PubMed Abstract \| Publisher Full Text\n\nBekelman J, Francis J, et al.: Lemierre’s Variant. Lancet Infect. Dis. 2004; 4(8): 518. Publisher Full Text\n\nPol H, Guerby P, Duazo Cassin L, et al.: Dangerous Liaisons: Pelvic Variant of Lemierre syndrome by Right Common Iliac Vein Thrombophlebitis After Sexual Intercourse. J. Low. Genit. Tract Dis. 2017; 21(3): e37–e39. PubMed Abstract \| Publisher Full Text\n\nPappenheimer AM Jr: The diphtheria bacillus and its toxin: a model system. J. Hyg (Lond). 1984; 93(3): 397–404. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHagelskjaer Kristensen L, Prag J: Human necrobacillosis, with emphasis on Lemierre's syndrome. Clin. Infect. Dis. 2000; 31(2): 524–532. PubMed Abstract \| Publisher Full Text\n\nBrazier JS: Human infections with Fusobacterium necrophorum. Anaerobe. 2006; 12(4): 165–172. Publisher Full Text\n\nLemierre A: On certain septicaemias due to anaerobic organisms. Lancet. 1936; 227(5874): 701–703. Publisher Full Text\n\nHagelskjaer Kristensen L, Prag J: Lemierre's syndrome and other disseminated Fusobacterium necrophorum infections in Denmark: a prospective epidemiological and clinical survey. Eur. J. Clin. Microbiol. Infect. Dis. 2008; 27(9): 779–789. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRiordan T: Human infection with Fusobacterium necrophorum (Necrobacillosis), with a focus on Lemierre's syndrome. Clin. Microbiol. Rev. 2007; 20(4): 622–659. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKanellopoulou T, Alexopoulou A, Theodossiades G, et al.: Pylephlebitis: an overview of non-cirrhotic cases and factors related to outcome. Scand. J. Infect. Dis. 2010; 42(11-12): 804–811. PubMed Abstract \| Publisher Full Text\n\nTariq T, Badwal K, Wilt J, et al.: Fusobacterium-Associated Pylephlebitis Complicated by Hepatic Abscess Following Roux-en-Y Gastric Bypass Surgery–Gastrointestinal Variant of Lemierre syndrome: A Case Report. Infect. Dis. Clin. Pract. 2020; 28(1): 48–50. Publisher Full Text\n\nJayasimhan D, Wu L, Huggan P: Fusobacterial liver abscess: a case report and review of the literature. BMC Infect. Dis. 2017; 17(1): 440. Published 2017 Jun 20. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHanda S, Panthagani A, Buddhdev A: Abdominal Lemierre syndrome–An Odd Presentation of a Rare Entity. J. Sci. Innov. Med. 2020; 3(3). Publisher Full Text\n\nWong K, Weisman DS, Patrice KA: Pylephlebitis: a rare complication of an intra-abdominal infection. J. Community Hosp. Intern. Med. Perspect. 2013; 3(2). Published 2013 Jul 5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChoudhry AJ, Baghdadi YM, Amr MA, et al.: Pylephlebitis: a Review of 95 Cases. J. Gastrointest. Surg. 2016; 20(3): 656–661. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "231202", "date": "03 Jan 2024", "name": "Zhou-Xiong Xing", "expertise": [ "Reviewer Expertise Gut microbiota and critical care" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1.Title:Abdominal variant of Lemierre’s syndrome Comments: The title does not summarize the main findings of the case. Lemierre’s syndrome contains the hallmark of venous thrombosis. The local hepatic venous thrombosis should be included in the title. Lemierre’s syndrome is generally defined as the thrombosis in the IJV. I an not sure other venous thrombosis can be called Lemierre’s syndrome.\n2. Are enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Comments: I suggest a timeline of the clinical course should be given.\n3.Is sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Comments: Liver abscess is prone to occur in patients with immunodeficiency. Please clarify the potential immunodeficiency of the patient, such as HIV. I suggest how the Fusobacterium bacteremia contribute to the formation of the thrombosis should be discussed.\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": [] } ]	1	https://f1000research.com/articles/12-859
https://f1000research.com/articles/12-858/v1	20 Jul 23	{ "type": "Research Article", "title": "All ions must serve: The role of various regimes of data acquisition in joint classifier for intraoperative mass spectrometry-based glial tumour identification  ", "authors": [ "Stanislav I. Pekov", "Denis S. Zavorotnyuk", "Anatoly A. Sorokin", "Denis S. Bormotov", "Mariya M. Derkach", "Dmitrii N. Starkov", "Igor A. Popov", "Denis S. Zavorotnyuk", "Anatoly A. Sorokin", "Denis S. Bormotov", "Mariya M. Derkach", "Dmitrii N. Starkov", "Igor A. Popov" ], "abstract": "Background: Ambient ionisation mass spectrometry, in combination with machine learning techniques, provides a promising tool for rapid intraoperative tumour tissue identification. However, deficiency of non-tumour control samples leads to the classifiers overfitting, especially in neurosurgical applications. Ensemble learning approaches based on the analysis of multimodal mass spectrometry data are able to overcome the overfitting problem through the extended time of data acquisition. In this work, the contribution of each regime of the data acquisition and the requirements for the metrics for further mass spectrometry set-up optimisation are evaluated. Methods: Two independent datasets of the multimodal molecular profiles, a total of 81 glial tumour and non-tumour pathological tissues, were analysed in a cross-validation set-up. The XGboost algorithm was used to build classifiers, and their performance was evaluated using different testing and validating sets. The individual classifiers for each mass spectrometry regime were aggregated into joint classifiers. The impact of each regime was evaluated by the exclusion of specific regimes from the aggregation. Results: The aggregated classifiers with excluded regimes show lower accuracy for most, but not all, excluded regimes. False positive rates have been found to be increased in most cases proving the strong effect of the ensemble learning approach on the overcoming of the “small sample size” problem. Conclusions: The impact of each group of regimes – with different ion polarity, resolution or mass range of spectra was found to be non-linear. It might be attributed to biochemical reasons as well as to the physical limitation of mass analysers. The required metrics for the evaluation of each regime contribution to the classification efficiency should be a numerical estimation of how the classifier depends on any given regime and could not be estimated only by excluding any group of regimes at all.", "keywords": [ "Mass spectrometry", "ambient ionisation", "glial tumours", "ion polarity", "ion suppression", "lipids" ], "content": "Introduction\n\nThe expanding capabilities of ambient ionisation mass spectrometry make metabolic molecular profiling a promising approach for various life science and medical applications.1,2 The simplicity and rapidity of sample collection, processing, and analysis are the key factors explaining the growing interest in ambient ionisation methods for diagnostics tasks inside and outside hospitals.3–7 On the other hand, the lack of sample purification or separation makes the resulting mass spectra interpretation a challenging task. It arouses interest in the application of machine learning techniques for data analysis.7–9 Indeed, molecular profiles obtained with ambient ionisation mass spectrometry is a multidimensional data which, however, represents only a part of the molecular composition of an analysed biological specimen. The different ionisation potential leads to competition for charge carriers during the ionisation process, while the limited dynamic range of the detector confines the simultaneous detection of all ions present in a wide range of concentration. Thus, the variety of the detected molecules (chemical space) became restricted, so only partial information on the underlying biological processes could be considered during the analysis.\n\nOncological surgery, especially neurosurgery, is one of the most demanding fields where new intraoperative tissue classification techniques are urgently needed.10–13 The resection volume is the most important characteristic for the patient outcome since complete resection significantly reduces the likelihood of the tumour reoccurrence. In the meantime, excessive resection is not appropriate in neurosurgery, especially in cases where functional centres of the central nervous system are affected by the malignancy. Multiple studies demonstrate the potential of an ambient ionisation molecular profiling implementation as an additional decision-making technique for neurosurgery.3,14,15 The classification of the resected tissue in these studies is based either on the lipid alterations16 accompanying the malignant transformation of cells or on the presence of specific water-soluble metabolites such as 2-hydroxyglutarate;16–18 however, the detection of different classes of molecules requires the specific ionisation regimes: ion polarities and mass ranges. Further translation of such studies into clinical practice not only requires the translation of methods from high-resolution mass spectrometers, which are common in the scientific institutes, to low-resolution instruments that prevail in clinical practice,19 but will confront the problem of high natural variability of the molecular composition of malignant and, especially, healthy tissues. The realisation of research on cells or animal models is not suitable in the case of metabolic profiling as cell cultures do not represent the physiological environment of cells, while an animal model does not provide sufficient genetic intra- and intertumoural variabilities.20\n\nThe development of classification models for intraoperative glial tumour tissue identification is suffering heavily from the limited availability of control samples, which could not be easily obtained due to medical and ethical reasons. In combination with the aforementioned limitations, it results in a “small sample size” problem which substantially reduces the accuracy of the classification models. As it was demonstrated earlier,21 the joint classifier that combines multiple weak learners fitted on the mass spectrometric data of various regimes boosts the classification accuracy significantly but parallel acquisition of multimodal data may slow down the analysis procedure substantially. Ensemble learning methods provide an opportunity to reduce the data set unbalancing impact on the classification model’s characteristics.22 Indeed, the concurrent consideration of ions detected in different regimes complements the chemical space with molecules of various classes, which is necessary to account for the natural molecular variability of intact and malignant tissues. In this work, we analyse the contribution of each regime of the data acquisition in attempt to evaluate their role in the joint classifier proposed and determine the requirements for the metrics for further mass spectrometry set-up optimisation.\n\n\nMethods\n\nThe clinical samples were analysed under an approved N.N. Burdenko National Scientific and Practical Center for Neurosurgery (NSPCN) Institutional Review Board protocol (order Nr. 131 from 17.07.2018) in accordance with the Helsinki Declaration as revised in 2013. The study was conducted in accordance with the recommendations of the ethical committee of the N.N. Burdenko NSPCN order Nr.40 from 12.04.2016 revised by order Nr. 131 from 17.07.2018. A signed written informed consent form explicitly noting that all removed tissues can be used for further research was obtained from all patients.\n\nTwo independent data sets of human glial tumour and non-tumour pathological tissues were analysed in this work. The first data set consisted of 55 biopsy samples from 41 glioblastoma patients and eight samples from eight non-tumour patients. The second, validation, data set consisted of 26 biopsy samples with a known tumour cell percentage (ranging from 0% to 100%) from 11 glioblastoma patients.3,21 It was specifically noted that all samples from the same patient were included only in one of the aforementioned data sets. The data sets were acquired with inline cartridge extraction mass spectrometry approach10,23 using a hybrid high- and low-resolution LTQ Orbitrap XL ETD mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) as described in a preceding work describing the proposed ensemble learning approach.21 Briefly, the brain tumour tissue sample was placed inside a disposable cartridge arranged in front of the vacuum interface of the mass spectrometer. The high voltage and solvent flow consisted of 3:3:3:1 (vol.) methanol:isopropanol:acetonitrile:water supplemented with 0.1% (vol.) acetic acid and was applied to the cartridge to perform extraction and ionisation of the molecules of interest. HPLC-grade solvents and acid were obtained from Merck (Merck KGaA, Darmstadt, Germany). Each molecular profile consisted of spectra acquired in eight different regimes of measurement – all combinations of (1) positive or negative ion mode; (2) high- (Orbitrap mass analyser, resolution 30,000 FWHM at m/z = 400) or low-resolution (linear ion trap mass analyser); (3) wide (100–2000) or narrow (500–1000) m/z range.21,24\n\nAll simulations were performed in a standard machine-learning cross-validation set-up. The spectra were normalised, aligned, and all peaks presented in less than ten scans per diagnosis were deleted. The resulting spectra were transformed into a feature matrix with individual scans as rows and peak intensities as columns.21 For the first data set, the resulting matrix rows were divided into training and testing subsets in a 60/40 ratio, ensuring that scans from the same tissue fragment are always assigned to the same set. For each analysed combination of regimes, 10% of all corresponding rows from the training set matrix were chosen at random and were used for the optimisation of XGboost algorithm metaparameters. An optimal set of metaparameters were then used to build a classifier using the training subset, and the classifier performance was evaluated using a testing subset. To assign a class (tumour or non-tumour) to the sample, predictions obtained for each scan corresponding to the sample were aggregated either using voting (Vote) or mean probability (MeanP) calculation.21 In voting, the class predicted by the majority of classifiers for the scan became the final prediction. In probability averaging, the probability of belonging to each class was calculated using XGboost for each scanб and these probabilities were averaged. These aggregated results characterise clinical samples, with all spectra from a sample contributing to the final prediction.21\n\nThe mass spectra data were preprocessed using the R environment version 4.0.4 with the R packages MALDIquant25 and the models analysis was performed with the KNIME Analytics Platform ver. 4.5.2. The classification algorithm was realised as the KNIME workflow26 and is available at the KNIME Community Hub via the link https://kni.me/w/dWtqs1_6S2XVP6EG.\n\n\nResults\n\nThe initial data set was used to train classifiers to evaluate the contribution of various regimes. The different subsets were selected from all data for each of the following:\n\n• all data obtained with positive or negative ion mode (despite the resolution and mass range)\n\n• all data obtained in high- or low-resolution (despite the polarity and mass range)\n\n• all data obtained in narrow or wide mass range (despite the polarity and resolution)\n\nThe results obtained on testing and validation data sets are shown in Table 1. For all the classifiers, the accuracy was found to be lower than for the joint classifier for all regimes.21 The accuracy obtained for the validation set was lower than for the corresponding training sets. However, the specificity and sensitivity of classifiers change variously through all the variations. The exclusion of positive polarity from the classification process significantly increases the false positive results, which means that many non-tumour samples have been incorrectly identified as tumour samples. In the case of the negative ion mode exclusion, the same effect was observed only for vote-aggregated classifies; however, the probability-based classifier trained solely on positive ion mode data did not show significant accuracy alteration but initially showed a poor false positive rate. Comparison of the impact of different resolutions on the classification demonstrates the tendency of false negative results for the probability-based classifier trained on high-resolution data in contrast to the tendency of false positive results for vote-based. In the case of low-resolution data, both aggregation types show some tendency to false positive tumour identification. The exclusion of any mass range from the data leads to a substantial loss of accuracy due to an increased rate of false positive identification. Such an effect is especially strong in the case of the analysis of narrow mass range data.\n\nAccuracy – the ratio of correctly identified samples to all samples; sensitivity – the ratio of correctly identified tumour samples to all tumour samples; specificity – the ratio of correctly identified non-tumour pathology samples to all non-tumour pathology samples.\n\n\nDiscussion\n\nThe impact of various data acquisition regimes on the classification model is not unexpected, but the reasons for declined accuracy are directly related to the chemical and physical limitations of each experimental regime. The most expected difference is obviously interconnected with the polarity of the data.27 Indeed, positive ions spectra are characterised by the presence of various types of phospholipids28 such as phosphatidylcholines, phosphatidylethanolamines, and phosphatidylserines. Other lipids, such as phosphatidic acids and phosphatidylinositols, could be ionised solely in negative ion mode, as well as many of the metabolites, including specific oncometabolite 2-hydroxyglutarate16–18 and nurometabolite N-acetylaspartate.16,29 The lipid metabolism is considerably altered during malignancy resulting in significant changes in the lipid content of the cells. Thus, the classifier based on one polarity only will be characterised with decreased accuracy. For all single-polarity classifiers, the decreased specificity (i.e. the rate of false positive identifications) and increased sensitivity (i.e. the rate of false negative identifications) is observed, which means the aggregation of different polarities into a single classifier substantially helps to overcome overfitting caused by a small sample size problem.\n\nHigh-resolution mass spectra could be transformed to the same dimension as the low-resolution data,19 but some details might be lost during the transformation. However, on the particular data set of glial tumour tissues analysed in this study, classifiers based on the high-resolution data show a significantly higher loss of accuracy during validation on the samples obtained from patients of the second cohort. The increased efficiency of the tumour tissue classification with the high-resolution-based models originated from the richer feature matrix as a high-resolution mass analyser provides peak-rich spectra, but the same fact negatively affects the classification results for validation data set as high-resolution-based classifiers are more sensitive to the natural molecular variability of the tissues.\n\nLimited dynamic range of various mass analysers could also affect the classification efficiency. The wide mass range allows the accumulation of more ions in each mass spectrum, but some minor ions could be lost due to the limited capacity of ion traps.30 The narrow mass range (from m/z 500 to 1000) is able to detect as many lipids as possible, which could be useful for the determination of the affected metabolic alterations in various lipid classes. However, it was found that the exclusion of the wide mass range from the training data set significantly reduces the classification accuracy. The model became substantially overfitted as the rate of false positive identifications increases significantly. The observed alterations between the lipid composition of the tumour and non-tumour tissues28 affect relatively abundant lipids, thus providing changes in the intensities of the relatively high peaks in mass spectra which could be determined on a wide mass range data. The contribution of the metabolites, which are mostly small molecules,16 to classification accuracy, appears to be important as the classifiers trained on narrow mass range data only lose accuracy more noticeably compared to the wide mass range classifiers.\n\nThe obtained results demonstrate the non-linear contribution of each data acquisition regime to the effectiveness of an aggregated classifier regardless of the aggregation method implemented. As the underlying reasons for the observed results are interconnected with the biochemical background of the malignancy and the physical limitations of the method, it is not possible to evaluate the impact of any of the regimes directly and independently. Since the aggregation of multiple regimes improves the accuracy of the classification, it is required to collect a lot of data in every experiment, which means an increase in the time required for data acquisition for each sample. As it is opposed to the main idea of ambient ionisation mass spectrometry – rapidity of the analysis, it is crucial to develop the method to assess the impact of each regime. The required metrics of such an impact should be a numerical estimation of how the classification accuracy and other characteristics change if any of the given regimes are included or excluded from the consideration, which allows one to determine the optimal set of regimes required for the accurate and high-performance implementation of ambient ionisation molecular profiling in clinical practice. It is proposed that the Shapley value31,32 calculation could be found as an appropriate metric; however, the current size of the data sets is supposed to be insufficient to make such calculations at this time, so the further collection of both tumour and control tissues is still required.", "appendix": "Data availability\n\nThe data described in the manuscript will not be made available in accordance with the indication of the N.N. Burdenko National Scientific and Practical Center for Neurosurgery Ethics Committee.\n\n\nReferences\n\nFeider CL, Krieger A, DeHoog RJ, et al.: Ambient Ionization Mass Spectrometry: Recent Developments and Applications. Anal. Chem. 2019; 91(7): 4266–4290. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi L-H, Hsieh H-Y, Hsu C-C: Clinical Application of Ambient Ionization Mass Spectrometry. Mass Spectrometry. 2017; 6(2): S0060–S0060. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPekov SI, Bormotov DS, Nikitin PV, et al.: Rapid Estimation of Tumor Cell Percentage in Brain Tissue Biopsy Samples Using Inline Cartridge Extraction Mass Spectrometry. Anal. Bioanal. Chem. 2021; 413(11): 2913–2922. PubMed Abstract \| Publisher Full Text\n\nLee C-W, Su H, Shiea J: Potential Applications and Challenges of Novel Ambient Ionization Mass Spectrometric Techniques in the Emergency Care for Acute Poisoning. TrAC Trends Anal. Chem. 2022; 157: 116742. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKöhler M, MacHill S, Salzer R, et al.: Characterization of Lipid Extracts from Brain Tissue and Tumors Using Raman Spectroscopy and Mass Spectrometry. Anal. Bioanal. Chem. 2009; 393(5): 1513–1520. PubMed Abstract \| Publisher Full Text\n\nPirro V, Alfaro CM, Jarmusch AK, et al.: Intraoperative Assessment of Tumor Margins during Glioma Resection by Desorption Electrospray Ionization-Mass Spectrometry. Proc. Natl. Acad. Sci. 2017; 114(26): 6700–6705. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchäfer KC, Balog J, Szaniszló T, et al.: Real Time Analysis of Brain Tissue by Direct Combination of Ultrasonic Surgical Aspiration and Sonic Spray Mass Spectrometry. Anal. Chem. 2011; 83(20): 7729–7735. PubMed Abstract \| Publisher Full Text\n\nSorokin A, Shurkhay V, Pekov S, et al.: Untangling the Metabolic Reprogramming in Brain Cancer: Discovering Key Molecular Players Using Mass Spectrometry. Curr. Top. Med. Chem. 2019; 19(17): 1521–1534. PubMed Abstract \| Publisher Full Text\n\nDu X, Hu H: The Roles of 2-Hydroxyglutarate. Front. Cell Dev. Biol. 2021; 9(March): 1–13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChou FJ, Liu Y, Lang F, et al.: D-2-Hydroxyglutarate in Glioma Biology. Cells. 2021; 10(9). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhvansky ES, Sorokin AA, Pekov SI, et al.: Unified Representation of High- and Low-Resolution Spectra to Facilitate Application of Mass Spectrometric Techniques in Clinical Practice. Clin. Mass Spectrom. 2019; 12: 37–46. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGlioblastoma, de Vleeschouwer S , editors. Codon Publications; 2017. Publisher Full Text\n\nSorokin AA, Bormotov DS, Zavorotnyuk DS, et al.: Aggregation of Multimodal ICE-MS Data into Joint Classifier Increases Quality of Brain Cancer Tissue Classification.2023; 8: 8. Publisher Full Text\n\nSchapire RE: The Strength of Weak Learnability. Mach. Learn. 1990; 5: 197–227. Publisher Full Text\n\nBormotov DS, Eliferov VA, Peregudova O v, et al.: Incorporation of a Disposable ESI Emitter into Inline Cartridge Extraction Mass Spectrometry Improves Throughput and Spectra Stability. J. Am. Soc. Mass Spectrom. 2022; 34: 119–122. PubMed Abstract \| Publisher Full Text\n\nZhvansky ES, Eliferov VA, Sorokin AA, et al.: Assessment of Variation of Inline Cartridge Extraction Mass Spectra. J. Mass Spectrom. 2021; 56(4): e4640. PubMed Abstract \| Publisher Full Text\n\nGibb S, Strimmer K: MALDIquant: A versatile R package for the analysis of mass spectrometry data. Bioinformatics. 2012; 28: 2270–2271. PubMed Abstract \| Publisher Full Text\n\nSorokin A, Zavorotnyuk D: KNIME workflow: Aggregation of Multimodal ICE-MS Glioblastoma Data into Joint Classifier.2023. Publisher Full Text\n\nWang C, Wang M, Han X: Applications of Mass Spectrometry for Cellular Lipid Analysis. Mol. BioSyst. 2015; 11(3): 698–713. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPekov SI, Sorokin AA, Kuzin AA, et al.: Analysis of Phosphatidylcholines Alterations in Human Glioblastomas Ex Vivo. Biochem. Mosc. Suppl. B. Biomed. Chem. 2021; 15(3): 241–247. Publisher Full Text\n\nBogner-Strauss JG: N-Acetylaspartate Metabolism Outside the Brain: Lipogenesis, Histone Acetylation, and Cancer. Front Endocrinol (Lausanne). 2017; 8(SEP): 1–5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHawkridge AM: Practical Considerations and Current Limitations in Quantitative Mass Spectrometry-Based Proteomics. In Quantitative Proteomics. 2014; 1–25. Publisher Full Text\n\nShapley LS: A Value for N-Person Games. Contributions to the Theory of Games (AM-28). Princeton University Press; 1953; Volume II. : pp. 307–318. Publisher Full Text\n\nGhorbani A, Zou J: Data Shapley: Equitable Valuation of Data for Machine Learning. Proceedings of the 36th International Conference on Machine Learning. 2019; p PMLR 97:2242–2251." }	[ { "id": "198058", "date": "04 Sep 2023", "name": "Per Malmberg", "expertise": [ "Reviewer Expertise 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\nThis is an interesting approach to glial tumor identification using ambient MS in all combinations of positive and negative ion mode, high- and low mass resolution and at different mass ranges. Much of this work has been published before and here the authors focus on the contribution of each regime of the data in attempt to evaluate its importance. Due to scarcity of samples, each regime remains necessary to achieve adequate classification accuracy which in itself is problematic since the analysis will be too time consuming to be efficient in a clinical setting.\nSome points to consider:\nIt would be interesting if the authors compared this work with what can be achieved by other ambient techniques with an included imaging component, such as DESI. What additional value would localization have since it has been demonstrated that glial tumors are very heterogenous (see e.g. https://doi.org/10.1021/acschemneuro.2c00776)1.\nHow would imaging compare time-wise when compared with your cartridge extraction mass spectrometry? Which is faster?\nThe DOI link for Ref 21 is not 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": [] } ]	1	https://f1000research.com/articles/12-858
https://f1000research.com/articles/12-856/v1	20 Jul 23	{ "type": "Data Note", "title": "The oxygen concentration data in a forest canopy in 2020 in Beijing Gongqing Forestry Farm", "authors": [ "ChangShan Xing" ], "abstract": "Background: With the outbreak of global climate problems in recent years, more and more countries have proposed carbon neutral plans. The measurement of forest carbon sinks is gradually becoming a research hotspot in the field of carbon sinks. Methods: Based on observations of the amount of change in oxygen concentration in the forest canopy, we propose a simple and accurate method of forest carbon sinks measurement. Conclusions: In this data note, we provide the data of oxygen concentration in the canopy of a 160-hectare forest in Beijing, and give a convenient equation for calculating the carbon sequestration and carbon sink according to the changes of 15 days oxygen concentration.", "keywords": [ "Forest Carbon Sinks", "Measurement", "Average oxygen concentration", "Carbon Sequestration" ], "content": "Introduction\n\nForest carbon sinks represent the ability of forest ecosystems to absorb and store carbon dioxide by quantifying the mass of carbon dioxide fixed by plants.1,2 It is an important indicator for assessing the impact of global climate change, management measures, and human disturbance on forest ecological function, growth, and survival.3,4 Therefore, accurate quantification of carbon sinks is essential for the effective assessment of forest function dynamics. However, the most common way to measure the changes in carbon sequestration right now is the stock-difference method, which calculates the forest gross primary productivity (GPP) rather than net ecosystem productivity.5 The gain-loss method6 is based on monitoring the changes of carbon dioxide in the air, which not only have large errors but also cannot be verified by test and measurement. Therefore, an accurate, accessible, low-cost, short-period observation method is useful for observing forest functional dynamics and convenient to promote in the forestry, agriculture, grass industry, and other related industries.\n\nIn this data note, we provide the data on oxygen concentration in the canopy of a 160-hectare forest in Beijing, and give a convenient equation for calculating the carbon sequestration and carbon sink according to the changes of 15 days’ oxygen concentration.\n\n\nMethods\n\nThe research was conducted in Beijing Gongqing Forestry Farm, which is located in the northeast of Beijing. This area was selected as the ecological environment here is very representative of northern China. The details of the forest are as follows:\n\n(1) The geographical coordinates are 166.40 E and 40.10 N;\n\n(2) The altitude is 25 meters;\n\n(3) The soil type is sandy soil;\n\n(4) The forest type is planted forest;\n\n(5) The main tree species are populus canadensis Moench. The average tree height of the poplars was 21 meters, the average canopy height was 12 meters, and the average tree age was 25 years;\n\n(6) The region has a warm, temperate, semi-humid, continental monsoon climate with four distinct seasons; it is dry and windy in spring, hot and rainy in summer, cool and crisp in autumn and cold and dry in winter;\n\n(7) The annual average temperature is 11.5 °C;\n\n(8) The annual sunshine is about 2750 hours;\n\n(9) The average annual rainfall is about 625 mm; the area is relatively arid.\n\nThe forest carbon sink was observed by a 30 meter high measuring tower which was set in the center of the 160-hectare forest. An oxygen concentration detector (HeNan ChiCheng Electric Co. Ltd, QB2000N) was installed 15 meters above ground on the measuring tower to ensure the detector was located in the middle of the canopy. This setup was designed specifically for this research. The error value of the oxygen concentration detectors had been adjusted to less than ±0.5%.\n\nThe oxygen concentration detector measured the oxygen concentration (% Vol.) every 5 minutes per day.7 Furthermore, we calculated the daily average oxygen concentration of the forest (Figure 1; Table 1). Since trees only begin to grow and release oxygen at a temperature higher than their biological zero (and the biological zero of poplar is more than 10 degrees Celsius), and the average temperature of Gongqing Forestry Farm from March 10th to March 24th is 10.17 degrees Celsius, the starting point of data recording in spring was March 10. The endpoint of data recording in autumn should be set at the time point when the oxygen concentration was higher than the starting point in spring, so the endpoint in autumn is October 5th.\n\n\nThe measurement of forest carbon sinks\n\nDuring photosynthesis, plants absorb carbon dioxide and release oxygen. Their amount of substance is equal to the mass divided by the molar mass. Therefore, the value of plant carbon sequestration can be calculated by the following formula:\n\nMco2 is the mass of plant fixed carbon dioxide, and ∑v is the accumulated value of oxygen concentration difference during a specific period (based on experience, 15 days is used as the most appropriate the measurement period), ρ is the oxygen density 1.43kg/m3, h is the average height of the photosynthetic part of the plant, s is the area of the plant, mrco2 is the molecular weight of CO2 (44), and mro2 is the molecular weight of O2 (32).", "appendix": "Data availability\n\nfigshare: The oxygen concentration data in Forest Canopy of 2020 in Beijing Gongqing Forestry Farm, https://doi.org/10.6084/m9.figshare.22735811.v1. 7\n\nThis project contains csv files of oxygen concentration data, labelled with the collection dates.\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 has previously been made available as a preprint (DOI: https://doi.org/10.21203/rs.3.rs-1141066/v1). Thanks to both authors JIANG LV and YUN SHI for their contributions to this article.\n\n\nReferences\n\nUNFCCC: Kyoto Protocol to the United Nations Framework Convention on Climate Change.1998. Acesso em: 25 out. 2019. Reference Source\n\nPan Y, Birdsey RA, Fang J, et al.: A Large and Persistent Carbon Sink in the World’s Forests. Science. 2011; 333: 988–993. PubMed Abstract \| Publisher Full Text\n\nGampe D, Zscheischler J, Reichstein M, et al.: Increasing impact of warm droughts on northern ecosystem productivity over recent decades. Nat. Clim. Chang. 2021; 11(9): 772–779. Publisher Full Text\n\nSitch S, Friedlingstein P, Gruber N, et al.: Recent trends and drivers of regional sources and sinks of carbon dioxide. Biogeosciences. 2015; 12: 653–679. Publisher Full Text\n\nForestry Carbon Sequestration Editorial Board: Forestry Carbon Sequestration: practice in Beijing. China Forestry Publishing House; 2016. (In Chinese).\n\nLi NY, Lv J: Carbon Inventory Methods. China Forestry Publishing House; 2009. (In Chinese).\n\nXing: The oxygen concentration data in Forest Canopy of 2020 in Beijing Gongqing Forestry Farm. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "194292", "date": "26 Oct 2023", "name": "Zheng-Hong Tan", "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\nI can not follow the logic or principle of calculating carbon sequestration by oxygen concentration data as provided by author. As shown in closed chamber method, we will calculate the flux by a linear fitting on concentration data. In this case, there less a confidential control volume below the sensor height where lateral flow might occur. More importantly, it is not reasonable to calculate flux with a too coarse interval (15 days).\nBy the way, authors did not provide enough information on measurement. i.e. calibrations, maintenance, sampling interval etc.\nThe major content should match to the title. Since authors want to show some oxygen concentration data, no need jumps into the carbon sequestration issues. If they want to, please provide more methodological information and apply appropriate and theoretically sounding method.\n\nIs the rationale for creating the dataset(s) clearly described? Partly\n\nAre the protocols appropriate and is the work technically sound? No\n\nAre sufficient details of methods and materials provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [ { "c_id": "10557", "date": "29 Nov 2023", "name": "ChangShan Xing", "role": "Author Response", "response": "First of all, thank you very much to the reviewers for their hard work on reviewing this paper. The reviewer has raised questions about the principle of this method, which have been addressed in the preprint paper available at https://doi.org/10.21203/rs.3.rs-1141066/v1. In response to the need for validation of the method in a closed space, I will provide the experimental data from experiments conducted in a closed greenhouse later, which fully demonstrates that the regularity of observation results in open and closed spaces is completely consistent. Whether in a closed or open space, the experimental verification of this method has demonstrated its practicality, operability, and accuracy: The reason for considering a 15-day period as the calculation unit for oxygen concentration is that the rate of photosynthesis is directly related to temperature. By conducting a one-way analysis of variance, we can determine that the temperature differences between 15-day intervals are significant. The following is the additional experimental data provided: An oxygen concentration detector was installed at the center position of a 11x6 square meter sunlit greenhouse. The detector was placed at a height of 25 centimeters above the ground. The greenhouse contained naturally growing wild plants. Depending on the drought conditions, intermittent irrigation was applied to water the wild plants. The oxygen concentration inside the greenhouse was continuously measured at a frequency of once every 5 minutes. The average daily oxygen concentration value for the wild plants was then calculated. The measurements were taken from February 24, 2020, to November 19, 2020. The oxygen concentration data for wild plants in an enclosed space： data \| 2.24-3.9 \| 3.10-3.24 \| 3.25-4.8 \| 4.9-4.23 \| 4.24-5.8 \| 5.9-5.23 \| 5.24-6.7 \| 6.8-6.22 \| 6.23-7.7 \| 7.8-7.22 \| 7.23-8.6 \| 8.7-8.21 \| 8.22-9.5 \| 9.6-9.20 \| 9.21-10.5 \| 10.6-10.20 \| 10.21-11.4 \| 11.4-11.19\| The average oxygen \| 20.676 \| 21.022 \| 21.068 \| 21.112 \| 21.172 \| 21.173 \| 21.178 \| 21.19 \| 21.189 \| 21.172 \| 21.147 \| 21.171 \| 21.201 \| 21.164 \| 21.083 \| 20.946 \| 20.84 \| 20.746 \| concentration difference \| +0.364 \| +0.046 \| +0.044 \| +0.06 \| +0.001 \| +0.005 \| +0.072 \| -0.001 \| -0.017 \| -0.025 \| +0.024 \| +0.03 \| -0.037 \| -0.081 \| -0.137 \| -0.106 \| -0.064 \| grass \| 0.3 \| 0.5 \| 0.6 \| 0.6 \| 0.6 \| 0.6 \| 0.6 \| 0.6 \| 0.6 \| 0.6 \| 0.6 \| 0.6 \| 0.6 \| 0.5 \| 0.4 \| 0.4 \| 0.4 \| 0.4 \| height The carbon sequestration of wild grass in an enclosed space： The variation of wild grass in an enclosed space over a continuous period of 15 days shows a noticeable increase and decrease at both ends with a relatively stable fluctuation in the middle. From February 24th to March 24th, the oxygen concentration gradually increased. From March 25th to October 5th, it showed a gradual and mild fluctuation. The peak occurred from August 22nd to September 5th during the summer, reaching 21.201 L/mol. Taking the average oxygen concentration from February 24th to March 9th, which is 20.676, as the starting point, we subtract the average oxygen concentration in the later period from the average in the earlier period. Then, using the highest oxygen concentration value as the threshold, we add up all the differences to obtain the total oxygen concentration. Using the formula , represents the mass of carbon dioxide fixed by plants, is the sum of the oxygen concentration, is the density of oxygen（1.43kg/m³），the average height h of the plant undergoing photosynthesis, and s is the area of the plant，mrCO2 is the molecular weight of CO2, which is 44, and mrO2 is the molecular weight of O2, which is 32.Calculate the total carbon sequestration mass of wild grass in a closed space during the growth period： MCO=1.429×0.364×0.4×66×(44/32)=18.88kg MCO=1.429×0.168×0.6×66×(44/32)=13.08kg MCO=18.88+13.08=31.96kg During the stage when the oxygen concentration gradually decreases after the inflection point, calculate the mass of oxygen consumed and the mass of carbon dioxide released during the growth process of wild grass.： MCO=1.429×0.037×0.55×66×(44/32)=2.64kg MCO=1.429×0.388×0.4×66×(44/32)=20.13kg MCO=2.64+20.13=22.77kg The carbon sink is the difference between the absorption of carbon dioxide before the inflection point and the release after the inflection point: MCO=31.96-22.77=9.19kg. During the growth period, the total carbon sequestration mass of wild grass is 31.96 kilograms. Harvesting 66 square meters of wild grass yields 41 kilograms of dry matter, and after measuring the organic carbon content, the total carbon sequestration mass is determined to be 20.067 kilograms. The measured carbon sequestration mass of the wild grass accounts for 62.8% of the calculated carbon sequestration mass, primarily due to the fact that the carbon sequestration mass of the roots and other plants in the soil was not measured, resulting in a lower measured value than the calculated carbon sequestration mass. From June 23rd to August 6th, the oxygen released by photosynthesis of the wild grass was less than the oxygen consumed by respiration, mainly due to the high temperature suppressing the photosynthesis of the wild grass." } ] } ]	1	https://f1000research.com/articles/12-856
https://f1000research.com/articles/12-488/v1	12 May 23	{ "type": "Case Report", "title": "Case Report: Simultaneous penetrating keratoplasty with autologous simple limbal epithelial transplantation as an alternative to keratoprosthesis", "authors": [ "Supriya Sharma", "Swati Singh", "Swapna S. Shanbhag", "Supriya Sharma", "Swati Singh" ], "abstract": "Introduction and importance: This case report highlights the multidisciplinary approach required to achieve successful anatomical and functional outcomes, in an eye with total limbal stem cell deficiency (LSCD) associated with underlying corneal scarring and thinning. Presentation of case: A 59-year-old gentleman had poor visual recovery in the right eye (RE) following accidental carbide blast, 1-year before presenting to us. The visual acuity was counting fingers and clinical examination revealed cicatricial entropion involving the upper eyelid, total LSCD, corneal scarring with a central descemetocele and cataract in the RE. Prior to ocular surface reconstruction, entropion correction was performed. Three months later, penetrating keratoplasty combined with cataract surgery and intraocular lens implantation (penetrating keratoplasty (PK) triple), with autologous simple limbal epithelial transplantation (SLET) was performed. The visual acuity was 20/100, 18 months after the surgery, with a clear well-epithelized corneal graft and stable ocular surface. Discussion: LSCD is caused by a decrease in the population and /or function of the limbal epithelial stem cells. Limbal stem cell transplantation (LSCT) is warranted in eyes with total LSCD. In eyes with coexisting corneal scarring, LSCT alone may be inadequate to restore the vision. These eyes require simultaneous or sequential lamellar or full-thickness corneal transplantation for visual rehabilitation. Though, the existing literature favors a sequential approach, where LSCT is performed first followed by corneal transplantation, under certain circumstances such as a thin underlying cornea like in our case, corneal transplantation may have to be combined with LSCT to achieve optimal outcomes. Conclusion: Combining autologous SLET with PK can be performed for visual rehabilitation in eyes with unilateral total LSCD and underlying corneal thinning. Corneal and limbal graft survival is prolonged if existing adnexal comorbidities are addressed before any surgical intervention is planned and adequate time interval is allowed for the surface inflammation to subside.", "keywords": [ "ocular burn", "limbal stem cell deficiency (LSCD)", "limbal stem cell transplantation (LSCT)", "cicatricial entropion", "descemetocele", "penetrating keratoplasty" ], "content": "Introduction\n\nOcular chemical injuries are often associated with poor long-term visual outcomes due to chronic sequelae such as limbal stem cell deficiency (LSCD), corneal scarring, and vascularization.1 Visual rehabilitation in these eyes is extremely challenging. To treat LSCD, limbal stem cell transplantation (LSCT) is required. This procedure can be autologous in cases of unilateral LSCD where the LESCs are harvested from the contralateral eye or this can be allogeneic where the LESC’s are harvested from a living-related donor or a cadaveric cornea.2–6 In eyes with total LSCD and underlying clear corneal stroma, only performing LSCT may stabilize the ocular surface and provide adequate visual outcomes.7 However, in eyes with underlying full-thickness corneal scarring, performing only LSCT may not be sufficient to achieve optimal functional outcomes. In such eyes, a deep anterior lamellar keratoplasty (DALK) or a penetrating keratoplasty (PK) is warranted to restore the corneal transparency.8 However, in the presence of LSCD, performing a PK or DALK alone is known to have very poor outcomes with a higher risk of graft rejection and failure associated with ocular surface inflammation causing persistent epithelial defects.9 In such eyes, optimal visual recovery can be achieved by performing a corneal transplantation either simultaneously with LSCT or sequentially after LSCT.\n\nThe published literature recommends that a corneal transplant should be performed once the surface inflammation has decreased, the corneal epithelium is stable and regular, and there is regression of stromal vascularization.2,10 Poor outcomes have been documented with simultaneous PK and LSCT, with the corneal graft survival ranging from 35% to 64%.11,12 At present, there are no existing guidelines supporting the relative timing of the two transplant procedures and whether they can be combined as a single stage procedure. In certain cases, performing LSCT and PK becomes inevitable as LSCT alone cannot be performed due to residual corneal thickness being inadequate. We report a case where PK was performed simultaneously with autologous LSCT in an eye with total unilateral LSCD with descemetocele with surrounding corneal scarring and cataract.\n\n\nCase presentation\n\nA 59-year-old Asian Indian male, a farmer by occupation, presented with gradual loss of vision in the right eye (RE) over a period of 1 year, associated with pain, watering and redness following accidental carbide blast. In the acute phase, amniotic membrane transplantation (AMT) was performed twice by the primary ophthalmologist. At presentation, the best corrected visual acuity (BCVA) was counting fingers close to face (CFCF) and 20/20 in the right and left eye (LE), respectively. On clinical examination, the RE showed cicatricial entropion involving the upper eyelid (Figure 1A, yellow arrows), diffuse conjunctival hyperemia, pseudopterygium involving two clock hours of the nasal limbus and five clock hours of the temporal limbus with peripheral corneal vascularization involving all quadrants (Figure 1B). Underlying leucomatous corneal scarring was seen with a central descemetocele measuring around 3×4 mm (Figure 1B). Anterior chamber examination was suggestive of a total cataract, although the details could not be clearly seen. The LE was unremarkable on clinical examination. The anterior segment optical coherence tomography (AS-OCT) of the RE showed corneal thickness of 94 microns in the area of the descemetocele, with surrounding corneal thinning and dense leucomatous corneal scarring (Figure 1C). Ultrasound B scan showed no obvious abnormality of the posterior segment. The Schirmer’s test revealed a wet ocular surface. Based on the clinical history and examination, a diagnosis of upper eyelid cicatricial entropion, total LSCD, central descemetocele, with full-thickness corneal scar and total cataract was established in the RE.\n\nPrior to performing any surface reconstruction, entropion correction of the upper eyelid with mucous membrane grafting was performed in the RE (Figure 1D, yellow dotted lines). No recurrence was noted three months post-surgery. Three months following entropion correction, PK triple (PK with cataract extraction and intraocular lens implantation) and autologous SLET was performed with one clock hour of limbus harvested from the superior limbus of the contralateral eye. After PK was performed and all sutures were placed, an amniotic membrane graft (AMG; Ramayamma International Eye Bank, Hyderabad) was secured to the perilimbal conjunctiva with 10-0 nylon sutures and fibrin glue (Tisseel Kit, Baxter AG, Vienna, Austria). The limbal biopsy was cut into multiple pieces and placed on the host cornea peripheral to the graft over the AMG and secured with fibrin glue. A central opening was made in the amniotic membrane.13 A bandage contact lens was placed over the corneal surface. Lateral paramedian permanent tarsorrhaphy was performed to promote epithelization and to protect the ocular surface. Postoperatively, prednisolone acetate (1%) eye drops 1 hourly and moxifloxacin eye drops (0.5%) four times daily were prescribed. After 1 week, antibiotic eye drop was discontinued and topical steroid drop was tapered gradually over the subsequent weeks to four times daily after 6 weeks, which was continued for 6 months of follow-up after which this was further stepped down to thrice daily.\n\nAfter complete epithelization of the ocular surface, the tarsorrhaphy was released. On further follow-ups post-surgery, raised intra-ocular pressure was documented with cup-to-disc ratio (CDR) of 0.8:1. A diagnosis of secondary glaucoma was established, and the patient has been managed on topical anti-glaucoma medications (combination of timolol maleate 0.5% and brimonidine tartrate 0.2% twice daily, dorzolamide 2% thrice daily) with good intra-ocular pressure control until the last follow-up visit. Patient was also started on topical cyclosporine 0.1% two times a day in view of having a high-risk graft. The patient has completed 18 months of postoperative follow-up and maintains a BCVA of 20/100 in the RE. Postoperatively, the graft is clear and well epithelized, with a stable ocular surface (Figure 1E). The AS-OCT of the RE revealed a compact cornea with a central corneal thickness of 434 microns and uniform corneal epithelium (Figure 1F). The LE only had discontinuity at the limbus at the site of limbal biopsy, otherwise the cornea was well epithelized and clear.\n\n\nDiscussion\n\nThe outcome of a corneal or limbal transplant is determined by presence of comorbidities such as tear film abnormalities, lid and lid margin related disease, uncontrolled intraocular pressure and presence of active surface inflammation.10 To reduce the risk of graft rejection and failure, it is important to address these existing comorbidities prior to performing any transplant procedure.9 In our case, prior to performing ocular surface reconstruction for visual rehabilitation, entropion correction with mucous membrane grafting was performed. This procedure of entropion correction with anterior lamellar recession and labial mucous membrane graft (MMG) is a well-established technique with modifications in the suturing technique. The risk of surgical failure increases in eyes with cicatricial entropion secondary to non-infectious etiology such as Stevens–Johnson syndrome, burns, and trauma.14 The modified technique used in this patient, has been described by Singh et al., where labial MMG is used for spacing the anterior lamella and reconstruction of the lid margin and the posterior lamella.15 This technique has shown promising long-term outcomes, particularly in eyes with cicatricial entropion secondary to ocular surface cicatricial disorders.\n\nOver several years, conjunctival limbal autograft (CLAU), cultivated limbal epithelial transplantation (CLET), keratolimbal allograft (KLAL) have been successfully performed in eyes with LSCD.2,12,16 However, limitations exist with different procedures such as the risk of iatrogenic LSCD in the contralateral healthy donor eye with CLAU, difficulty in the surgical procedure with the need for life long systemic immunosuppression and need for a donor cornea with KLAL, and the need for an expensive laboratory setting to allow ex vivo expansion of LESCs in CLET.17 Autologous simple limbal epithelial transplantation (SLET) introduced in 2012, has quickly gained popularity as it uses minimal limbal tissue from the contralateral healthy eye, allows in vivo expansion of stem cells without the risk of iatrogenic LSCD in the donor eye, and also alleviates the need for systemic immunosuppression.6 However, in eyes with LSCD and corneal scarring, the results of LSCT procedures combined with PK have not been encouraging. Shimazaki et al. and Solomon et al. published outcomes of simultaneous KLAL and PK in eyes with total LSCD.11,18 Inferior outcomes were seen in eyes where simultaneous procedure was performed as compared to those eyes where two-staged surgery was performed (KLAL followed by PK) with higher rate of corneal graft rejection. Corneal graft rejection has been attributed to increased exposure of the host immune system to the donor corneal antigens through the limbal allograft antigens, which are derived from the same donor as the central graft. Also, simultaneous PK increases the surface inflammation and the wound healing response. Both studies recommended a time interval of 3–6 months after KLAL to allow stabilization of the ocular surface before performing keratoplasty.11,18\n\nIn 2011, Basu et al. compared anatomical and functional outcomes of simultaneous PK and CLET with two-staged procedure in eyes with unilateral total LSCD secondary to ocular burns.19 They concluded that a two-staged surgical approach of first transplanting the cultivated limbal stem cells, followed by PK, resulted in superior outcomes in restoring the ocular surface stability and vision, as compared to single-staged procedure. Also, once the surface was well epithelized, which usually takes around 6 weeks, the time interval between CLET and PK did not affect the corneal graft survival. This was in accordance with the outcomes published by Baradaran-Rafii et al. and Sangwan et al., where a two-staged sequential surgical approach showed favorable outcomes in terms of corneal graft survival and final visual acuity, as compared to simultaneous surgeries.20,21\n\nThe existing literature reporting outcomes of simultaneous autologous SLET and PK have also been discouraging. Simultaneous PK is an established risk factor for recurrence of LSCD and failure of SLET in eyes with total unilateral LSCD in adults and children.8,22 The cause for poor visual recovery in eyes is complications like secondary glaucoma, amblyopia and infectious keratitis, rather than the surgical procedure itself. Encouraging outcomes have been reported in eyes where sequential ocular surface reconstruction by SLET followed by keratoplasty was performed in eyes with unilateral total LSCD.23,24 Simultaneous allogeneic SLET with PK has been described in a case of sterile keratolysis following severe ocular chemical burn, as an emergency procedure to preserve the globe tectonicity.25\n\nSurgical decision making in such cases depends on the status of the contralateral eye. Of the various techniques described earlier for ocular surface reconstruction, in our case, autologous SLET was preferred over CLAU, CLET or allogeneic SLET. The need for a CAG or CLAU was eliminated in our case as there was no co-existing symblepharon. As our patient had a healthy contralateral eye, autologous LSCT was preferred to avoid the need for systemic immunosuppression. Similarly, for visual rehabilitation, PK was preferred over Boston type 1 keratoprosthesis (BKpro1), which is often reserved in patients who are bilaterally blind. Though BKpro1 has shown to provide rapid visual recovery in eyes with LSCD secondary to chemical burns, glaucomatous optic neuropathy is common in these eyes and may reduce the long-term visual potential post BKpro1.26 Also, when BKpro1 is performed in a patient with a contralateral healthy eye, these patients may not be aware of the decreased vision in the operated eye, secondary to any complication, as the contralateral eye maintains a good vision.27\n\nHence, in our case, we chose to perform autologous SLET combined with PK. Although sequential surgery would have been ideal, this was not possible in our case due to the underlying cornea being thin. Additionally, while performing SLET, the explants were placed peripherally over the host cornea. This surgical modification can prevent the loss of explants, in eyes where a repeat penetrating keratoplasty is required. An allogeneic SLET was not performed as the recipient will then be exposed to antigens from two donors versus a single donor.10 Another option would be choosing to take a larger graft and include the limbus from the donor graft, however, this would also require systemic immunosuppression.28 Simultaneous intervention in our case also allowed for faster visual recovery, reduced multiple follow-up visits for the patient, reduced the cost of surgery, and allowed for an earlier diagnosis and management of secondary glaucoma. We also believe that addressing the adnexal abnormalities prior to ocular surface reconstruction helped us achieve the desired outcome of a clear graft with a stable ocular surface which was maintained for a follow-up period of 18 months.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nMendeley: CARE checklist for ‘Case Report: Simultaneous penetrating keratoplasty with autologous simple limbal epithelial transplantation as an alternative to keratoprosthesis’. https://doi.org/10.17632/m299chb22v.2\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\nWagoner MD: Chemical injuries of the eye: current concepts in pathophysiology and therapy. Surv. Ophthalmol. 1997; 41(4): 275–313. PubMed Abstract \| Publisher Full Text\n\nKenyon KR, Tseng SC: Limbal autograft transplantation for ocular surface disorders. Ophthalmology. 1989 May; 96(5): 709–723. discussion 722-723. PubMed Abstract \| Publisher Full Text\n\nPellegrini G, Traverso CE, Franzi AT, et al.: Long-term restoration of damaged corneal surfaces with autologous cultivated corneal epithelium. Lancet Lond. Engl. 1997 Apr 5; 349(9057): 990–993. PubMed Abstract \| Publisher Full Text\n\nDua HS, Azuara-Blanco A: Limbal stem cells of the corneal epithelium. Surv. Ophthalmol. 2000; 44(5): 415–425. Publisher Full Text\n\nSangwan VS, Vemuganti GK, Singh S, et al.: Successful reconstruction of damaged ocular outer surface in humans using limbal and conjuctival stem cell culture methods. Biosci. Rep. 2003 Aug; 23(4): 169–174. PubMed Abstract \| Publisher Full Text\n\nSangwan VS, Basu S, MacNeil S, et al.: Simple limbal epithelial transplantation (SLET): a novel surgical technique for the treatment of unilateral limbal stem cell deficiency. Br. J. Ophthalmol. 2012 Jul; 96(7): 931–934. PubMed Abstract \| Publisher Full Text\n\nShanbhag SS, Nikpoor N, Rao Donthineni P, et al.: Autologous limbal stem cell transplantation: a systematic review of clinical outcomes with different surgical techniques. Br. J. Ophthalmol. 2020 Feb; 104(2): 247–253. PubMed Abstract \| Publisher Full Text\n\nBasu S, Sureka SP, Shanbhag SS, et al.: Simple Limbal Epithelial Transplantation: Long-Term Clinical Outcomes in 125 Cases of Unilateral Chronic Ocular Surface Burns. Ophthalmology. 2016 May; 123(5): 1000–1010. Publisher Full Text\n\nMaguire MG, Stark WJ, Gottsch JD, et al.: Risk factors for corneal graft failure and rejection in the collaborative corneal transplantation studies. Collaborative Corneal Transplantation Studies Research Group. Ophthalmology. 1994 Sep; 101(9): 1536–1547. PubMed Abstract \| Publisher Full Text\n\nDua HS, Rahman I, Jayaswal R, et al.: Combined limbal and corneal grafts: should we or should we not? Clin. Exp. Ophthalmol. 2008 Aug; 36(6): 497–498. PubMed Abstract \| Publisher Full Text\n\nShimazaki J, Maruyama F, Shimmura S, et al.: Immunologic rejection of the central graft after limbal allograft transplantation combined with penetrating keratoplasty. Cornea. 2001 Mar; 20(2): 149–152. PubMed Abstract \| Publisher Full Text\n\nTseng SC, Prabhasawat P, Barton K, et al.: Amniotic membrane transplantation with or without limbal allografts for corneal surface reconstruction in patients with limbal stem cell deficiency. Arch. Ophthalmol. 1998 Apr; 116(4): 431–441. Publisher Full Text\n\nSingh A, Murthy SI, Gandhi A, et al.: “Doughnut” Amniotic Membrane Transplantation With Penetrating Keratoplasty for Vernal Keratoconjunctivitis With Limbal Stem Cell Disease. Cornea. 2021 Jul 1; 40(7): 914–916. PubMed Abstract \| Publisher Full Text\n\nSodhi PK, Yadava U, Pandey RM, et al.: Modified grey line split with anterior lamellar repositioning for treatment of cicatricial lid entropion. Ophthalmic Surg. Lasers. 2002; 33(2): 169–174. PubMed Abstract \| Publisher Full Text\n\nSingh S, Narang P, Mittal V: Labial mucosa grafting for lid margin, anterior lamellar, and posterior lamellar correction in recurrent cicatricial entropion. Orbit Amst Neth. 2021 Aug; 40(4): 301–305. Publisher Full Text\n\nTseng SC, Tsai RJ: Limbal transplantation for ocular surface reconstruction--a review. Fortschritte Ophthalmol. Z. Dtsch. Ophthalmol. Ges. 1991; 88(3): 236–242.\n\nKate A, Basu S: A Review of the Diagnosis and Treatment of Limbal Stem Cell Deficiency. Front. Med. 2022; 9: 836009. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSolomon A, Ellies P, Anderson DF, et al.: Long-term outcome of keratolimbal allograft with or without penetrating keratoplasty for total limbal stem cell deficiency. Ophthalmology. 2002 Jun; 109(6): 1159–1166. Publisher Full Text\n\nBasu S, Mohamed A, Chaurasia S, et al.: Clinical outcomes of penetrating keratoplasty after autologous cultivated limbal epithelial transplantation for ocular surface burns. Am. J. Ophthalmol. 2011 Dec; 152(6): 917–924.e1. PubMed Abstract \| Publisher Full Text\n\nBaradaran-Rafii A, Ebrahimi M, Kanavi MR, et al.: Midterm outcomes of autologous cultivated limbal stem cell transplantation with or without penetrating keratoplasty. Cornea. 2010 May; 29(5): 502–509. Publisher Full Text\n\nSangwan VS, Matalia HP, Vemuganti GK, et al.: Early results of penetrating keratoplasty after cultivated limbal epithelium transplantation. Arch. Ophthalmol. 2005 Mar; 123(3): 334–340. PubMed Abstract \| Publisher Full Text\n\nGupta N, Joshi J, Farooqui JH, et al.: Results of simple limbal epithelial transplantation in unilateral ocular surface burn. Indian J. Ophthalmol. 2018 Jan; 66(1): 45–52. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGupta N, Farooqui JH, Patel N, et al.: Early Results of Penetrating Keratoplasty in Patients With Unilateral Chemical Injury After Simple Limbal Epithelial Transplantation. Cornea. 2018 Oct; 37(10): 1249–1254. PubMed Abstract \| Publisher Full Text\n\nSingh D, Vanathi M, Gupta C, et al.: Outcomes of deep anterior lamellar keratoplasty following autologous simple limbal epithelial transplant in pediatric unilateral severe chemical injury. Indian J. Ophthalmol. 2017 Mar; 65(3): 217–222. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKunapuli A, Fernandes M: Successful Outcome of Simultaneous Allogeneic Simple Limbal Epithelial Transplantation With Therapeutic Penetrating Keratoplasty (PKP) for Limbal Stem Cell Deficiency and Sterile Keratolysis After Chemical Injury. Cornea. 2021 Jun 1; 40(6): 780–782. Publisher Full Text\n\nShanbhag SS, Saeed HN, Paschalis EI, et al.: Boston keratoprosthesis type 1 for limbal stem cell deficiency after severe chemical corneal injury: A systematic review. Ocul. Surf. 2018 Jul; 16(3): 272–281. PubMed Abstract \| Publisher Full Text\n\nShanbhag SS, Saeed HN, Colby KA, et al.: Comparative Outcomes of Boston Keratoprosthesis Type 1 Implantation Based on Vision in the Contralateral Eye. Cornea. 2018 Nov; 37(11): 1408–1413. PubMed Abstract \| Publisher Full Text\n\nJain N, Kate A, Basu S: Deep anterior lamellar limbo-keratoplasty for bilateral limbal stem cell deficiency with corneal scarring in chemical injury sequelae: Two case reports. Int. J. Surg. Case Rep. 2022 Aug; 97: 107409. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "173526", "date": "25 May 2023", "name": "Sotiria Palioura", "expertise": [ "Reviewer Expertise Cornea" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 nicely documents the sequence of rehabilitative procedures that need to be done in order to restore vision in an eye with cicatricial entropion, corneal thinning, cataract and total LSCD following thermal injury. They should be congratulated for a great outcome on an eye that would otherwise be lost.\nAlthough the cited literature suggests that a two stage procedure has better long-term outcomes in terms of graft survival, in certain cases, such as the one described by the authors, this cannot be done due to the significant corneal thinning and the risk of perforation during pannus dissection for the LSCT.\nThe authors should discuss in more detail why corneal thinning precludes a sequential procedure. Moreover, they should discuss how they modified their technique. It seems that they did not perform a 360 peritomy as is commonly done in SLET and pannus dissection, but rather performed the PK and then secured the AMT over the peripheral conjunctiva.\nFinally, the authors should discuss why they performed a central opening in the ΑΜΤ and whether, in their experience, this leads to better visual quality in the long term. Why did they choose to do that in this case? Or is it something they always perform in their SLET procedures?\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": "9894", "date": "29 Nov 2023", "name": "Swapna Shanbhag", "role": "Author Response", "response": "1) This case report nicely documents the sequence of rehabilitative procedures that need to be done in order to restore vision in an eye with cicatricial entropion, corneal thinning, cataract and total LSCD following thermal injury. They should be congratulated for a great outcome on an eye that would otherwise be lost. Reply: Thank you for your comments. 2) Although the cited literature suggests that a two stage procedure has better long-term outcomes in terms of graft survival, in certain cases, such as the one described by the authors, this cannot be done due to the significant corneal thinning and the risk of perforation during pannus dissection for the LSCT. The authors should discuss in more detail why corneal thinning precludes a sequential procedure. Reply: Thank you for your suggestion. We have added the following lines towards the end of the Discussion: ‘Corneal thinning increases the risk of frank perforation of the cornea during pannus dissection for SLET, thus necessitating PK. Thus, performing SLET alone was not a possibility. Although performing PK alone could have been a possibility, this would have led to recurrence of LSCD over the graft, thus, leading to failure of the PK procedure.’ 3) Moreover, they should discuss how they modified their technique. It seems that they did not perform a 360 peritomy as is commonly done in SLET and pannus dissection, but rather performed the PK and then secured the AMT over the peripheral conjunctiva. Reply: Thank you for your suggestion. In this case, a complete pannus was not seen over the entire cornea. And hence a pannus dissection as performed in SLET was not necessary. We performed pannus dissection nasally and temporally and allowed the conjunctiva in this area to recess posteriorly. We have added the following lines in the Case Report section in the second paragraph: ‘Pannus dissection was first performed nasally and temporally, and this conjunctiva was allowed to recess from over the cornea.’ We have added the following lines in the Discussion section: ‘Also, in our case, there were certain modifications to the surgical procedure. Pannus dissection was not performed 360 degrees, as is performed in SLET as a complete pannus was not seen over the cornea. Hence pannus dissection was performed only in the areas of the pannus nasally and temporally and this conjunctiva was allowed to recess. Sutures were used to anchor the AMG on the perilimbal sclera as the underlying cornea was epithelized and it is possible that the AMG would not have been stable otherwise. Also, as the pannus dissection was not performed 360 degrees, it was not possible to tuck the AMG under the surrounding conjunctiva, as is performed in SLET. Hence, sutures were deemed to be necessary.’ 4) Finally, the authors should discuss why they performed a central opening in the ΑΜΤ and whether, in their experience, this leads to better visual quality in the long term. Why did they choose to do that in this case? Or is it something they always perform in their SLET procedures? Reply: Thank you for your suggestion. This is anecdotal data, unpublished. We have previously done a SLET with PK where the central opening was not created, which led to central haze, and the visual acuity never improved beyond 20/200 in spite of having a clear graft. Hence, the patient had to be taken to the operating room 3 months after the surgery, to create a central opening in the AMG, after which the patient's visual acuity improved. We have added the following in the Discussion section: ‘Also, in these cases, it may be more important to support the paracentral area and the limbal area in the form of a doughnut AMG.(13) The central area of the corneal graft may have healthy donor corneal epithelium which need not be debrided. Hence, AMG may not be required centrally, and a central opening was created in the AMG, thus allowing for better visual acuity.(13) Also, it has been reported that AMG may persist as a subepithelial membrane in some cases leading to haze and poor visual acuity post-operatively.(28) This central opening is not created in SLET cases as the underlying cornea is devoid of epithelium and if the AMG does not cover this area, then this area of the corneal stroma may not get epithelized as there is no continuous scaffold to grow over.’ We have cited the following papers: Reference no 13: Singh A, Murthy SI, Gandhi A, Sangwan VS. “Doughnut” Amniotic Membrane Transplantation With Penetrating Keratoplasty for Vernal Keratoconjunctivitis With Limbal Stem Cell Disease. Cornea. 2021 Jul 1;40(7):914–6. Reference number 28: Dua HS, Gomes JA, King AJ, Maharajan VS. The amniotic membrane in ophthalmology. Surv Ophthalmol. 2004 Jan-Feb;49(1):51-77." } ] }, { "id": "180027", "date": "10 Jul 2023", "name": "Denise Loya Garcia", "expertise": [ "Reviewer Expertise Cornea", "Ocular Surface", "Dry Eye." ], "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 present a very interesting case highlighting the advantages of autologous simple limbal epithelial transplantation combined with penetrating keratoplasty as a single-stage procedure.\nDespite the evidence supporting a two-stage procedure, the authors clearly explained and justified the use of combined surgery by a multidisciplinary team and an organized surgical approach in a well-selected patient such as the one described in this case report. Underscoring the importance of addressing the adnexal abnormalities before any ocular surface reconstruction is key.\nThe authors used the “Doughnut” amniotic membrane transplantation, my suggestion is that they could explain the benefits of using this technique for retaining a clear central cornea after AMT transplantation.\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": "9895", "date": "29 Nov 2023", "name": "Swapna Shanbhag", "role": "Author Response", "response": "Response: Thank you for your comments.. The authors used the “Doughnut” amniotic membrane transplantation, my suggestion is that they could explain the benefits of using this technique for retaining a clear central cornea after AMT transplantation Response: Thank you for your comment. We have added points in the Case Report section and the Discussion section regarding the creating of the central opening in the amniotic membrane and also added references for the technique of 'doughnut' amniotic membrane transplantation in the Discussion section." } ] } ]	1	https://f1000research.com/articles/12-488
https://f1000research.com/articles/12-251/v1	08 Mar 23	{ "type": "Systematic Review", "title": "Meta-analysis of the prevalence of Carpal Tunnel Syndrome (CTS) among dental health care personnel", "authors": [ "Deepika Chenna", "Medhini Madi", "Mathangi Kumar", "Vijay Kumar", "Sitaram Chopperla", "Abhinav Tadikonda", "Kalyana Pentapati", "Deepika Chenna", "Medhini Madi", "Mathangi Kumar", "Vijay Kumar", "Sitaram Chopperla", "Abhinav Tadikonda" ], "abstract": "Background: Carpal Tunnel Syndrome (CTS) is one such common disorder among dental health care personnel caused due to the entrapment neuropathy of the median nerve in the carpal tunnel. We aimed to evaluate the pooled estimates of the CTS among dental healthcare personnel. Methods: We systematically reviewed the existing literature from six databases till January 1st, 2022. Studies reported in English along with the prevalence of CTS or where prevalence could be calculated were included. Independent screening of title and abstracts, and the full text was done by two examiners. Information collected was authors, year of publication, geographic location, type of dental healthcare personnel, sample size, distribution of age, sex, CTS, method of diagnosis, and risk of bias. The random effect model was used to estimate the pooled estimates. Results: Thirty-seven studies yielded 38 estimates. A total of 17,152 dental health care personnel were included of which 2717 had CTS. The overall pooled prevalence of CTS among the included studies was 15%, with a high heterogeneity. Meta-analysis showed no significant difference in the pooled estimates of CTS between male and female dental healthcare personnel (OR: 0.73; 95% CI: 0.52 -1.02; I2= 69.71). The pooled estimates among the dentist and dental auxiliaries were 20% and 10%, respectively. The pooled prevalence of CTS with self-reported measures, clinical examination and NCS were 21%, 13% and 8% respectively. Meta-regression showed that the prevalence estimates were significantly associated with publication year (coefficient: 0.006; 95% CI= 0.002-0.01). Conclusion: One out of seven dental health care personnel may be affected by CTS. No significant difference was seen in the prevalence of CTS between male and female dental healthcare personnel.", "keywords": [ "Carpal Tunnel", "Pain", "Dentist", "Dentist", "Dental students", "Dental auxiliaries" ], "content": "Introduction\n\nDentistry involves complex procedures with repetitive movements, firm grasp, and fine tactile movements with prolonged static postures often with poor illumination and access. Due to this dental healthcare personnel are prone to various musculoskeletal disorders.1–7\n\nCarpal Tunnel Syndrome (CTS) is one such common disorder among dental health care personnel caused due to the entrapment neuropathy of the median nerve in the carpal tunnel. It can cause sensorimotor symptoms like pain, numbness, tingling, and weakness in the hand leading to loss of grip strength and dexterity. CTS can have negative effects on the individual quality of life, functional disability, limitation of daily living, poor sleep quality, decreased productivity, and the discontinuation of the profession. It can have a significant impact on the individual’s family and the community.\n\nNumerous risk factors like repetitive actions,8 use of vibrating instruments,8,9 pregnancy, diabetes,10 obesity,10 trauma, smoking,11 increasing age,8,12 female sex,9,10,13–16 wrist diameter ratio,9 clinical experience12 and the number of working hours per day14 have been linked to the development of CTS. Studies have used different modalities for the assessment of CTS. Self-reported measures (for ex: Boston carpal tunnel questionnaire, Nordic questionnaire, hand diagram, Clinical questionnaire by Kamath and Stothard) are the most used methods of assessment. This was followed by nerve conduction studies (NCS) and clinical examination using variety of tests (Tinel’s test, Phalen’s test, or Durkan compression test) and a combination of any of the above methods.\n\nThe prevalence of CTS among dental healthcare personnel was reported to be high akin to musculoskeletal disorders when compared to the general population. However, no attempt was made to consolidate the estimates of CTS among dental healthcare personnel. Considering this, our goal was to compile the estimates of the CTS among dental healthcare professionals reported from the literature.\n\n\nMethods\n\nWe systematically reviewed the existing literature to evaluate the prevalence of CTS among dental healthcare personnel. The protocol for this study was registered with “International Platform of Registered Systematic Review and Meta-analysis Protocols” (INPLASY202210084)17 and was reported as per the “PRISMA” guidelines.\n\nA methodical search of six databases (“PubMed, Embase, Dentistry and Oral Sciences Source, CINAHL, Web of Science, and Scopus”) was conducted without any date restrictions till January 1st, 2022. The keywords used were “dentist” OR “dental student” OR “dental auxiliary” OR “dental hygienist” OR “dental personnel” AND “carpal tunnel syndrome” or “carpal tunnel” or “medial nerve entrapment” or “CTS.”\n\nStudies written in English that reported the prevalence of CTS or where the prevalence could be determined were included. Studies reported as letters, commentaries, and short communications were excluded.\n\nStudies obtained from various databases were added to “Rayyan – a web-based application” for duplicate removal and title and abstract screening. This was followed by full-text screening and data extraction. Two review authors did the screening independently, and the disagreements, if any, were resolved by a third review author.\n\nTwo review authors independently performed the data extraction. Information that was collected was authors, year of publication, country, type of dental personnel, age and sex distribution, sample size, number of participants with CTS, method of diagnosis used (self-reported, clinical examination, or NCS), the sex distribution of CTS and risk of bias.\n\nTwo review authors independently evaluated the risk of bias using a nine-item questionnaire developed by Hoy et al.18 The total score was obtained based on which the studies were graded as low (0-3), moderate (4-6), or high risk of bias (7-9).\n\nAll the analysis was done using OpenMeta software (Metafor Package 1.4, 1999). The random effect model (Restricted maximum likelihood method) was used to estimate the pooled estimates. Subgroup analysis was performed for the type of dental personnel, geographic location, and type of diagnosis. The distribution of the prevalence of CTS between males and females was evaluated using the Binary Random effect model, and the Odds ratio was calculated. Publication bias was assessed using a funnel plot and Fail-Safe N analysis using the Rosenthal approach. Meta-regression was done with publication year to evaluate time trends in the prevalence estimates. Sensitivity analysis was performed using the Leave one out method. Heterogeneity among the studies was assessed using I2 statistics. Underlying data for this review is available at Mendeley datasets.19\n\n\nResults\n\nThe search of six databases (Embase (n=77), Scopus (n=54), PubMed (n=120), CINAHL (n=465), DOSS (n=570), and Web of Science (n=95)) yielded 1381 studies, of which 249 were duplicates. A total of 1131 studies were subjected to title, and abstract screening out of which 43 studies were eligible for full-text screening. Another nine studies were obtained from manual searching of reference lists at the end of publications resulting in a total of 52 studies for full-text screening. After screening full-text, 15 studies were further excluded due to missing outcome (n=7), the secondary publication (n=3), or inappropriate study design (n=4) and full-text unavailable (n=1).20 Data extraction was performed for 37 studies which yielded 38 estimates (Figure 1, Table 1).9,12–16,21–51\n\nA total of 17,152 dental health care personnel were included in 37 studies of which 2717 had CTS. The prevalence ranged from 0 to 86%.21,42,50,51 The overall pooled prevalence of CTS was 15%, with a high heterogeneity (I2=99.18) (Figure 2).\n\nNine studies have not reported the age distribution.14,16,25,30,44–46,48,49 The age-specific estimates of CTS lacked uniformity in reporting. The mean age ranged from 21-50 years.\n\nEight studies have not reported the sex distribution of the participants.21,22,26,30,48–51 Twelve studies reported the prevalence of CTS concerning the sex of which one study had only female participants and was excluded from analysis.12 Meta-analysis showed no significant difference in the pooled estimates of CTS between male and female dental healthcare personnel (OR: 0.73; 95% CI: 0.52-1.02; P=0.07; I2=69.71) (Figure 3).\n\nAlmost half of the studies were reported from North America (n=17)12,16,21–23,25,27–29,31,32,34,46,48–51 followed by Asia (n=15)9,14,15,30,33,35–39,41–43,45,47 and Europe (n=4).13,24,26,40 Only one study was reported from South America.44 High pooled prevalence was seen among studies that were reported from Asia (25%), followed by North America (9%) and Europe (8%) (Table 2).\n\nMore than half of the included studies were reported among dentists (n=18)9,13–15,27,28,30,33,35–40,42–44,47 followed by dental auxiliaries (n=16).12,21–24,27,28,31,32,34,41,48–51 The pooled estimates among the dentist and dental auxiliaries were 20% and 10%, respectively (Table 2).\n\nThe majority of the included studies (n=21) had used only self-reported measures for estimating the prevalence of CTS.13–16,22,23,29,30,37–49 Nine studies have used nerve conduction studies9,12,24,27–29,32,34,36 out of which four studies used clinical examination along with NCS.9,32–34 Only five studies have used clinical examination.25,26,31,33,35 Three studies conducted have used Vibrometry and have reported nil prevalence.21,50,51 The pooled prevalence of CTS with self-reported measures, clinical examination and NCS were 21%, 13% and 8% respectively (Table 2).\n\nMajority of the studies (n=30) were in the low-risk category with a pooled prevalence of 17% (Tables 1 and 2).9,12–16,25–36,38,39,41–48,50,51\n\nThe funnel plot showed publication bias (Fail safe N=26129; P-value<0.001) (Figure 4).\n\nThere was no change in the overall pooled estimate of CTS using the Leave-one out method.\n\nA meta-regression was performed to evaluate the pooled estimates of CTS with publication year. The prevalence estimates were significantly associated with publication year (coefficient: 0.006; 95% CI=0.002-0.01; P=0.002) (Figure 5).\n\n\nDiscussion\n\nWe conducted a systematic review of the prevalence of CTS among dental healthcare personnel. Many systematic reviews reported a high prevalence of musculoskeletal disorders among these professionals1–7 without emphasizing the CTS.\n\nHigh heterogeneity was observed among the studies that were included in this review. The overall pooled prevalence of CTS was 15% obtained from 38 estimates. It was higher among dentists than dental auxiliaries. The prevalence was higher than the reported studies among other professionals (9.6%).52,53 The age-standardised prevalence rates of confirmed clinical and NCS were 2.1 and 3% among males and females, respectively.54 A study among Danish office workers reported a confirmed CTS prevalence of 5%.55 It was reported that repetitive activity and firm gripping could be a major risk factor for the development of CTS.52 This suggests that dental healthcare personnel have a higher risk of CTS than the general population. In our analysis, only six studies reported a prevalence of less than 5%.21,24,27,29,50,51 More than half of the studies showed higher than 10% prevalence.9,14,16,23,25,30–44,46,47 There was substantial variation in the estimates of CTS with geographic location. Studies reported from Asia showed a high pooled prevalence of CTS.\n\nThe pooled prevalence among male and female dental healthcare personnel was 14 and 17%, respectively. Few studies have reported female predilection to CTS among dental healthcare personnel9,13–16 and the general population.56 However, we found no significant difference between male and female dental healthcare personnel.\n\nThere were substantial variations in the assessment of CTS among the included studies. Methods like self-reported measures, clinical examination (Tinels test, Phalen’s test, or compression test), Vibrometry and NCS were used for the assessment of CTS. Studies that used self-reported measures showed higher pooled prevalence than those studies that used clinical examination and NCS for the diagnosis of CTS. NCS is a useful tool and can be used as complimentary methods with clinical examination in the assessment of CTS. It is not recommended to be used as a sole method of diagnosis as it has limitations like difficulty in the assessment of nerve injuries that are very distal or proximal to the extremity, timing of the test, expertise of the examiner, multi-level injury along the course of nerve or systemic polyneuropathy. Also, the nerve latency is mainly due to the available myelinated fibers than the affected fibers. Due to the above reasons, a thorough physical examination of hand is a prerequisite for the diagnosis of CTS.\n\nOur review included studies over four decades and it was seen that there was an increasing trend in the prevalence estimates of CTS. This could be attributed to many factors like increasing workload, increasing awareness about CTS, comorbidities etc.\n\nFurther high-quality studies using clinical examination for the identification of CTS among a representative sample of dental health care personnel using STROBE guidelines are required for calculating robust prevalence estimates. High heterogeneity among the included studies, inclusion of only studies that were reported in English, lack of age specific estimates, variations in the assessment of CTS are some of the limitations.\n\n\nConclusion\n\nOne out of seven dental health care personnel may be affected by CTS. There was no difference in the prevalence of CTS between male and female dental healthcare personnel. Dentists more than dental auxiliaries are affected by CTS.", "appendix": "Data availability\n\nMendeley Data: Pooled prevalence of Carpal Tunnel syndrome among dental health care providers, https://doi.org/10.17632/m2tytmjdzf.2. 19\n\nThis project contains the following underlying data:\n\n- Data CTS mendeley.xlsx\n\nMendeley Data: PRISMA checklist ‘Pooled prevalence of Carpal Tunnel syndrome among dental health care providers’, https://doi.org/10.17632/m2tytmjdzf.2. 19\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nZakerJafari HR, YektaKooshali MH: Work-Related Musculoskeletal Disorders in Iranian Dentists: A Systematic Review and Meta-analysis. Saf. Health Work. 2018; 9(1): 1–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLeggat PA, Kedjarune U, Smith DR: Occupational health problems in modern dentistry: A review. Ind. Health. 2007; 45(5): 611–621. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShaffer SW, Moore R, Foo S, et al.: Clinical and electrodiagnostic abnormalities of the median nerve in US Army Dental Assistants at the onset of training. U.S. Army Med. Dep. J. 2012; 72–81. PubMed Abstract\n\nEhsan MA, Ehsan S, Arshad HS: Frequency of Carpal Tunnel Syndrome in Dentists Working in Government Hospitals of Lahore. Int. J. Sci. Res. 2016; 5(5): 1672–1675.\n\nBorhan Haghighi A, Khosropanah H, Vahidnia F, et al.: Association of dental practice as a risk factor in the development of carpal tunnel syndrome. J. Dent. (Shiraz, Iran). 2013; 14(1): 37–40.\n\nMunirah M, Normastura A, Azizah Y, et al.: Prevalence of Probable Carpal Tunnel Syndrome and itsAssociated Factors among Dentists in Kelantan. Int. J. Collab. Res. Intern. Med. Public Heal. 2014; 6(8): 247–259.\n\nPai MB, Shenoy R, Rao A, et al.: Symptoms of Carpal Tunnel Syndrome in a dental work force of a developing country. Int. J. Adv. Res. 2014; 2(2): 87–94.\n\nAhmed KA, Siddiqui AZ, Ahmed MR, et al.: Prevalence of carpel tunnel syndrome in the dentists working in Karachi. Pakistan Oral Dent J. 2014; 34(4): 588–591.\n\nHodacova L, Sustova Z, Cermakova E, et al.: Self-reported risk factors related to the most frequent musculoskeletal complaints among Czech dentists. Ind. Health. 2015; 53(1): 48–55. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNurfarah Wahidah MN, Nurul SN, Munirah MANAR, et al.: Probable carpal tunnel syndrome and its coping Hospital Universiti Sains Malaysia. J. Sch. Dent. Sci. USM. 2016; 11(2): 31–38.\n\nPrasad DA, Appachu D, Kamath V, et al.: Prevalence of low back pain and carpal tunnel syndrome among dental practitioners in Dakshina Kannada and Coorg District. Indian J. Dent. Res. 2017; 28(2): 126–132. PubMed Abstract \| Publisher Full Text\n\nInbasekaran D, Sankari M, Nambi G: Prevalence of carpal tunnel syndrome among dentists in Chennai, India. Drug Invent. 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "165926", "date": "24 Mar 2023", "name": "Dileep Nag Vinnakota", "expertise": [ "Reviewer Expertise Implantology", "Full mouth 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\nI have gone through the meta-analysis sent for peer review. The topic seems interesting, but there are lot of flaws which are of concern. I have mentioned the possibilities of changing the manuscript section wise.\nTitle: The authors have mentioned the title as “Meta-analysis of the prevalence of carpal tunnel syndrome among dental health care personnel”. I feel the title can be improved as “Prevalence of carpal tunnel syndrome among dental health care personnel worldwide - A systematic review and meta-analysis”\nIntroduction: The need for the study has been focused by the authors properly. However, can elaborate on the clinical diagnosis of the condition (including the sensitivity and specificity of the tests), and a note on the differential diagnosis. A systematic review is also published on the diagnosis of this condition. This part is important as it has a link with the way the authors can mold the quality of the present systematic review.\nMethodology: Many sections are poorly written.\nThe authors can mention the keywords separately as MeSH words and alternate words employed for the search.\n\nThe inclusion and exclusion criteria are not proper. The authors can consider only those studies that have employed nerve conduction tests, instead of considering those with self-report. There are definite chances of bias, if the self-reported measures are considered for diagnosis. Also many factors like number of years practised in dentistry, number of working hours, the knowledge of ergonomics, and age of the dental personnel all play a key role on prevalence. The authors did not take any step to cut down the effect of confounding factors in their criteria for inclusion.\n\nUnder extraction of data, in text, the authors have mentioned that ‘information regarding country of study’, but in the table the authors have considered only continent.\n\nUnder risk of bias assessment, the authors have mentioned that risk was evaluated using a nine item questionnaire. The authors have to elaborate the items in a tabular form along with the total scores obtained by individual studies. Need to mention the reason for not considering the STROBE guidelines for evaluation? I think they can add this part also.\n\nUnder statistical analysis, the authors did not mention the test employed for the publication bias. Is it Begg and Egger test?\nResults:\nIt is clearly evident from Table 1 that the prevalence is more in studies that have diagnosed the condition using self-reported measures. The type of dental health care personnel also cannot be combined; the work done by dentists is different from dental assistants. The mean age as mentioned in the review is in the range of 21-50 years, which is too long. All these have an influence on the overall estimate mentioned.\n\nClarity of the forest plot showing gender differences is not clear. The authors need to mention the sides as male and female, so that the readers can easily depict the side which is favoured.\n\nUnder publication bias, the authors did not explain about the symmetry of the funnel plot. What is inverse standard error? Also, the reason for selecting the inverse standard error needs mentioning. The scatter plot needs explanation regarding the precision of individual studies.\n\nUnder sensitivity analysis, the authors need to mention the outliers and the explanation of difference in the overall estimate after removal of studies with high prevalence like Prasad et al (2017).\nDiscussion: Discussion is not enough. Authors can discuss the importance of case control studies to know whether dentists are really more prone for this condition compared to normal population. Authors can discuss about the ergonomics to prevent these conditions. Can discuss about differential diagnosis of this condition and discuss about other neurologic, musculoskeletal and vascular conditions that have similar symptoms as carpal tunnel syndrome. Also, management of this condition (non-surgical and exercises) needs mentioning.\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", "responses": [ { "c_id": "9890", "date": "20 Jul 2023", "name": "Kalyana Pentapati", "role": "Author Response", "response": "Thank you for the effort and time take in reviewing this manuscript. Below are our responses to your comments. Reviewer 1: I have gone through the meta-analysis sent for peer review. The topic seems interesting, but there are lot of flaws which are of concern. I have mentioned the possibilities of changing the manuscript section wise. Title: The authors have mentioned the title as “Meta-analysis of the prevalence of carpal tunnel syndrome among dental health care personnel”. I feel the title can be improved as “Prevalence of carpal tunnel syndrome among dental health care personnel worldwide - A systematic review and meta-analysis” Response: We will edit the same in our manuscript “Worldwide prevalence of carpal tunnel syndrome among dental health care personnel - A systematic review and meta-analysis” Introduction: The need for the study has been focused by the authors properly. However, can elaborate on the clinical diagnosis of the condition (including the sensitivity and specificity of the tests), and a note on the differential diagnosis. A systematic review is also published on the diagnosis of this condition. This part is important as it has a link with the way the authors can mold the quality of the present systematic review. Response: Thank you for your valuable insight. We had gone through MacDermid and Wessel to understand the value-added points. They concluded that the primary limitation of establishing a gold standard diagnosis for CTS. This difficulty, combined with methodologic flaws, made interpretation difficult. Also, there was no guarantee that these choices increased the validity of our results. It was also stated that we should not consider the findings of this review to be conclusive concerning the value of clinical tests in the diagnosis of CTS. Furthermore, a systematic review requires that issues be addressed using specific and documented methods. Therefore, discussions on why certain tests may be better in specific situations or relevant in different stages of CTS are beyond the scope of this review. Our review focussed on the burden of disease (CTS) among dental health professionals which was by pooling the estimates that have been reported from the literature. Various methods are available in the literature for the diagnosis of CTS which are broadly categorized as self-reported, clinical, and nerve conduction studies. All these tests have their own advantages and limitations that are discussed by the authors of these primary studies. Methodology: Many sections are poorly written. Query: The authors can mention the keywords separately as MeSH words and alternate words employed for the search. Response: MeSH words are only specific for Pubmed. We have used All fields option for all the databases and have not restricted our search to title, abstract and keywords search. Based on our previous review experience on musculoskeletal disorders, we noticed that few studies that reported prevalence estimates of musculoskeletal disorders have reported carpal tunnel syndrome. If we restrict our search to title, abstract and keywords, these studies would be missed during the first stage of screening. We will reframe the sentence as search terms instead of keywords in the manuscript. Query: The inclusion and exclusion criteria are not proper. The authors can consider only those studies that have employed nerve conduction tests, instead of considering those with self-report. There are definite chances of bias, if the self-reported measures are considered for diagnosis. Also many factors like number of years practiced in dentistry, number of working hours, the knowledge of ergonomics, and age of the dental personnel all play a key role on prevalence. The authors did not take any step to cut down the effect of confounding factors in their criteria for inclusion. Response: There is no consensus or gold standard for the diagnosis of carpal tunnel syndrome. Nerve conduction studies are a useful tool and can be used as complementary methods with clinical examination in the assessment of CTS. Use of such methods in epidemiological surveys is quite challenging as it is costly, requires trained personnel to perform and interpret and cannot be used alone for the diagnosis of CTS. Hence, there were many attempts to develop self-reported measures and clinical examination for the diagnosis of CTS. Self-reported measures like boston carpal tunnel questionnaire has been used widely and was shown to have acceptable validity and reliability in many previous studies. We agree that there were will be bias, hence we reported the estimates of CTS as per the diagnostic method used in the primary studies. We have revised the sentence: Studies written in English that reported the prevalence of CTS using self-reported or clinical tests or NCS or where the prevalence could be determined were included. Studies reported as letters, commentaries, and short communications were excluded. We agree with reviewers that there are many factors (years practiced in dentistry, number of working hours, the knowledge of ergonomics, and age of the dental personnel) on the prevalence estimates. The main aim of this review was to quantify the prevalence estimates obtained from the published literature. To look at these factors that may have the effect of confounding, it is imperative that published literature reports that prevalence estimates as per age groups, work experience, level of ergonomics, etc. We have reviewed the included studies and extracted data on age, clinical experience, and gender distribution as per the CTS distribution. Response: We will include the information below in the manuscript. Based on the data from the included studies, age estimates with respect to CTS and No CTS was reported by only six studies. Studies that reported age as categorical data could not be analysed as there was no similarity in the categories used (Table 2). Three studies reported age as continuous variable. Meta-analysis showed that there was no significant difference in the age between CTS and No CTS groups (SMD: 0.1; 95%CI: -0.17 – 0.38) (figure 3). Image 1; Image 2 A total of seven studies reported clinical experience which was either continuous (n=3) or categorical (n=4). Meta-analysis showed that there was no significant difference in the mean clinical experience between the groups (SMD: -0.03; 95%CI: -0.31 – 0.24) (Figure 5). Categorical data on clinical experience was categorized as < 10 years and > 10 years for analysis. Meta-analysis showed no significant difference in the pooled estimates between different levels of clinical experience (OR: 0.76; 95%CI: 0.39-1.47) (Figure 6). Image 3; Image 4 Query: Under extraction of data, in text, the authors have mentioned that ‘information regarding country of study’, but in the table the authors have considered only continent. Response: Yes. We have collected the information on country. However, country wise estimates were not feasible. Hence, we pooled the estimates as per the continent. Query: Under risk of bias assessment, the authors have mentioned that risk was evaluated using a nine-item questionnaire. The authors have to elaborate the items in a tabular form along with the total scores obtained by individual studies. Need to mention the reason for not considering the STROBE guidelines for evaluation? I think they can add this part also. Response: Thank you for your comments. We will incorporate the item-wise scores for individual studies. The questionnaire used for quality assessment was validated and primarily developed for the assessment of risk of bias for systematic reviews on prevalence studies. STROBE guidelines are primarily intended as a checklist for reporting cross-sectional studies. The valid overall risk of bias scores cannot be computed so that studies can be rated as high or low risk of bias from STROBE guidelines. Hence, it was not used in this study. Image 5 Query: Under statistical analysis, the authors did not mention the test employed for the publication bias. Is it Begg and Egger test? Response: We have used Fail-Safe N analysis using the Rosenthal approach. We will add this information also in the manuscript. Statistical analysis: Publication bias was assessed using a funnel plot and Fail-Safe N analysis using the Rosenthal approach and Egger regression test. Publication bias: Egger Regression Test for Funnel Plot Asymmetry showed asymmetry (Z=2.187; P=0.029). Query: It is clearly evident from Table 1 that the prevalence is more in studies that have diagnosed the condition using self-reported measures. The type of dental health care personnel also cannot be combined; the work done by dentists is different from dental assistants. The mean age as mentioned in the review is in the range of 21-50 years, which is too long. All these have an influence on the overall estimate mentioned. Response: Yes, we agree with the reviewer that self-reported measures have yielded higher estimates and we have reported the estimates as per the diagnostic criteria used in the studies. We also agree with the fact that type of dental health care personnel cannot be combined as all have different range of work but all these personnel do activities that requires repetitive movements, firm grasp, and fine tactile movements with prolonged static postures. Many studies which were included in this review have included all types of dental health personnel. Studies that reported prevalence separately were captured separately. In our review, we have mentioned the estimates as per the type of healthcare personnel. We understand that all these factors along with age and clinical experience have potential influence. This review is focussed on the burden of CTS among these dental health care personnel. Query: Clarity of the forest plot showing gender differences is not clear. The authors need to mention the sides as male and female so that the readers can easily depict the side which is favoured. Response: We will edit the figure in the manuscript as per your recommendation. Image 6 Query: Under publication bias, the authors did not explain about the symmetry of the funnel plot. What is inverse standard error? Also, the reason for selecting the inverse standard error needs mentioning. The scatter plot needs an explanation regarding the precision of individual studies. Response: We will add the following details to the manuscript. Inverse standard error in the y-axis depicts the precision of the studies. It helps in identifying the studies with lower precision which will be distributed at the bottom. Inverse standard error was selected as there was no inversion required when compared to plots that use standard error in the y-axis where studies with large sample sizes and lower standard error are placed at the top of the graph. The plot showed asymmetry where in large studies showed higher precision and lower prevalence estimates whereas smaller studies had lower precision and higher prevalence estimates. Query: Under sensitivity analysis, the authors need to mention the outliers and the explanation of difference in the overall estimate after the removal of studies with high prevalence like Prasad et al (2017). Response: We performed a sensitivity analysis using Leave -one out method. The prevalence estimate marginally decreased to 13% after the removal of Prasad et al. We will add this information in the manuscript. Query: Discussion is not enough. Authors can discuss the importance of case-control studies to know whether dentists are really more prone to this condition compared to the normal population. Authors can discuss the ergonomics to prevent these conditions. Can discuss about differential diagnosis of this condition and discuss about other neurologic, musculoskeletal and vascular conditions that have similar symptoms as carpal tunnel syndrome. Also, the management of this condition (non-surgical and exercises) needs mentioning. Response: The below information will be added in the manuscript. Further case-control studies are required to understand the role of the dentistry profession as a risk factor for the development of CTS are needed. During training years, emphasis should be on the potential role of the dental profession in the development of CTS and other musculoskeletal disorders. There is a need for the development and implementation of preventive strategies for early detection and prevention of CTS. Comprehensive preventive strategies like workplace postural requirements and adoption of ergonomic postures, use of ergonomically designed instruments and equipment to reduce strain on the hand and wrist, the importance of intermittent breaks between patients, an alternation between the activities, keeping wrists in a neutral position, strengthening and stretching daily which aid in alleviating the muscular tension and promote blood circulation, minimize repetitive movements and management of patient flow can be incorporated into the curriculum during training years to prevent or minimize the onset of musculoskeletal disorders. Regular monitoring and evaluation of musculoskeletal disorders need to be mandated for high-risk individuals. Workplace-associated CTS must be identified earlier, and care should be exercised on the prevention and progression of the development of CTS. Active referral should be initiated by the employer who is at risk of development of CTS. It is important for the dental health care professional to be aware of the symptoms of CTS. Many conditions like systemic neurologic disorders (motor neuron disease, multiple sclerosis, and hereditary neuropathy), cervical spine disorders (cervical spondylotic myelopathy, cervical radiculopathy, and syringomyelia), tumors (Pancoast tumors, benign peripheral nerve tumors, malignant peripheral nerve sheath tumors, intraneural ganglia), inflammatory and autoimmune disorders. The management of CTS includes conservative methods like wrist splinting in the neutral position at night, analgesics, corticosteroid injections, and nerve and tendon gliding exercises with varying degrees of results. Also, the carpal tunnel can be surgically decompressed to relieve the symptoms when there is a lack of response to the above. Early diagnosis will help in initiating early interventions like medication, splinting, and changes in daily activities and can be relieved without surgical interventions. Therefore, a multi-pronged approach with ergonomic guidelines, workload management strategies, and health education and prevention can significantly reduce the risk of CTS among dental personnel and enhance their occupational well-being." } ] }, { "id": "178238", "date": "19 Jun 2023", "name": "Y. Ravi shankar Reddy", "expertise": [ "Reviewer Expertise Musculosketal 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\nTitle: Meta-analysis of the prevalence of Carpal Tunnel Syndrome (CTS) among dental health care personnel.\n\nProvide a clear rationale for conducting the study and highlight the gap in the existing literature that the study aims to address.\n\nClearly define the inclusion and exclusion criteria for the selection of studies to ensure transparency and reproducibility.\n\nDiscuss the methods used for data extraction and risk of bias assessment in more detail, including the specific items evaluated in the risk of bias assessment tool.\n\nAddress the high level of heterogeneity among the included studies and discuss potential reasons for this heterogeneity. Explore possible sources of variation, such as differences in study design, participant characteristics, diagnostic methods, or geographic location.\n\nProvide a more comprehensive discussion of the limitations of the study, including the potential impact of publication bias, language restriction, and the quality of the included studies.\n\nDiscuss the implications of the findings in more depth, including the potential impact of CTS on the quality of life, functional disability, and productivity of dental healthcare personnel.\n\nConsider the potential confounding factors or interactions that could influence the relationship between CTS and dental healthcare personnel, such as the duration of practice, specific dental procedures performed, or the use of ergonomic interventions.\n\nProvide recommendations for future research based on the identified limitations and gaps in knowledge. Discuss the need for studies with larger sample sizes, more rigorous study designs, and standardized diagnostic criteria.\n\nDiscuss the practical implications of the findings and potential interventions that can be implemented to reduce the risk of CTS among dental healthcare personnel. Consider the development of guidelines for ergonomic practices, workload management, and education on early detection and prevention of CTS.\n\nEnsure that the conclusion aligns with the findings of the study and emphasizes the key takeaways for researchers, clinicians, and policymakers.\n\nConsider the broader implications of the study findings, such as the potential impact on healthcare policy, occupational health and safety regulations, and professional training programs for dental healthcare personnel.\n\nFinally, acknowledge any limitations of the study not previously discussed and provide suggestions for further research in the field of CTS among dental healthcare personnel.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [ { "c_id": "9891", "date": "20 Jul 2023", "name": "Kalyana Pentapati", "role": "Author Response", "response": "We thank your efforts in reviewing the manuscript. Below are the responses for your comments. Query: Provide a clear rationale for conducting the study and highlight the gap in the existing literature that the study aims to address. Response: We added the following information: Data pertaining to the pooled prevalence of CTS and associated risk factors is lacking among dental healthcare personnel. Query: Clearly define the inclusion and exclusion criteria for the selection of studies to ensure transparency and reproducibility. Response: we have revised as follows: Studies written in English that reported the prevalence of CTS using self-reported or clinical tests or NCS or where the prevalence could be determined were included. Studies reported as letters, commentaries, and short communications were excluded. Query: Discuss the methods used for data extraction and risk of bias assessment in more detail, including the specific items evaluated in the risk of bias assessment tool. Response: Revised the information as below: Two review authors independently performed the data extraction. Information that was collected was authors, year of publication, country, type of dental personnel (Dentist, dental auxiliary or Mixed population), age and sex distribution, age, sex and clinical experience distribution with respect to the distribution of CTS, sample size, number of participants with CTS, method of diagnosis used (self-reported, clinical examination, or NCS), the sex distribution of CTS and risk of bias. The first four questions (representative target population and sampling frame, random selection and non-response bias) assessed the external validity and the later five questions (participant or proxy data collection, acceptable case definition, validity and reliability of the instrument, similar data collection for all participants and specifying the numerators and denominators) assessed the internal validity of the study. All the questions were rated as low or high risk. Query: Address the high level of heterogeneity among the included studies and discuss potential reasons for this heterogeneity. Explore possible sources of variation, such as differences in study design, participant characteristics, diagnostic methods, or geographic location. Response: We attempted to explore the reasons for heterogeneity using sub-group analysis. The nature of the study design was same for all the studies. With respect to participant characteristics, we analysed based on the type of dental health care personnel which also showed high heterogeneity. Similar, was the case with geographic location. With respect to type of diagnosis, clinical examination showed lower levels of heterogeneity (<50%) than other modalities of diagnosis. However, the number of studies that used clinical examination were less (n=5). Query: Provide a more comprehensive discussion of the limitations of the study, including the potential impact of publication bias, language restriction, and the quality of the included studies. Response: Added the following information: Publication bias was due to less precise studies with high prevalence estimates which could have distorted the overall estimates. Language bias due to inclusion of studies that were reported in English could have over or under-estimated the overall pooled estimates. Although, most of the studies had low risk of bias, the lack of acceptable diagnostic standard could have caused considerable heterogeneity. Query: Discuss the implications of the findings in more depth, including the potential impact of CTS on the quality of life, functional disability, and productivity of dental healthcare personnel. Response: Added the following information: Implications of CTS can be at an individual, family or workplace level. Symptoms like pain, numbness, tingling and weakness in the hand and fingers can lead to significant functional disability to the dental personnel while performing the dental procedures. There by substantially affecting the individuals’ quality of life in performing daily activities and decreased productivity at workplace leading to loss of work, work place absenteeism along with financial losses. Indirectly, employers can face decreased productivity and loss of time in hiring new professionals. This can affect the overall productivity. Moreover, CTS can have a profound impact on the outside of the work, affecting simple tasks like writing, typing and grasping objects which may become challenging and be a limitation in their professional and personal activities alike. Query: Consider the potential confounding factors or interactions that could influence the relationship between CTS and dental healthcare personnel, such as the duration of practice, specific dental procedures performed, or the use of ergonomic interventions. Response: We agree with reviewers about the role of potential confounders. We have included the data specific to age and clinical experience with respect to CTS. However, data on other factors like type of dental procedures and use of ergonomic interventions have not been reported in relation to the CTS prevalence among the included studies. It is crucial for further research to account for these confounding factors and assess their relationship between CTS and dental healthcare personnel. Query: Provide recommendations for future research based on the identified limitations and gaps in knowledge. Discuss the need for studies with larger sample sizes, more rigorous study designs, and standardized diagnostic criteria. Response: Added information as below: Further large high-quality studies using clinical examination for the identification of CTS among a representative sample of dental health care personnel using STROBE guidelines are required for calculating robust prevalence estimates. A larger sample would allow for a more representative distribution of demographic and professional characteristics, enabling researchers to explore potential subgroups that may be more susceptible to CTS. Also, a larger sample size would provide more statistical power to detect significant associations and to examine the effects of potential confounding factors. Case control studies are required to understand the role of dental profession as risk factor for the development of CTS. Studies can use self-reported questionnaires to screen potential participants following which a clinical examination using various tests need to be adopted to diagnose CTS. Furthermore, adapting standardized, validated diagnostic criteria for CTS across studies would facilitate more apt comparisons of different studies and enhance the reliability of the study findings. Query: Discuss the practical implications of the findings and potential interventions that can be implemented to reduce the risk of CTS among dental healthcare personnel. Consider the development of guidelines for ergonomic practices, workload management, and education on early detection and prevention of CTS. During training years, emphasis should be on the potential role of dental profession in the development of CTS and other musculoskeletal disorders. There is need for the development and implementation of preventive strategies for early detection and prevention of CTS. Comprehensive preventive strategies like workplace postural requirements and adoption of ergonomic postures, use of ergonomically designed instruments and equipment to reduce strain on the hand and wrist, the importance of intermittent breaks between patients, an alternation between the activities, keeping wrists in a neutral position, strengthening and stretching daily which aid in alleviating the muscular tension and promote blood circulation, minimize repetitive movements and management of patient flow can be incorporated into the curriculum during training years to prevent or minimise the onset of musculoskeletal disorders. Regular monitoring and evaluation of musculoskeletal disorders need to be mandated for high-risk individuals. Workplace-associated CTS must be identified earlier and care should be exercised on the prevention and progression of the development of CTS. Active referral should be initiated by the employer who is at risk of development of CTS. It is important for the dental health care professional to be aware of the symptoms of CTS. Early diagnosis will help in initiating early interventions like medication, splinting, and changes in daily activities and can be relieved without surgical interventions. Therefore, a multi-pronged approach with ergonomic guidelines, workload management strategies, and health education and prevention can significantly reduce the risk of CTS among dental personnel and enhance their occupational well-being. Query: Ensure that the conclusion aligns with the findings of the study and emphasizes the key takeaways for researchers, clinicians, and policymakers. Response: Future studies should explore the relationship between various potential risk factors and CTS. There is a need to develop and incorporate guidelines for the prevention of work-related musculoskeletal disorders into the training curriculum. Continuing dental education programs for the prevention of musculoskeletal disorders need to be conducted for the benefit of dental health care personnel. Query: Consider the broader implications of the study findings, such as the potential impact on healthcare policy, occupational health and safety regulations, and professional training programs for dental healthcare personnel. Response: Findings of this review highlight the potential impact of CTS among dental healthcare personnel. Policymakers need to ensure the development and implementation of the guidelines for the prevention of work-related musculoskeletal disorders and the incorporation of the same into the curriculum. Occupational Safety and Health Administration guidelines on the prevention of work-related musculoskeletal disorders have elements like management support, involvement of staff, training, identification of problems, early reporting, solutions to control hazards and evaluation. It should also emphasize the importance of the number of patients seen and attended, periodic breaks, task rotation, workflow and workload in the prevention of musculoskeletal disorders. Query: Finally, acknowledge any limitations of the study not previously discussed and provide suggestions for further research in the field of CTS among dental healthcare personnel. Response: The information below was added: Further large high-quality studies using clinical examination for the identification of CTS among a representative sample of dental health care personnel using STROBE guidelines are required for calculating robust prevalence estimates. A larger sample would allow for a more representative distribution of demographic and professional characteristics, enabling researchers to explore potential subgroups that may be more susceptible to CTS. Also, a larger sample size would provide more statistical power to detect significant associations and to examine the effects of potential confounding factors. Case control studies are required to understand the role of the dental profession as a risk factor for the development of CTS. Studies can use self-reported questionnaires to screen potential participants following which a clinical examination using various tests need to be adopted to diagnose CTS. Furthermore, adapting standardized, validated diagnostic criteria for CTS across studies would facilitate more apt comparisons of different studies and enhance the reliability of the study findings. High heterogeneity among the included studies, inclusion of only studies that were reported in English, publication bias, lack of age specific estimates, and variations in the assessment of CTS are some of the limitations. Publication bias was due to less precise studies with high prevalence estimates which could have distorted the overall estimates. Language bias due to the inclusion of studies that were reported in English could have over or under-estimated the overall pooled estimates. Although, most of the studies had low risk of bias, the lack of acceptable diagnostic standards could have caused considerable heterogeneity." } ] } ]	1	https://f1000research.com/articles/12-251
https://f1000research.com/articles/10-926/v1	15 Sep 21	{ "type": "Research Article", "title": "Hearing aid through skin sensory for profound deaf people", "authors": [ "Yasothei Suppiah", "M Chandran Maruthan", "Fazly Salleh Abas", "M Chandran Maruthan", "Fazly Salleh Abas" ], "abstract": "An individual with profound deafness or total hearing loss has a hearing threshold of 80dB or more. The ineffectiveness of hearing aids, surging costs and complex surgeries for cochlear implants have discouraged many to opt for these types of treatments. Hence, this research aims to provide an alternative hearing aid that stimulates “hearing” through the skin sensory, which is more affordable and accessible for the profoundly deaf or total hearing loss community. We have developed four initial vibrating transducers with single spectrum, which are strapped to a belt. The transducers pick up audible sounds through a microphone, amplifies the sound to a high-level signal, stimulating a vibration pattern on the human skin sensory. The belt was tested on 30 random people who identified as normal, partial, and profoundly deaf. When the belt was strapped to the individual’s waist, audible sound was played (stimulus) and the individual was asked whether\n\nhe/she can feel a stimulation or vibration on their skin, and if so, state the sound source direction. Based on the test, all individuals were able to feel the vibrating stimulation on their skin, and they were also able to state the directions accurately. The various vibrating pattern that stimulates the human sensory system for the profoundly deaf can be learned over time, which could serve as useful information. However, interpreting and identifying the different types of vibrating pattern perceived through the skin remains a huge challenge for profoundly deaf people. As hearing through skin sensory is a very new area of research, there are very limited research articles published in this field. Thus far, this is the first study to evaluate the method of audio spectrum to develop hearing aid through skin sensory.", "keywords": [ "profound deaf", "sound", "hearing device", "vibrating pattern", "skin sensory", "stimulation", "transducers", "spectrum" ], "content": "Introduction\n\nThe World Health Organization (WHO) has adopted a grading system based on audiometric measurements to standardize the way in which severity of hearing loss of a person is reported. According to WHO,1 a profound deafness is defined as a person who has a hearing threshold of 80 to 95 decibels (dB). A person with complete or total hearing loss has a threshold of 95dB or more. On the other hand, a normal hearing person has a hearing threshold of less than 20dB. Furthermore, they stated that almost 30 million people worldwide have profound or complete hearing loss in both ears. Based on their reported statistics on number of people with moderate or higher levels of hearing loss, 80% are from low income and middle-income countries as opposed to 20% that are from high-income countries.1\n\nA hearing aid or a cochlear implant is the common solution for induvial that are profoundly or severely deaf.2 The purpose of hearing aid is sound amplification; therefore, it is more suitable for mild hearing impairment.3,4 Besides that, the treatment based on cochlear implant is too costly and involves complex and risky surgery. In addition, hearing-impaired users still encounter substantial practical and social challenges with the use of this aid. At present, sign language5-7 and speech-reading8 are commonly applied in schools for the deaf.\n\nRecent studies show that the human ear and the auditory nerve are not the only channel for gaining audio signals.10,11 There are several processes such as obtaining sound signals, translating voice signals to electrical signals, and producing frequency resolution can be achieved through the advancement of electronic devices. In other words, this additional tactile stimulus could help the profoundly deaf person wearing the electronic device to perceive sounds.\n\nA study on multi-channel array skin-hearing technology was proposed which involved the stimulation of the skin by the electrical signal based on the sound.9 This enabled the profoundly deaf person to receive sound signals through the skin to accomplish the purpose of hearing the sound. The advantages of their technology were that it does not rely on intact hearing, and it was cost-effective. Furthermore, Li, J et al.10 showed that voice signal can be transferred using the cutaneous sensory nerves and it can also distinguish different speech signals. Their findings demonstrate that skin sensory nerves are a reliable replacement for the auditory nerve in the challenges facing individuals with severe-to-profound hearing loss.\n\nA very recent study11 has shown that these individuals can learn to identify sounds that are algorithmically translated into patterns of vibration on the skin on the wrist. Furthermore, the users of the device could identify different sounds from the vibrations alone, which gradually improved over the course of one month. The analysis on the wearable sensory device unlocks the gateway to auditory stimuli, which could be interpreted through skin.11\n\nThe aim of this study was to develop a hearing aid that stimulates “hearing” through skin sensory, which is more affordable and accessible for the profoundly deaf or total hearing loss community. Hence, we embarked into this research as studies on hearing through skin sensory seems to be a promising area for the beneficial of the society of profound hearing people in terms of safety and affordability.\n\n\nMethods\n\nThe first phase of this study was to design a skin sensory stimulator by using a hand phone coin vibrator or micro actuator (MEMS) that allows the sound vibrations to be detected through the user’s skin. Figure 1 briefly demonstrates the stages of designing the human sensory stimulator.\n\nA Sound Transducer uses electrical energy to produce mechanical vibrations to disturb the surrounding air to produce sound regardless of whether the frequency is audible or inaudible. Audio Sound Transducer includes an input sensor that transforms sound into an electrical signal such as a microphone, and an output actuator that transforms the electrical signals back into sound, such as a loudspeaker. A preamplifier converts a weak electrical signal into an output signal, which is powerful enough to be noise tolerant. Absence of this will cause the output signal to be noisy or misleading. Due to this, the preamplifier is frequently located near to the sensor which reduces the effects of noise and other interference. A frequency filter is an electrical circuit that either stops or passes frequency from electrical signal with respect to specific frequency needed for further process. There are two types of filters, passive filter which uses passive components, and active filter that uses active components. Audio spectrum analysers are commonly used by sound engineers for various applications. Measuring the frequency response and analysing distortion characteristics of different types of audio tools are some of these applications. Micro actuators are active devices proficient of producing mechanical motion of solids or fluids. Hand phone coin vibrator is taken from the concept of cell phone vibration motor. We developed a simple single audio signal vibration array, which is based on the LM3915 Dot/Bar Display Driver and an electret microphone.\n\nSound sensor module gives a simple method to detect sound and it is usually used for the purpose of detecting sound intensity. It uses a microphone as a transducer which supplies the input audio signal to an amplifier, peak detector, and buffer. This module is made of three functional elements, the sensor on the front of the module will perform the pick-up (transducer), then the analogue signal is sent to the amplifier to amplify the signal. Accommodated with the adjustable voltage reference and an accurate ten-step voltage divider is the IC LM3915. The advantage of substituting conservative meters with a light-emitting diode (LED) bar graph is that it provides a quicker response, and a more rugged display with high visibility that provides the ease of interpretation of an analog display. As an initial test device, a transducer vibrating device circuit is designed to study the response of subjects to vibrating motor or actuator to skin sensory. The circuit (Figure 2) utilises a LM358 operational amplifier. An electret microphone preamplifier will pick-up the audible signal from the surrounding and amplifies it through a first stage operational amplifier to a process able signal. The signal will then pass through a second stage amplifier comparator to increase the voltage level high enough to drive the vibrator or actuator. A transistor interface is used to drive the vibrator or actuator in accordance with the sound received from the electret microphone.\n\nIn this research, the initial testing model was designed based on the LM3915 audio level indicator with LEDs converted to hand phone coin vibrating devices. The circuit design development and drawing were done with the NI Multisim Electronic computer-aided design (CAD) software. The circuit is then simulated to produce a printed circuit board (PCB). The schematic circuit diagram is shown in Figure 3. The initial design (Figure 3) will be upgraded to an audio spectrum analyser (Figure 4), by using the Arduino processor for a multichannel wearable spectrum vibrator.\n\nThe spectrum analyser measures and displays the amplitude of a given input signal set verses the full frequency ranges of the instrument. Its main purpose is to measure the strength of the spectrum of both known and unknown signals. This audio spectrum analyser enables us to see the frequencies present in audio or sound and produces the graph of all the frequencies that are present in a sound source at any given time. The Arduino is a microcontroller board that contains everything needed to support the microcontroller to create a led audio spectrum matrix. The board is equipped with sets of digital and analogue input/output (I/O) pins that may be interfaced to various expansion boards (shields) and other circuits.\n\nThe initial experiment uses a single overall sound to vibrate the device which will be used to stimulate the skin sensory. The electret microphone will pick up audio or sound signal which will feed to a preamplifier with adjustable gain of sound. This is to test the subject whether they can perceive sound through the vibrating motor or actuator. The single vibrating device then will be upgraded to Audio spectrum vibrators in respond to a visible led matrix. The led matrix would then be replaced with coin vibrator or actuator to give more precise vibrating pattern. The sound sensor can detect the frequency range from 20hz -20khz as this is the normal human hearing range. By using this type of sound sensor, it will enable the profoundly deaf people to “hear” the sound through their skin. The hand phone coin vibrators or micro actuator acts as an audio spectrum vibrator to create a vibrating pattern. This vibrating pattern will then be used to stimulate the human sensory system such as the skin for the profoundly deaf person, so they can use the vibration pattern as information. This repeating vibrating pattern stimulation will create a memory of a particular vibrating pattern for future recognition when similar sound is “heard” through the microphone.\n\nThe LED Matrix will have different types of frequency columns and its own vibrating devices with different sound intensity (dB) levels. Each column will indicate the frequency level representation based on how it is programmed. For example, if there is a sound present, the frequency of the led matrix column will be activated to the maximum dB level which was picked up by the electret microphone. By changing the LEDs to vibrating stimulation, the profoundly deaf person can feel and “hear” the sound through his or her skin sensory system.\n\n\nResults\n\nDue to the recent outbreak of covid-19 pandemic, profoundly deaf individuals from different institutions, schools, or hospitals were not able to participate in our study.\n\nTherefore, we randomly selected 30 people: 20 normal, seven partially deaf and three profoundly deaf (Underlying data) (12), who were mostly friends and relatives that lived within a 10 km radius of the authors residential area. All the 30 participants have given a written consent and they voluntarily agreed to participate in this study. We developed four initial vibrating transducers with single spectrum, which were strapped to a belt. Once the individuals wore the belt on his/her waist, the four transducers were placed at the front, back, left, and right side of the individual’s waist (Figure 5). Audible sound was played (stimulus) and the individual was asked whether he/she felt a stimulation at the point of the transducer and if so, state the direction of the sound source. Based on the experiments, both normal and the partial or profoundly deaf individuals felt the vibrating stimulation on their skin and accurately stated the directions of the sounds. This initial experiment was successful, which is an important direction for the future development of a hearing aid through human sensory skin. Further advancement of a more comprehensive device using the concept of spectrum analyser is now in progress. The sound signals will then be fed to multiple audio filters and audio spectrum analyser to produce sound audio spectrum to drive multiple vibration on motors or actuators of the device.\n\n\nConclusions\n\nDespite the advancement of various hearing devices that improve the life of profoundly deaf people around the globe, there are still many limitations and drawbacks, which emphasizes the need to further improve such technologies. The study of “hearing through the skin” is very promising and leads to affordable and safe solutions for the profoundly deaf and completely deaf people. As far as we are aware, adopting the concept of audio spectrum analyser for developing hearing aid has not been previously studied. By wearing the device, a profoundly deaf person can perceive sound through their skin. Future studies should investigate and address how various types of sound stimulated through the skin by devices such as the belt used in this study, can be interpretated and identified by the the profoundly deaf individual.\n\n\nEthical approval\n\nThe Research Ethics committee of Technology Transfer Office, Multimedia University has granted ethics approval for this study. Ethical Approval Number: EA1992021. All participants of this study gave informed written consent to take part in the research.\n\n\nData availability\n\nOpen Science Framework (OSF): Hearing aid through skin sensory for profoundly deaf people.\n\nDOI: 10.17605/OSF.IO/MHWFP.12\n\nThis project contains the following underlying data:\n\nData file. Data contains the participants’ age, sex, hearing level, and ability to feel the vibration of the belt.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAuthor contributions\n\nYasothei Suppiah: Conceptualization, investigation, supervision. M Chandran Maruthan: investigation, methodology, resources. Fazly Salleh Abas: validation, visualization, writing-original draft.", "appendix": "References\n\nWorld Health Organization (WHO): World report on hearing. 2021. Reference Source\n\nZhang M, Gao Y: Hearing level of deaf children in deaf- mute schools. Zhonghua Erbiyanhou Toujing Waike Zazhi (Chinese Journal of Otorhinolaryngology Head and Neck Surgery). 2008; 15: 671–673.\n\nLi JW, Tang T: Applications in the Skin-Hearing Aid Compact by Embedded Technique. Microelectronics Computer. 2009; 5: 239–241.\n\nCui J, Xiao L, Wang Y, et al.: A kind of design criterion for WOLA filterbanks used in digital hearing aids. Yingyong Shengxue. 2010; 29(1): 36–42. Publisher Full Text\n\nDu QL, Zhu ZW: Sign language in special art education. J Changchun University. 2010; 2: 81–82.\n\nJiang HQ, Pan H: Key frame based multi-level classification of sign language recognition. Jisuanji Yingyong Yanjiu. 2010; 2: 491–493.\n\nZheng X: Lingual status of Chinese finger language. Tinglixue ji Yanyu Jibing Zazhi. 2010; 1: 57–58.\n\nYan W: An exploration of round-mouth characters of zhi- system read in labiodental sound in shandong. Shandong Daxue Xuebao Zhexue he Shehui kexue (J Shandong University (Philosophy and Social Sciences)). 2006; 2: 151–155.\n\nLi JW, Liu W, Han XJ: Response of skin to audible signals. Shengxue Jishu. 2006; 25(3): 253–257.\n\nLi J, Li Y, Zhang M, et al.: Cutaneous sensory nerve as a substitute for auditory nerve in solving deaf- mutes’ hearing problem: an innovation in multi-channel- array skin-hearing technology. Neural Regeneration Res. 2014; 9(16): 1532–1540. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMichael VP, Thorhildur A, David ME: Deciphering Sounds Through Patterns of Vibration on the Skin. Neuroscience. 2021; 458, 77–86. Publisher Full Text\n\nSuppiah Y: Data for hearing aid through skin sensory.2021. Publisher Full Text" }	[ { "id": "96595", "date": "19 Oct 2021", "name": "Quar Tian Kar", "expertise": [ "Reviewer Expertise I am an expert in Audiology", "a branch of science that studies hearing", "balance and related disorders. My research interest include hearing aid evaluation and validation. The technical aspects of this research is beyond my expertise." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study developed a device that converts sound patterns into patterns of vibrotactile stimulation. Overall, the article is well written, and the information presented in the article is well explained, organized and relevant to the study. The ideas are well-organized and coherent, making it easy for readers to follow and understand. This is an interesting study as it explains the development of a sensory device that has the potential to provide benefits to people diagnosed with profound hearing loss that cannot be aided either with conventional hearing aids or cochlear implant. The research design is appropriate, adequate, and novel in the sense it was developed by the researchers and validated.\nSome comments:\nIn the abstract, the second sentence mentions a hearing aid's ''ineffectiveness” for those who are profoundly deaf. This is perhaps not accurate and should not be generalized to all individuals with hearing loss. With the advancement of technology, today's hearing aids are found to be useful even for profoundly deaf people. Perhaps it should be replaced with 'limitations' of hearing aids.\nIn the second paragraph of the Introduction section, it would be good if the authors can elaborate a bit more why hearing aids are suitable only for mild hearing loss and not helpful for other degrees of hearing loss. \"Individual\" is misspelled in the first sentence.\nThere are few comments from me on the results section where it would be good if the authors could elaborate a bit more, so that readers can have a better understanding. It was mentioned that 30 subjects were recruited for the study. Seven were partially deaf. Please explain the meaning of 'partially deaf'. Please explain the purpose of recruiting subjects with different degrees of hearing loss. Would individuals with different degrees of loss have different experiences of the vibration stimulation? The reader might be interested to know what kind of sound (stimulus) was used in the experiment and how the stimulus contributed to the ability of the subjects to tell the direction of the sound source.\nIt will be interesting for future studies to explore the possibilities of developing what the authors have suggested, the concept of audio spectrum analyzer that enables profoundly deaf persons to interpret sounds through tactile hearing aids.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "99668", "date": "17 Jan 2022", "name": "Lindsey E. Jorgensen", "expertise": [], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting study and the background is very good. However, the methods lack significantly.\n1. It is not made clear how the signal was processed, and this causes issues with replication. The authors should include frequency, ranges of frequencies, and intensity. What filtering did they use in the FFT?\n2. While it is understood that COVID was a factor, it is of concern that the person was able to “hear” while also feeling, given that the subjects were not hard of hearing. Therefore, they could also hear the signal and not just feel it. This is difficult for validation.\n3. The authors also did not demonstrate how the person’s response was intended, and did not give a criteria by which the subjects response was to be measured? (awareness, perception, recognition, etc).\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "8032", "date": "20 Jul 2023", "name": "Yasothei Suppiah", "role": "Author Response", "response": "It is not made clear how the signal was processed, and this causes issues with replication. The authors should include frequency, ranges of frequencies, and intensity. What filtering did they use in the FFT? The human ideal listening frequency range or bandwidth is from 20hzto 20Khz, and this is a preliminary study on the device. The frequency of sound received from the microphone is directly fed to a signal preamplifier and a power amplifier and later couple to activate the actuator motor to as a vibrating device. At this point the study is just to test whether the sound can be converted to a vibration pattern according to sound being picked up by the microphone. While it is understood that COVID was a factor, it is of concern that the person was able to “hear” while also feeling, given that the subjects were not hard of hearing. Therefore, they could also hear the signal and not just feel it. This is difficult for validation. The “hearing” here is referring to the vibration produced by the device being feel by the subjects, at this point the subject would not understand the meaning of this vibrating pattern, just like when we hear an unknown language, we only perceive the sound but we do not understand the meaning. The test only to know whether the subject can feel the vibration upon a sound fed to the microphone. The authors also did not demonstrate how the person’s response was intended, and did not give a criteria by which the subjects response was to be measured? (awareness, perception, recognition, etc). The subject was to respond or recognise to the vibration being felt produced by the device at the stimulated direction of the sound. The subject will respond to a “yes” meaning they felt the vibration or “No” if they do not feel any vibration at the stimulated part of their body." } ] } ]	1	https://f1000research.com/articles/10-926
https://f1000research.com/articles/12-219/v1	27 Feb 23	{ "type": "Research Article", "title": "Political representation of medical doctors in Switzerland’s executive and legislative branches in 2023", "authors": [ "Alexander Smith", "Anna Buadze", "Petra Stute", "Michael Liebrenz", "Anna Buadze", "Petra Stute", "Michael Liebrenz" ], "abstract": "Background: Healthcare policy is an important societal concern in Switzerland, often dominating the national agenda. In other countries, studies have explored the influence of physicians in public office on healthcare policies, but little is known about the representation of medical doctors in Switzerland's political structures, despite ongoing health-related debates.\n\nMethods: In January 2023, we examined the proportion of registered doctors currently serving in Swiss governmental branches: the executive (the Federal Council) and the legislative (the Council of States and the National Council, together the United Federal Assembly). We used publicly available information to demarcate Federal, State, and National Councillors with professional medical backgrounds. We subsequently verified physician registrations using the Federal Office of Public Health’s “Register of Medical Professionals” (MedReg) Results: Six physicians registered in MedReg were identified across the Federal Council and the United Federal Assembly in 2023, equivalent to 2.37% of the total number of Councillors in these chambers. This corresponds to 14.20% of members in the Federal Council (the executive chamber) and 2.03% of members in the United Federal Assembly (the legislative chamber). Conclusions: Rates of physicians sitting in Switzerland’s Federal Council and United Federal Assembly are higher than general population trends for doctors per person. Nonetheless, physicians in Swiss legislative positions are proportionally lower than comparative data from the United States. We highlight how existing professional frameworks may already ensure medical doctors are sufficiently participating in Swiss healthcare debates outside of formal roles. We also suggest that more international evidence is needed to determine the benefits of physicians serving in public office.", "keywords": [ "Healthcare policy", "Physicians and politics", "Political representation", "Medical societies", "Switzerland" ], "content": "Introduction\n\nThe COVID-19 pandemic and rising living costs have reanimated socioeconomic concerns about health policies in Switzerland, which regularly capture the national agenda.1 Owing to an ageing population and growing technological advancements, Swiss health insurance premiums were set to increase substantially in 2022,2 with possible consequences for long-term fiscal sustainability.3 Additional factors like pharmaceutical prices4 and procedural backlogs2 are exacerbating this situation. Recently, politicians have attempted to address these circumstances. For instance, the Swiss political party, The Centre, have suggested a federal vote on cost control measures and different lawmakers have recommended alternative initiatives.1,5 However, at the time of writing, no consensus exists around potential interventions,1 and historical proposals to modify the Swiss health system have not passed.6\n\nIn other countries where healthcare is an important national issue, notably the United States, researchers have explored the role of physicians in governmental proceedings. In clinical subdisciplines recurrently exposed to legal matters, like forensic psychiatry, Piel has discussed expert advocacy.7 Separately, professional organisations and medical practitioners frequently engage in lobbying activities.8,9 In more formalised frameworks, physicians in political positions have historically attracted much inquiry, with papers dedicated to this issue from over fifty10,11 and one hundred years ago.12 For example, Oberstar has outlined various cases of US doctors occupying legislative seats and their influence on health policy.13 For Kraus and Suarez, physician lawmakers and first-hand medical insights could be useful within political domains, particularly as research funding and care delivery can often be legislatively determined.9 Moreover, anecdotally, Australian doctors have advocated for better representation across public office.14\n\nPrevious work has examined the prevalence of medical doctors serving in state and federal legislative branches in the United States [e.g., Refs. 9, 15, 16]. Others have focussed on German physician-trained health ministers,17 doctors in the United Kingdom’s parliament,18 and biographical investigations into the medical background of various national leaders.19 Nonetheless, to the authors’ knowledge, despite these studies in different national settings and ongoing Swiss healthcare policy concerns, there is scant awareness about registered physicians fulfilling formal political roles in Switzerland. Whilst Swiss media outlets accentuated the clinical expertise of the 2022 Federal President, Ignazio Cassis, during the COVID-19 pandemic,20 there is limited scholarly evidence about the holistic representation of medical doctors in national governmental spheres.\n\nUsing secondary biographical information, we sought to identify the rates of registered physicians serving in Switzerland’s national executive branch (the Federal Council) and the legislative branches (the Council of States and the National Council, together the United Federal Assembly) in 2023. As Switzerland’s governmental tradition is distinctive for individuals holding jobs outside of politics,21 our hypothesis was that the rates of serving physician-politicians would be higher than other geographical settings.\n\n\nMethods\n\nIn January 2023, we analysed publicly available information from the Swiss government and parliamentary websites, which list biographical records for executive and legislative positions: Federal Councillors, State Councillors and National Councillors (n=253).22–24 Through these resources, we were able to gather vocational data for n=206 national politicians, with no specific filters or access restrictions. However, for certain State and National Councillors, secondary professional data were not displayed by these parliamentary sources. In these cases (n=47), two authors collected occupational details separately through an internet search of multiple sources, including the official websites of these Councillors and media reports. Full data for n=253 Councillors were then exported into a Microsoft Excel file and from this total sample, we demarcated politicians with relevant medical backgrounds.\n\nSubsequently, we cross-referenced the information we collected by searching the “Register of Medical Professionals” (MedReg), which is managed by the Swiss Federal Office of Public Health.25 This enabled us to validate the biographical data against registrations as medical physicians in MedReg, and ascertain age, clinical specialties, and gender; specifically, the latter was determined based on information presented in MedReg. Following this process of cross-comparison and validation, descriptive statistics were calculated using Microsoft Excel, which are displayed in our results.\n\nThis investigation did not entail primary research involving human participation or confidential data and thus approval from an institutional review board and informed consent were not sought. Furthermore, our study was based on publicly available web resources managed by third parties, with no access requirements or permissions. This followed existing protocols used by recently published research articles that identified physician-politicians in different geographical domains [e.g., Refs. 15, 16].\n\n\nResults\n\nOur results are summarised in Table 1, which shows the total number of Federal Councillors, State Councillors, and National Councillors in 2023, alongside those who are registered doctors in MedReg.\n\nWe found that 2.37% (n=6) of the total number of Councillors (n=253) across the executive and legislative domains of Swiss national politics were registered physicians in MedReg. This corresponds to registered medical doctors representing 14.20% of members in the Federal Council, 2.17% in the Council of States, and 2.00% in the National Council in 2023; or per each governmental branch, 14.20% of Switzerland’s national executive body and 2.03% of the national legislative body. These six physicians consisted of two females (33.33%) and four males (66.66%). Ages ranged from 45-49 (16.66%), 55-59 (25%), 60-64 (16.66%) and 65-69 (25%). In respect of their medical field of expertise, three were board-certified specialists in general internal medicine (50.00%), one was board-certified in general internal medicine and prevention and public health (16.66%), one was an expert in general internal medicine and endocrinology (16.66%), and one was board-certified as an ophthalmologist (16.66%).\n\n\nDiscussion\n\nWhilst rates of registered physicians serving in national political positions may appear insignificant, they are higher than demographic trends for doctors per person in Switzerland,26 suggesting an overrepresentation compared to this general population-based metric. This is notable since practising physician numbers may be declining nationwide per previous studies.27 Nevertheless, the number of doctors in the Swiss federal legislature is proportionally lower than contemporaneous results in other countries; in 2022, 3.10% of federal legislators in the US had professional backgrounds as physicians,15 as compared to our finding of 2.03% in Switzerland’s United Federal Assembly in 2023. Using gender-based figures from the Swiss Medical Association (FMH), 44.90% of registered doctors in Switzerland are female,28 indicating that they might be underrepresented in national public office per our study. Likewise, this could be apposite for medical subspecialties other than general internal medicine based on occupational statistics from the FMH.28\n\nIn the authors’ opinion, broader political representation of doctors in Switzerland may prove advantageous for civil society and professional medical associations.13 This could be especially timely given political and socioeconomic debates surrounding Swiss healthcare policies [e.g., Refs. 1, 2]. Significantly, medical expenditure was estimated to account for 11.80% of the country’s gross domestic product in 202029 and a recent survey of 26,298 Swiss residents identified healthcare as a preeminent political concern.30 Amidst these contexts, physicians could raise awareness about health-related issues and influence relevant policies as elected officials. For doctors, this could include discussions around insurance, research funding provisions, and patient care, where first-hand vocational experience of these notions has been beneficial in separate settings.9,13 Further, physicians can be particularly valuable in high office positions; for instance, evidence shows that medically trained German health ministers improved hospital capacities, capital, and health insurance funding.17\n\nNonetheless, the extensive coverage of medical societies and professional groups in Switzerland might mean that doctors are engaging at a political level outside of formal positions. Such organisations regularly provide policy guidance and undertake advocacy activities; notably, the FMH has a resource devoted to political matters.31 Additionally, Switzerland’s distinctive consultation process of law-making (Vernehmlassung) aims to involve stakeholders in legislative procedures32 and may therefore already encompass physicians’ perspectives. Here, again, associations periodically facilitate responses to consultative requests around legislative considerations; for example, the FMH publicly declares its positions,33 as does the Swiss Society of General Medicine,34 amongst others. Correspondingly, participation within Federal Commissions can also facilitate dialogues between doctors and governmental administrations. These extra-parliamentary institutions are founded to provide advice on specific topics and are often dedicated to specialised medical areas [e.g., Refs. 35, 36].\n\nWe deemed our study to be the best available method to explore current levels of registered physicians in Switzerland’s executive and legislative political bodies; yet our approach has its limitations. Firstly, although other investigations into physicians in US governmental structures have adopted similar methodologies,15,16 secondary analysis can invoke data availability and reproducibility questions.37 For example, during data gathering, occupational information was not available on governmental or parliamentary websites for certain State (n=15) and National Councillors (n=32), and a supplementary internet search was required. This had the potential to introduce discrepancies; to mitigate against this, two authors consulted multiple internet sources, including official websites and press reports, to corroborate biographical information and the MedReg database was screened to validate physician registrations.\n\nMoreover, we investigated Federal, State, and National Councillors in 2023 and not longitudinal trends. Due to data availability constraints, we deemed this appropriate to present current insights amidst contemporaneous healthcare debates; a comparative follow-up study after the Swiss Federal Elections in October 2023 could allow for more insights. Nonetheless, samples over a broader timeframe would allow for historical comparisons. Our work only captured physicians registered in MedReg and did not include other health-related professions or qualifications. Future research could encompass additional stakeholders involved in healthcare policy, such as nurses or insurance experts, and cantonal-level politicians for more exhaustive evaluations.\n\nMore generally, the extent to which physicians feel they are sufficiently participating in the governmental process through multiple professional mechanisms could form the basis for additional investigations. Whilst our study presents quantitative data about physicians in formal federal roles, qualitative findings about the wider political representation of Swiss physicians could better contextualise their influence on civil and health-related issues. This could be further complimented by extensive research in different countries and about how doctors serving in other national political structures can influence health policy debates.\n\n\nConclusion\n\nHealthcare policy is a substantial socio-political and economic concern in Switzerland, frequently capturing the national agenda. However, there is limited knowledge about the number of registered physicians serving in the Swiss Federal, State, and National Councils, despite similar studies in other countries.\n\nBased on our findings, national political representation of medical doctors was above populational trends in Switzerland. Nevertheless, the number of physicians serving in the Swiss legislature (the United Federal Assembly) was lower than in the United States’ federal legislature, where comparable investigations have occurred. Further, females and clinical subspecialties other than general internal medicine may be professionally underrepresented in formal political roles.\n\nDetailed work is needed to understand the implications of medical doctors occupying political offices and their representative mechanisms outside of formal federal positions in Switzerland. Moreover, further investigations should be encouraged in different political systems internationally. In general, this may help determine whether more physicians should be encouraged to run for elected office.", "appendix": "Data availability\n\nPublicly available biographical information is obtainable from the Swiss government and parliamentary websites, which list occupational records for executive and legislative positions. Information about physician registrations is available by searching The Register of Medical Professionals. Data used in this study are:\n\nThe “The seven members of the Federal Council” dataset of 2023, available from The portal of the Swiss government.\n\nThe “National Council Members A–Z” dataset of 2023, available from The Federal Assembly – The Swiss Parliament.\n\nThe “Council Of States Members A–Z” dataset of 2023, available from The Federal Assembly – The Swiss Parliament.\n\nThe “Register of Medical Professionals” dataset of 2023, available from the Swiss Federal Office of Public Health.\n\n\nReferences\n\nO’Dea C: How spiralling costs are jeopardising Switzerland’s healthcare system. [Accessed 15 Jan 2023]. Reference Source\n\nSwissInfo: Health insurance premiums to take biggest jump in a decade. [Accessed 24 Dec 2022]. Reference Source\n\nBrändle T, Bruchez PA, Colombier C, et al.: Do the COVID-19 Crisis, Ageing and Climate Change Put Swiss Fiscal Sustainability at Risk? Int. Econ. 2022; 57(1): 48–55. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKaiser B, Schmid C: Does Physician Dispensing Increase Drug Expenditures? Empirical Evidence from Switzerland. Health Econ. 2016; 25(1): 71–90. PubMed Abstract \| Publisher Full Text\n\nBundeskanzlei BK: Federal popular initiative 'For lower premiums - cost control in healthcare (cost control initiative)' [Eidgenössische Volksinitiative 'Für tiefere Prämien – Kostenbremse im Gesundheitswesen (Kostenbremse-Initiative)']. [Accessed 16 Nov 2022]. Reference Source\n\nDe Pietro C, Crivelli L: Swiss popular initiative for a single health insurer … once again! Health Policy. 2015; 119(7): 851–855. PubMed Abstract \| Publisher Full Text\n\nPiel J: Legislative Advocacy and Forensic Psychiatry Training. J. Am. Acad. Psychiatry Law. 2018; 46(2): 147–154. PubMed Abstract \| Publisher Full Text\n\nVolgman AS: It’s essential for doctors to be involved in politics. [Accessed 15 Jan 2023]. Reference Source\n\nKraus CK, Suarez TA: Is there a doctor in the house? … Or the Senate? Physicians in US Congress, 1960-2004. JAMA. 2004; 292(17): 2125–2129. PubMed Abstract \| Publisher Full Text\n\nEditor: Doctors in Politics. Can. Med. Assoc. J. 1933; 29(5): 557–558.\n\nGlaser W: Doctors and Politics. Am. J. Sociol. 1960; 66(3): 230–245. Publisher Full Text\n\nWhalen C: The Doctor as a Politician. JAMA. 1899; XXXII(14): 756–759. Publisher Full Text\n\nOberstar JV: Physician-legislators: physicians practicing public service. JAMA. 1999; 281(9): 862. PubMed Abstract \| Publisher Full Text\n\nAustralian Medical Association: Doctors in politics. [Accessed 30 Dec 2022]. Reference Source\n\nVarma T, Goldenberg M: Physician-Legislators in Federal and State Government in 2022 [in press]. JAMA. 2022; 328: 2450–2452. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKumar B, Suneja M, Swee ML: The Doctors in the House: Examining Physician Legislators in the US Congress from 2011 to 2020. South. Med. J. 2022; 115(5): 322–327. PubMed Abstract \| Publisher Full Text\n\nPilny A, Roesel F: Are Doctors Better Health Ministers? American Journal of Health Economics. 2020; 6(4): 498–532. Publisher Full Text\n\nMoberly T, Iacobucci G: General election: 10 doctors are elected as MPs. BMJ. 2019; 367: l6976. PubMed Abstract \| Publisher Full Text\n\nLass P, Szarszewski A, Gaworska-Krzemińska A, et al.: Lekarze w roll prezydentów i premierów--analiza biograficzna [Medical doctors as the state presidents and prime ministers--a biographical analysis]. Przegl. Lek. 2012; 69(8): 642–646.\n\nSwissInfo: President Ignazio Cassis: a man who resembles Switzerland. [accessed 11 Jan 2023]. Reference Source\n\nSwissInfo: Swiss politicians: just don’t call me a professional. [accessed 18 Jan 2023]. Reference Source\n\nThe Federal Council: The seven members of the Federal Council. [accessed 5 Jan 2023]. Reference Source\n\nThe Federal Assembly – The Swiss Parliament: Council of States Members A-Z. [accessed 5 Jan 2023]. Reference Source\n\nThe National Assembly – The Swiss Parliament: National Council Members A-Z. [accessed 5 Jan 2023]. Reference Source\n\nFederal Office of Public Health: MedReg register of medical professionals. [accessed 6 Jan 2023]. Reference Source\n\nThe Global Economic: Switzerland: Doctors per 1,000 people. [accessed 15 Jan 2023]. Reference Source\n\nStreit S, da Costa BR , Christensen S, et al.: One in seven Swiss physicians has left patient care - results from a national cohort study from 1980-2009. Swiss Med. Wkly. 2019; 149: w20116. PubMed Abstract \| Publisher Full Text\n\nSwiss Medical Association FMH: Practicing physicians by main discipline and gender; 2021 [Médecins en exercice par discipline principale et par sexe; 2021]. [accessed 15 Jan 2023]. Reference Source\n\nFederal Statistic Office: Total health expenditure in 2020 at CHF 83.3 billion. [accessed 14 Jan 2023]. Reference Source\n\nLe News: The 3 biggest current concerns in Switzerland, based on survey. [accessed 15 Jan 2023]. Reference Source\n\nSwiss Society of General Internal Medicine: Consultations/Positions [Vernehmlassungen/Positionen]. [accessed 16 Jan 2023]. Reference Source\n\nSchwarz D: Switzerland: Agenda-Setting Power of the Government in a Separation-of-Powers Framework.Björn ER, Tsebelis G, editors. The Role of Governments in Legislative Agenda Setting. London: Routledge; 2011; 127–143\n\nSwiss Medical Association FMH: Political Business [Politische Geschäfte]. [accessed 15 Jan 2023]. Reference Source\n\nSwiss Medical Association FMH: Consultation Responses [Vernehmlassungsantworten]. [accessed 15 Jan 2023]. Reference Source\n\nFederal Administration: Federal Commission for Quality Assurance in Medical Assessment. [Eidgenössische Kommission für Qualitätssicherung in der medizinischen Begutachtung]. [accessed 15 Jan 2023]. Reference Source\n\nFederal Office for Public Health: Federal Commission for Issues relating to Sexually Transmitted Infections (FCSTI). [accessed 14 Jan 2023]. Reference Source\n\nVartanian TP: Secondary Data Analysis. Oxford: Oxford University Press; 2010." }	[ { "id": "167296", "date": "18 Apr 2023", "name": "Valerie Seror", "expertise": [ "Reviewer Expertise Health 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\nThis is a very well-written manuscript that explored the issue of the influence of physicians in political positions on health policy. As a first step, this study aimed at providing insight based on data gathered from publicly information accessible on the Internet without requirements or permissions. Data on age and gender of the members of the Federal, State and National Councils had been collected as well as data on the medical background of the physicians involved in these councils. Among a total number of 253 Councillors in 2023, 6 had been identified as medical doctors.\nMain comments:\nConsidering the relatively low number of physicians involved in the Councils, the authors pointed out a likely over-representation of the members of the Councils with medical background as compared to their rates in the general population. In order to get more insight on this issue, the authors could also question whether and to what extent occupational backgrounds of the members of the councils are representative of the Swiss population.\n\nConsidering the major issue of potential influence of physicians in political positions on health policy, the Discussion section could provide suggestions on whether to appraise such influence.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "9588", "date": "28 Apr 2023", "name": "Alexander Smith", "role": "Author Response", "response": "Authors: Dear Dr Seror, we would like to thank you for taking the time to review our paper and providing constructive and supportive feedback. We very much appreciate your valuable insights and have responded to the feedback you raised point-by-point below. We believe that these suggestions now strengthen the paper by providing additional contextualisation and reinforcing the theoretical basis for future international studies. Reviewer: Considering the relatively low number of physicians involved in the Councils, the authors pointed out a likely over-representation of the members of the Councils with medical background as compared to their rates in the general population. In order to get more insight on this issue, the authors could also question whether and to what extent occupational backgrounds of the members of the councils are representative of the Swiss population. Authors: This is an excellent point, thank you for raising this. In paragraph 1 of the discussion, we have now added other occupational comparisons (namely to farmers and lawyers from sources showing national trends) to better frame the representation of doctors in a national context. Reviewer: Considering the major issue of potential influence of physicians in political positions on health policy, the Discussion section could provide suggestions on whether to appraise such influence. Authors: Thank you for this suggestion, which will strengthen the basis for further studies. At the end of paragraph 2 of the discussion, we have included information about how to assess the political influence of doctors from a related study, alongside some suggestions from the political science literature. We have also acknowledged this at the end of the “Limitations and directions for future research section”. Thank you again for this important point." } ] } ]	1	https://f1000research.com/articles/12-219
https://f1000research.com/articles/12-426/v1	20 Apr 23	{ "type": "Research Article", "title": "Single-cell transcriptional uncertainty landscape of cell differentiation", "authors": [ "Nan Papili Gao", "Olivier Gandrillon", "András Páldi", "Ulysse Herbach", "Rudiyanto Gunawan", "Nan Papili Gao", "Olivier Gandrillon", "András Páldi", "Ulysse Herbach" ], "abstract": "Background: Single-cell studies have demonstrated the presence of significant cell-to-cell heterogeneity in gene expression. Whether such heterogeneity is only a bystander or has a functional role in the cell differentiation process is still hotly debated. Methods: In this study, we quantified and followed single-cell transcriptional uncertainty – a measure of gene transcriptional stochasticity in single cells – in 10 cell differentiation systems of varying cell lineage progressions, from single to multi-branching trajectories, using the stochastic two-state gene transcription model. Results: By visualizing the transcriptional uncertainty as a landscape over a two-dimensional representation of the single-cell gene expression data, we observed universal features in the cell differentiation trajectories that include: (i) a peak in single-cell uncertainty during transition states, and in systems with bifurcating differentiation trajectories, each branching point represents a state of high transcriptional uncertainty; (ii) a positive correlation of transcriptional uncertainty with transcriptional burst size and frequency; (iii) an increase in RNA velocity preceding the increase in the cell transcriptional uncertainty. Conclusions: Our findings suggest a possible universal mechanism during the cell differentiation process, in which stem cells engage stochastic exploratory dynamics of gene expression at the start of the cell differentiation by increasing gene transcriptional bursts, and disengage such dynamics once cells have decided on a particular terminal cell identity. Notably, the peak of single-cell transcriptional uncertainty signifies the decision-making point in the cell differentiation process.", "keywords": [ "single cell", "gene expression", "cell differentiation", "transcriptional uncertainty", "RNA velocity" ], "content": "Introduction\n\nCell differentiation is the process through which unspecialized stem cells become more specialized. Because of its important roles in development, cellular repair, and organismal homeostasis, the molecular mechanisms of cell differentiation has been the subject of intense scrutiny. Since roughly 50 years ago – along with the promulgation of the central dogma of molecular biology by Francis Crick and the characterization of the lactose operon by François Jacob and Jacques Monod – the existence of a genetic program has become a prevailing explanation for the cell differentiation process. Although the details were originally not defined, at least not formally, such a genetic program purports a constellation of master genes (i.e., transcription factors) that orchestrate the transcription of downstream target genes in a precise spatiotemporal fashion, resulting in long-lasting alterations in the gene expression patterns (Herskowitz, 1989; Lewis, 1992; Ohno et al., 1979). A notable experimental evidence substantiating this view is the overexpression of myoD inducing a myogenic phenotype in seemingly naive cells (Davis et al., 1987). Over the past few decades, the repertoire of such master genes across numerous stem cell systems, such as Nanog, Oct4, Sox2, BATF and MyoD, has begun to coalesce (Papili Gao et al., 2017; Sartorelli & Puri, 2018; Whyte et al., 2013).\n\nRecent advances in single-cell technologies has revealed new aspects of the cell differentiation that are incompatible with the idea of ordered and programmed (i.e., deterministic) gene expression. More specifically, single-cell data paint a stochastic differentiation process that increases cell-to-cell variability of gene expression. Such an observation has been made for a wide variety of cell differentiation systems, including chicken erythroid progenitors (Richard et al., 2016), erythroid myeloid lymphoid (EML) cells (Mojtahedi et al., 2016), mouse embryonic stem cells (mESCs) (Semrau et al., 2017; Stumpf et al., 2017), and human CD34+ cells (Moussy et al., 2017). Interestingly, a similar increase of gene expression variation was also observed during the de-differentiation of somatic cells into iPSCs (Buganim et al., 2012). Stochastic gene expression also appears to have a functional role beyond cell differentiation systems. For example, an increase in cell-to-cell variability of gene expression has been reported during a forced adaptation of budding yeast cells to unforeseen challenges (Braun, 2015).\n\nIn 1957, Conrad Waddington proposed the presently well-known epigenetic landscape that likens the cell differentiation process to a ball rolling on a downward sloping surface, starting from a state of high cell potency and ending at one of possibly several states of low cell potency. The landscape itself is shaped by the action of the genes and gene network – depicted in the less-frequently-shown part B of Waddington’s original figure as a network of ropes that are tied to the surface, creating valleys and hills. Although the epigenetic landscape was originally proposed only as a metaphor of how gene regulation governs the cell differentiation process, this landscape has been formalized within the framework of dynamical systems theory (Huang, 2009). The valleys in the Waddington’s epigenetic landscape are equated to stable states of a dynamical system, called attractors, while the hills are often interpreted as energetic barriers.\n\nA number of recent studies provided a graphical representation of the differentiation process based on single-cell transcriptomic data that conforms with the Waddington’s epigenetic landscape (Fard et al., 2016; Guo & Zheng, 2017; Shi et al., 2018; Zhang & Zhou, 2018; Zwiessele & Lawrence, 2017). More specifically, these studies reconstructed the epigenetic landscape from single-cell gene expression data using probabilistic and quasi-potential methods, for example by applying Hopfield neural networks (Fard et al., 2016; Guo & Zheng, 2017), a cell-density based strategy (Zhang & Zhou, 2018), network entropy measurements (Shi et al., 2018) or more recently Large Deviation Theory (Lv et al., 2014). However, with the exception of Fard et al. (2016) and Lv et al. (2014), the aforementioned studies produced monotonic descent passages during cell differentiation, mimicking closely the Waddington’s epigenetic landscape metaphor (see for example (Bhattacharya et al., 2011; Shi et al., 2018)). Also, none of the above studies consider directly the cellular mechanism that generates stochastic gene transcriptional bursts.\n\nIn the present work, we aimed to shed light on the gene transcriptional mechanism behind the rise-then-fall trajectory of cell-to-cell variability in gene expression observed during the cellular differentiation process (Richard et al., 2016). To this end, we analyzed a collection of published single-cell transcriptomic datasets from various cell differentiation systems, comprising both single-cell RT-qPCR (scRT-qPCR) (Bargaje et al., 2017; Guo et al., 2010; Moignard et al., 2013; Moussy et al., 2017; Richard et al., 2016; Stumpf et al., 2017) and single-cell RNA-sequencing (scRNA-seq) (Nestorowa et al., 2016; Treutlein et al., 2016). We employed a likelihood-based analysis using a recent method CALISTA (Clustering And Lineage Inference in Single-cell Transcriptomics Analysis) (Papili Gao et al., 2020). The analysis relied on a mechanistic model of the stochastic gene transcriptional bursts to describe single-cell gene expression distribution. Specifically, we introduced a new concept of transcriptional uncertainty at single cell level, and by applying CALISTA, we reconstructed the transcriptional uncertainty landscapes for the aforementioned cell differentiation systems. Further, by leveraging the stochastic gene transcriptional model behind CALISTA, we were able identify possible mechanisms behind the overt trajectories of cell differentiation on the transcriptional uncertainty landscapes (Coulon et al., 2010). For two additional single-cell datasets, we also evaluated the single-cell RNA-velocity using the recently published Velocyto method (La Manno et al., 2018). The two-state model parameter analysis, combined with RNA-velocities, provided insights into the mechanism regulating cell fate decisions, specifically on the role of stochastic gene transcriptions in the differentiation processes and on the possible mechanism generating this stochasticity.\n\n\nMethods\n\nHerein, we briefly describe the main steps involved in the calculation of single-cell transcriptional uncertainty using CALISTA (Papili Gao et al., 2020).\n\nPre-processing. Given an N×G single-cell expression matrix M, where N denotes the number of cells and G the number of genes, the pre-processing in CALISTA involves two steps: a normalization of the expression data mn,g – i.e. the number of transcripts of gene g in the n-th cell, and a selection of the most variable genes (Papili Gao et al., 2020).\n\nCell clustering. CALISTA clustering follows a two-step procedure. The first step involves a greedy optimization strategy to find cell clustering that maximizes the total cell likelihood, i.e. the sum of the likelihood value for all cells. The single-cell likelihood value is computed as the joint probability of the cell’s gene expression data, which is set equal to the product of the probabilities of the mRNA counts for the selected genes based on the mRNA distribution from the two-state stochastic gene transcription model. To avoid issues with numerical overflow, we use the logarithm of the cell likelihood. By performing the greedy optimization multiple times, a consensus matrix containing the number of times two cells in the dataset are put in the same cluster, is generated. In the second and final step, CALISTA generates the cell cluster assignments by using k-medoids clustering based on the consensus matrix. The final outcome of CALISTA’s clustering is the assignment of cells into K clusters and the optimal model parameters for the two-state gene transcription model: θgk=θonθoffθtgk. for each gene g in cluster k (Papili Gao et al., 2020). In this case, θon is the normalized rate of the promoter activation, θoff is the normalized rate of the promoter inactivation, and θt is the normalized rate of mRNA production when the promoter is active. These parameters are normalized by the rate constant of mRNA degradation θd, so that θd=1.\n\nLineage progression inference. In CALISTA, cell lineage progression is inferred based on cluster distances – a measure of dissimilarity between two clusters. The cluster distance of two cell clusters is defined as the average decrease in the cell likelihood value if the cells from these two clusters are grouped as one cluster, as opposed to the original clustering. The lineage progression graph is built by adding transition edges between pairs of clusters in increasing magnitude of cluster distance until all clusters are connected to at least one other cluster, or based on user-specified criteria.\n\nSingle-cell transcriptional uncertainty. The last step in our analysis is to compute the final single-cell likelihood. Briefly, for each cell, we consider all edges in the lineage progression graph that are adjacent to the cell’s respective cluster, i.e. edges that eminate from or pointing to the cluster to which the cell belongs. The likelihood of a cell along an edge is evaluated by interpolating the likelihood values of the cell’s gene expression using the mRNA distributions from the two adjacent clusters. Each cell is then assigned to the edge along which its interpolated likelihood value is maximum, and the final cell likelihood is set to this maximum value. As mentioned above, the single-cell transcriptional uncertainty is evaluated as the negative logarithm of the cell likelihood value (NLL).\n\nPseudotimes calculation. We can evaluate the pseudotimes for the cells according to the following procedure. First, a pseudotime is given to each cluster with a value between 0 (initial cell state) and 1 (final cell fate). Subsequently, we determine the linear fractional position of each cell along its respective edge at which its interpolated likelihood value is maximum (see Single-cell transcriptional uncertainty). The pseudotime of a cell is computed by a linear interpolation of the pseudotimes of the two clusters adjacent to its assigned edge according to the cell’s linear fractional position on this edge.\n\nEpigenetic landscape reconstruction. To visualize the 3D transcriptional uncertainty landscape, we apply dimensional reduction techniques such as principal component analysis (PCA) or t-SNE on the z-scored expression data, to project the gene expression of each individual cell on two dimensional axis, which gives the x-y axis of the landscape plot. For the z axis, we plot the NLL values. The transcriptional uncertainty landscape surface is reconstructed by estimating local approximation of individual cell 3D coordinates on a regular 30×30 grid by using a publicly available Matlab (R2020a) surface fitting package called gridfit.\n\nBargaje et al. scRT-qPCR dataset. The dataset includes the expression profiles of 96 genes from 1896 single cells at eight different time points (day 0, 1, 1.5, 2, 2.5, 3, 4, 5) during the differentiation of human pluripotent stem cells (iPSCs) into either mesodermal (M) or endodermal (En) fate (Bargaje et al., 2017). By employing CALISTA, we obtained five cell clusters and detected a bifurcation event, which gives rise to the two final cell fates. After lineage inference, we pseudotemporally ordered cells along the inferred differentiation paths (for more details, see (Papili Gao et al., 2020)).\n\nTreutlein et al. scRNA-sequencing dataset. The dataset includes the gene expression profiles of 405 cells during reprogramming of mouse embryonic fibroblast (MEF) into a desired induced neural (iN) and an alternative myogenic (M) cell fate (Treutlein et al., 2016). We pre-processed the data using CALISTA to select the 40 most variable genes (10% of the number of cells) for the transcriptional uncertainty analysis. CALISTA identified four different subpopulations and successfully recovered the bifurcation event (for more details, see (Papili Gao et al., 2020)).\n\nRichard et al. scRT-qPCR dataset. The dataset contains the expression profile of 91 genes measured from 389 cells at six distinct time points (0, 8, 24, 33, 48, 72 h) during the differentiation of primary chicken erythrocytic progenitor cells (T2EC) (Richard et al., 2016). Following the CALISTA pre-processing step, we removed cells in which less than 75% of the genes are expressed. Then, we selected the subset of genes with at least one non-zero expression values. A total of 354 cells and 88 genes were considered in the transcriptional uncertainty analysis. Based on eigengap heuristics (Papili Gao et al., 2020; von Luxburg, 2007), we grouped cells into six optimal clusters and ordered cells along the inferred linear trajectory (see the Extended data S8 Figure (Gao et al., 2023)).\n\nStumpf et al. scRT-qPCR dataset. The dataset comprises the single-cell expression of 97 genes at seven time points (0, 24, 48, 72, 96, 120, 168 h) during neural differentiation of mouse embryonic stem cells (E14 cell line) (Stumpf et al., 2017). In the data pre-processing, we excluded cells in which less than 70% of genes are expressed. Then, we selected genes with at least one non-zero expression values. A total of 276 cells and 93 genes were considered for for the transcriptional uncertainty analysis. Based on eigengap heuristics (Papili Gao et al., 2020), we grouped cells into five optimal clusters and ordered cells along the inferred linear trajectory (Extended data S9 Figure (Gao et al., 2023)).\n\nMoussy et al. scRT-qPCR dataset. The single-cell expression dataset includes normalized Ct values for 91 genes in 435 cells captured at five distinct time points (0, 24, 48, 72, 96 h) during human cord blood-derived CD34+ differentiation (Moussy et al., 2017). We employed CALISTA to group cells into seven clusters, reconstruct the developmental trajectory and calculate pseudotimes (Extended data, S10 Figure (Gao et al., 2023)).\n\nGuo et al. scRT-qPCR dataset. The dataset comprises the single-cell expression values of 48 genes from 387 individual cells isolated at four distinct developmental cell stages, from 8-cell stage mouse embryos to 64-blastocyst (Guo et al., 2010). By applying CALISTA, we identified seven different subpopulations along the differentiation process, and the inferred lineage hierarchy pinpointed two bifurcations events at 32- and 64-cell stage (Extended data, S11 Figure (Gao et al., 2023)). The timing of the lineage bifurcations coincides with two well-known branching points: one at 32-cell stage when totipotent cells differentiate into trophectoderm (TE) and inner cell mass (ICM), and another at 64-cell stage when ICM cells differentiate into primitive endoderm (PE) and epiblast (E).\n\nNestorowa et al. scRNA-sequencing dataset. The dataset comprises single-cell gene expression of 1656 cells from mouse hematopoietic stem cell differentiation (Nestorowa et al., 2016). We pre-processed the data by removing genes with non-zero values in less than 10% of the cells. Then, we selected 433 most variable genes, which is 10% of the number of genes after the previous pre-processing step, for the transcriptional uncertainty analysis (Papili Gao et al., 2020). We set the optimal number of clusters based on the original study (Nestorowa et al., 2016), which reported six different subpopulations and two bifurcation events: the first one producing common myeloid progenitor (CMP) from lymphoid-primed multipotent progenitors (LMPP), and the second one generating granulocyte–monocyte progenitors (GMP) from megakaryocyte-erythroid progenitors (MEP) (Extended data, S12 Figure (Gao et al., 2023)).\n\nMoignard et al. scRT-qPCR dataset. The dataset contains the single-cell expression level of 18 transcription factors measured in a total of 597 mouse bone marrow cells during hematopoietic differentiation. By applying CALISTA, we successfully identified the five subpopulations and the two branching points detected in the original study (Moignard et al., 2013): long-term hematopoietic stem cells (HSC) differentiating into megakaryocyte–erythroid progenitors (PreM) or lymphoid-primed multipotent progenitors (LMPP); LMPP cells differentiating into granulocyte–monocyte progenitors (GMP) and common lymphoid progenitors (CLP) (for details see (Papili Gao et al., 2020)).\n\nWe defined gene transcriptional burst size and burst frequency using the two-state model parameters, as follows:\n\nThe burst sizes and burst frequencies were evaluated using the cluster parameters θgk=θonθoffθtgkobtained from single-cell clustering analysis of CALISTA. Meanwhile, the average gene-wise NLL values for each single-cell cluster was computed as:\n\nwhere NLLgn is the negative log-likelihood of cell n based only on the expression of gene g, and Nk is the total number of cells in cluster k.\n\nCells and genes were first filtered based on the pre-processing strategy in the original publication by La Manno and colleagues (La Manno et al., 2018), which resulted in a total of 1720 cells and 1448 genes from human glutamatergic neurogenesis, and a total of 18140 cells and 2141 genes from the mouse hippocampus dataset. We further reduced the number of genes to only the top 500 highly variable genes for the transcriptional uncertainty analysis. The cell cluster assignments generated by Velocyto – the algorithm for computing RNA velocity from the original publication (La Manno et al., 2018) – were considered, instead of using CALISTA. Based on the clustering, we employed CALISTA to generate the lineage progression and cell pseudotimes (Extended data, S13 Figure (Gao et al., 2023)). The RNA velocity and transcriptional uncertainty values for the top 500 genes were calculated by employing Velocyto and CALISTA, respectively. The cell-wise RNA velocity was set to the Euclidean norm of the vector of RNA velocities for each cell, while the cell-wise NLLs was\n\n\nResults\n\nIn this work, we used CALISTA (Papili Gao et al., 2020), a likelihood-based bioinformatics toolbox designed for an end-to-end analysis of single-cell gene expression data, to evaluate the transcriptional uncertainty of each individual cell based on its gene expression data (see the Extended data, Supplementary Notes S1 (Gao et al., 2023)). CALISTA uses the two-state model of stochastic gene transcription bursts to characterize the steady state distribution of mRNA counts in individual cells (Peccoud & Ycart, 1995). In the model, a gene promoter stochastically switches between the ON and OFF state, and only in the ON state can gene transcription occur. The distribution of mRNA depends on four model parameters: θon (the rate of promoter activation), θoff (the rate of promoter inactivation), θt (the rate of mRNA production when the promoter is in the ON state), and θd (the rate constant of mRNA degradation) (Herbach et al., 2017; Kim & Marioni, 2013) (see Figure 1a). For example, when θoff >>θon and θoff >>θd, keeping θt/θoff fixed, mRNA are produced through bursts of short but intense transcription, which is a typical case observed for gene transcriptions in single cells (Munsky et al., 2012) (Suter et al., 2011). As the mRNA distribution is linked to mechanistically interpretable parameters, CALISTA is able to give insights into the possible mechanism driving the cell heterogeneity dynamics during cell differentiation.\n\n(a) The illustration depicts the landscape of single-cell transcriptional uncertainty during a differentiation process over the (pseudo) time (from blue to yellow). Each dot corresponds to a cell in the single-cell transcriptomic dataset. Cells start their journey from a valley in the landscape, through a hill, before ending at one of the final valleys/states. (b–f) Analysis of single-cell transcriptional profiles during iPSC differentiation into cardiomyocytes (Bargaje et al., 2017). (b) Boxplots of the negative log-likelihood (NLL) values for each single-cell cluster. (c–d) Moving-window average NLL along (c) endoderm and (d) mesoderm fate trajectory. (e) NLL of each gene and cell for every single-cell cluster. (f) Protein-protein interaction network of top variable genes inferred by STRING (Szklarczyk et al., 2015). Blue nodes represent transcription factors, while red nodes denote proteins involved in signal transduction. The width of the edges denotes the confidence for the inferred relationship (thicker edge = higher confidence).\n\nCALISTA employs a maximum likelihood approach and assigns a likelihood value to each cell based on its gene expression based on the mRNA distribution governed by the two-state model of stochastic gene transcription. The single-cell transcriptional uncertainty is evaluated as the negative logarithm of the likelihood (NLL) value for a cell. The single-cell likelihood value reflects the joint probability of its gene expression repertoire. A cell with a low likelihood value may indicate that the gene expression of the cell is different from its neighboring cells, i.e. the cell is an outlier. But, more interestingly, a low likelihood value may also correspond to a cell state of high uncertainty in the gene expression. The group of cells in such a high uncertainty state have gene expressions that are dissimilar to each other, and thus, the gene expression distribution will have a high entropy. By visualizing the single-cell transcriptional uncertainty over the two-dimensional projection of the single-cell transcriptomics data—for example, using the first two principal components from PCA—we constructed a transcriptional uncertainty landscape in the form of a surface plot of the NLL value. In this way, we studied the landscape of transcriptional uncertainty during cell differentiation at single-cell resolution. On such single-cell transcriptional uncertainty surface, an aberrant cell can be easily distinguished from a cell of high uncertainty state, since such an aberrant cell will appear isolated from its neighboring cells with a high NLL.\n\nIn the following, we demonstrated an application of our procedure described above to a single-cell transcriptional dataset from cardiomyocytes differentiation from human induced pluripotent stem cells (iPSCs) (Bargaje et al., 2017). The single-cell clustering of CALISTA returned five clusters (Papili Gao et al., 2020) and identified one bifurcation event in the lineage progression, which led to two cell lineages (Bargaje et al., 2017), in good agreement with the number of cell types reported in the original study. The estimated uncertainty landscape shows cells exiting the initial epiblast state that is characterized by a valley in the landscape, passing through a hill of high transcriptional uncertainty corresponding to primitive streak (PS)-like progenitor state, before ending up at one of the low transcriptional uncertainty terminal states corresponding to either mesodermal (desired) or endodermal (undesired) fate (see the Extended data, S1 Figure (Gao et al., 2023)). As depicted in Figure 1b, the intermediate cell cluster (cluster 2) comprising PS-like cells have higher cell uncertainty (lower single-cell likelihood) than the other clusters. Figure 1c and d give the moving-averaged uncertainty values for pseudotemporally ordered cells using a moving window of 10% of the total cells for both endodermal and mesodermal paths, respectively. The moving-averaged transcriptional uncertainty for the two differentiation paths follows a rise-then-fall trajectory where the peak of uncertainty coincides with the lineage bifurcation event.\n\nWe explored whether the rise-then-fall in uncertainty is an artefact from using the two-state model to evaluate the cell likelihood values. To this end, we implemented a modified version of the algorithm for ordering cells by calculating the cell likelihood values using the empirical (observed) distribution, instead of the analytical distribution from the two-state model. As shown in the Extended data S2 Figure (Gao et al., 2023), the transcriptional uncertainty landscape from the modified implementation shows a strong resemblance to the original one. We also investigated whether the number of clusters may affect the landscape, in which using too few of the clusters may artificially inflate the uncertainty due to the mixing of cells from different states. We reran CALISTA by using a higher number of clusters (set to nine based on the eigengap heuristic (von Luxburg, 2007)). The hill in the uncertainty landscape is again seen around the bifurcation event upon using a higher number of cell clusters (Extended data, S3 Figure (Gao et al., 2023)). Finally, we used a different algorithm to cluster cells, specifically using a Laplacian-based clustering algorithm called single-cell interpretation via multikernel learning (SIMLR) (Wang et al., 2017), to test whether the shape of the transcriptional uncertainty landscape changes with the clustering algorithm. The single-cell clusters can be interpreted as the transitional states that the differentiating cells go through. Starting with the result of SIMLR cell clustering, we then generated the lineage progression and estimated the cell likelihood values using CALISTA. The transcriptional uncertainty landscape from SIMLR cell clustering has the same shape as that in Extended data S1 Figure (Gao et al., 2023), demonstrating that the transcriptional uncertainty landscape observed above is not dependent on using CALISTA for cell clustering (Extended data, S4 Figure (Gao et al., 2023)).\n\nTo further elucidate the role of specific genes in shaping the transcriptional uncertainty landscape, we looked at the transcriptional uncertainty associated with individual genes. Figure 1e depicts the NLL distribution of each gene for the five single-cell clusters. As expected, cells in cluster 2 have generally higher NLL than those in the other clusters. Figure 1e clearly illustrates that within cluster 2, some genes show higher NLL values than the others (Extended data, S5 Figure (Gao et al., 2023)). To identify the important genes related to transcriptional uncertainty, we identified genes with NLL values exceeding a threshold δ for at least 30% of the cells in each cluster, where δ is set to 3 standard deviation above the overall mean NLL for all cells and genes in the dataset (see Methods equation (2)). None of the genes in clusters 1, 4 and 5 have a NLL above the threshold. Meanwhile, 16 and eight genes in clusters 2 and 3, respectively, pass the above criterion for high uncertainty with four common genes between the two gene sets (Extended data, S1 Table (Gao et al., 2023)). Genes with high transcriptional uncertainty in cluster 2 may have functional roles in cell fate determination. The gene set of cluster 2 includes known genes upregulated only in the PS-like state (e.g. EOMES, GSC, MESP1 and MIXL1), as well as markers of mesodermal and endodermal cells (e.g. BMP4, HAND1, and SOX17) (Bargaje et al., 2017; Papili Gao et al., 2020) (Extended data, S6 Figure (Gao et al., 2023)). Meanwhile, the main contributors to cell uncertainty in cluster 3 (e.g. BMP4 and MYL4 (Bargaje et al., 2017; Papili Gao et al., 2020)) are known transition genes between PS-like cells and the final mesoderm fate (Extended data, S7 Figure (Gao et al., 2023)). Figure 1f depicts the protein-protein interaction (PPI) network related to the gene set of cluster 2 using STRING (minimum required interaction score of 0.4) (Szklarczyk et al., 2015), indicating that these genes form a strongly interconnected hub of known transcription factors and molecules involved in the signal transduction of embryonic development (Extended data, Table S1 (Gao et al., 2023)).\n\nWe further applied the procedure above to seven additional single-cell transcriptomic datasets that were generated using scRT-qPCR (Guo et al., 2010; Moignard et al., 2013; Moussy et al., 2017; Richard et al., 2016; Stumpf et al., 2017) and scRNA-sequencing (Nestorowa et al., 2016; Treutlein et al., 2016), to assess the universality of the rise-then-fall feature of single-cell transcriptional uncertainty landscape during cell differentiation. The first of these datasets came from 405 cells during mouse embryonic fibroblast (MEF) reprogramming into induced neural (iN) and myogenic (M) cells (Treutlein et al., 2016). Like the iPSC differentiation above, the lineage progression has a single bifurcation point. As depicted in Figure 2a, the single-cell transcriptional uncertainty increases from the initial MEF state and reaches a peak around the bifurcation before decreasing toward two end-point cell fates. The rise-then-fall of transcriptional uncertainty in the MEF reprogramming is in good agreement with what we observed in the iPSCs differentiation above. Higher entropy of gene expression distribution in a cell population has also been reported in the reprogramming of iPSCs (Buganim et al., 2012).\n\n(a–c) Landscape plots (based on cell clusters and pseudotime) and moving-averaged negative log-likelihood (NLL) values for each differentiation path of (a) single-branching trajectory (Treutlein et al., 2016), (b) linear trajectories (Moussy et al., 2017; Richard et al., 2016; Stumpf et al., 2017), (c) multi-braching trajectories (Guo et al., 2010; Moignard et al., 2013; Nestorowa et al., 2016). Green and red vertical arrows in moving-averaged NLL plots indicate the first and second peak in cell uncertainty, respectively. Abbreviations: (a) MEF: mouse embryonic fibroblast, iN: induced neuronal, M: myocyte, (b) T2EC: chicken erythocytic progenitor cell, ESC: embryonic stem cell, NPC: neuroprogenitor cell, HSC: haematopoietic stem cell, CMP: common lymphoid progenitor, (c) 8C: eighth cell stage, 16C: sixteenth cell stage, ICM: inner cell mass, TE: trophectoderm, PE: primitive endoderm, E: endoderm, MPP: multipotent progenitor, LMPP: lymphoid multipotent progenitor, CMP: common myeloid progenitor, MEP/PreM: megakaryocyte-erythrocyte progenitor, GMP: granulocyte-monocyte progenitor, CLP: common lymphoid progenitor.\n\nNext, we analyzed datasets from cell differentiation processes without a lineage bifurcation and with multiple lineage bifurcations. Three scRT-qPCR datasets came from differentiation systems without bifurcation, including the Richard et al. study on chicken erythrocytic differentiation of T2EC cells (Richard et al., 2016), the Stumpf et al. study on differentiation of mouse embryonic stem cells (ESC) to neural progenitor cells (NPC) (Stumpf et al., 2017), and the Moussy et al. study during CD34+ cell differentiation (Moussy et al., 2017). The single-cell clustering and lineage progression by CALISTA produced the expected cell differentiation trajectory (see Extended data, S8 to S10 Figures (Gao et al., 2023)). The single-cell transcriptional uncertainty landscapes of these three differentiation systems, as shown in Figure 2b, exhibit a rise-then-fall profile, creating a hill that the cells traverse through in the differentiation process. A transitory increase in single-cell gene expression uncertainty was reported either directly or indirectly in the original publications. In Richard et al. (2016) and Stumpf et al. (2017), the authors adopted the Shannon entropy to quantify cell-to-cell variability (uncertainty), while Moussy et al. (2017) reported an unstable transition state with ‘hesitant cells’ flipping their morphology between polarized and round shapes before committing to the common myeloid progenitors-like fate. Morphological uncertainty therefore corresponded to a higher transcriptional uncertainty. Note that the Moussy et al. study looked at only the initial phase of the (hematopoietic) cell differentiation, and thus, it is likely that the differentiation process had not completed for the cells in the dataset.\n\nThe next set of single-cell gene expression data came from differentiation systems with multi-branching lineage, including the Guo et al. study during mouse embryo development from zygote to blastocyst (Guo et al., 2010), Nestorowa et al. (2016) and Moignard et al. (2013) studies on hematopoietic stem cell differentiation. Figure 2c shows the single-cell transcriptional landscape for each of the datasets. For the Guo et al. study, we identified seven cell clusters and identified two bifurcations in the lineage. Here, we observed two hills in the transcriptional uncertainty landscape, each coinciding with a bifurcation event in the lineage progression – one at 32-cell stage (cluster 2 to cluster 3 and 4) and another at 64-cell stage (cluster 4 to cluster 6 and 7) (see the Extended data, S11 Figure (Gao et al., 2023)). For the Nestorowa et al. (2016) (Extended data, S12 Figure (Gao et al., 2023)) and Moignard et al. (2013) (see Methods and (Papili Gao et al., 2020)) datasets, we again observed peaks in the transcriptional uncertainty landscape that colocalize with the bifurcation points in the lineage progression.\n\nThe use of the two-state mechanistic gene transcriptional model within CALISTA enabled us to probe into a mechanistic explanation for the observed shape of the transcriptional uncertainty landscape. Table 1 show the pairwise Pearson correlations between the cell-averaged NLL of each cluster with two biologically interpretable model parameters, namely transcriptional burst size (number of transcripts generated in each burst) and burst frequency (occurrence of burst per unit time) (Nicolas et al., 2017) (see Methods). The Pearson correlations indicate that the single-cell gene expression uncertainty increases with higher burst size and burst frequency (p-value ≤ 0.01). Higher transcriptional burst size and frequency are associated with a lower θoff – a lower rate of promoter turning off – and a greater θon – higher rate of promoter turning on. One possible explanation for such a change in model parameters is a higher chromatin accessibility during the transition period of cell differentiation. This finding is consistent with the view that stem cells increase its gene expression uncertainty or stochasticity by adopting a more open chromatin state to enable the exploration of the gene expression space (Antolović et al., 2017; Fritzsch et al., 2018; Nicolas et al., 2017; Zhang & Zhou, 2018).\n\nIn a recent paper (La Manno et al., 2018), La Manno and colleagues introduced the concept of RNA velocity, which involves computing the rate of change of mRNA from the ratio of unspliced to spliced mRNA. A positive RNA velocity indicates an induction of gene expression, while a negative RNA velocity indicates a repression of gene expression. La Manno et al. demonstrated that RNA velocities are able to predict the trajectory of cells undergoing a dynamical transition, such as in circadian rhythms or cell differentiation. In the following, we explored the relationship between RNA velocities and single-cell transcriptional uncertainty.\n\nWe evaluated the single-cell transcriptional uncertainty and RNA velocity for two single-cell gene expression datasets that were previously analyzed in La Manno et al. (2018). The first dataset came from human glutamatergic neurogenesis which has a linear (non-bifurcating) lineage progression. Figure 3 (top row) depicts the cell clustering, single-cell transcriptional uncertainty, and RNA velocities (see also Extended data, S13 Figure (Gao et al., 2023)). The single-cell transcriptional uncertainty landscape again has the rise-then-fall shape, as in the other cell differentiation systems discussed above. Interestingly, the same rise-then-fall profile is also seen in the RNA velocity. As illustrated in Figure 3, the increase and decrease of the RNA velocity preceed the transcriptional uncertainty, and the peak of RNA velocity occurs prior to those of the transcriptional uncertainty (see the Extended data S1 File for animated illustration (Gao et al., 2023)). Furthermore, a gene-wise cross-correlation analysis confirms a positive correlation between RNA velocity and single-cell transcriptional uncertainty with a delay for individual genes (see the Extended data, Figure S14 (Gao et al., 2023)).\n\n(Top row) Human glutamatergic neurogenesis and (Bottom row) mouse hippocampal neurogenesis (La Manno et al., 2018). (First column) Cell clustering assignments evaluated from Velocyto (La Manno et al., 2018). Normalized values for Euclidean norm of RNA velocities (2nd column), CALISTA single-cell transcriptional uncertainty (NLL; 3rd column). The colors in the first column indicate the cell clusters, and those in the second-third columns indicate the normalized cell-wise RNA velocities and NLL values respectively.\n\nWe also compared RNA velocity and single-cell transcriptional uncertainty for another dataset from mouse hippocampal neurogenesis with a multi-branching lineage (La Manno et al., 2018). Figure 3 (bottom row) shows that like in the neurogenesis dataset earlier, the RNA velocity increases and then decreases during cell differentiation, and the change in the RNA precede that of the transcriptional uncertainty (see the Extended data, S2 File for animated illustration (Gao et al., 2023)). Also, the RNA velocity peaks take place before the transcriptional uncertainty peaks. The rise-then-fall dynamic of the RNA velocity seen in the two datasets above is consistent with the view that cells engage in exploratory stochastic dynamics as they leave the progenitor state, and disengage this explorative mode as they reach toward the final cell state.\n\n\nDiscussion\n\nAlthough Waddington’s epigenetic landscape was originally proposed only as a metaphor, the landscape has helped stem cell researchers to conceptualize the cell differentiation processes through canalization of cell lineages. As mentioned earlier, much of the existing literature on the analytical reconstruction of the epigenetic landscape relied on either a dynamical system theory applied to a simple gene network, or a thermodynamic interpretation based on the potential energy of a reaction (Bhattacharya et al., 2011; Rebhahn et al., 2014). In this study, we did not make any prior assumptions on the gene regulatory network driving the differentiation process nor on the characteristics of the landscape, such as the existence of a stable valley or that of an energetic barrier (hill). Rather, we assumed that the gene transcription at the single-cell level occurs via stochastic transcriptional bursts that described by a two-state stochastic gene transcription model (Peccoud & Ycart, 1995). We defined single-cell transcriptional uncertainty based on the likelihood of the cell’s gene expression, computed using the steady-state mRNA distribution from the stochastic transcriptional model above. While high transcriptional uncertainty may reflect a cell with an aberrant gene expression signature with respect to other cells of the same state, such a cell will have little effect on the shape of the transcriptional uncertainy landscape. More importantly, high single-cell transcriptional uncertainty also reflects a cell state that is characterized by high level of heterogeneity in gene transcription. These cells together form the hill region of our transcriptional uncertainty landscape. Thus, the transcriptional uncertainty landscape in our study is a reflection of the dynamic trajectory of gene transcriptional stochasticity during the cell differentiation process.\n\nThe two-state model used in CALISTA captures the essential features of stochastic transcriptional bursts – an ON/OFF promoter state and an mRNA transcription only during the ON state. The model is able to reproduce the characteristic negative binomial distribution of mRNA commonly observed in single-cell transcriptomic data. More detailed modelling of gene transcriptional bursts that includes RNA polymerase recruitment and paused release, maturation of nascent mRNA, and cell divisions (Bartman et al., 2019; Cao et al., 2020; Suter et al., 2011), demonstrates how various aspects of gene transcription contribute to the overt cell-to-cell heterogeneity in gene expression. Under conservative simplifying assumptions, the mRNA distribution from the more detailed models can be reduced to that of the two-state model. Thus, the parameters of the two-state model, for example the rate constants of promoter activation (OFF-to-ON state) and deactivation (ON-to-OFF), should be interpreted as effective constants – i.e. not fundamental biophysical constants – that capture the aggregate impact of various sources of gene transcriptional stochasticity. Note that while we used the two-state model for single-cell clustering and transcriptional uncertainty calculations, as we demonstrated in the iPSC cell differentiation, the rise-then-fall of the transcriptional uncertainty landscape is still valid when using SIMLR clustering algorithm and when using the empirical distribution of mRNA, rather than the two-state model distribution, for computing single-cell transcriptional uncertainty.\n\nThe reconstruction of the transcriptional uncertainty landscapes from 10 single-cell transcriptomic datasets of various cell differentiation processes in our study reveals a universal rise-then-fall trajectory in which cells start from a high potency state with a uniform gene expression pattern in the cell population, then progress through transitional cell state(s) marked by increased transcriptional uncertainty (i.e., higher cell-to-cell variability), and eventually reach one of possibly several final cell states with again a uniform gene expression pattern among the cells. Furthermore, the peaks of the transcriptional uncertainty landscape colocalize with forks in the cell lineage. The rise-then-fall in cell uncertainty agrees well with other reports from different cell differentiation systems (Han et al., 2020; Mojtahedi et al., 2016; Moussy et al., 2017; Richard et al., 2016; Semrau et al., 2017; Stumpf et al., 2017), suggesting that stem cells go through a transition state of high gene expression uncertainty before committing to a particular cell fate. Notably, an increase of variability is a known early warning signal associated with critical transitions in stochastic dynamical systems that are driven by slow, monotonic change in the bifurcation parameter (Kuehn, 2011; Sarkar et al., 2019). While the results of our analysis are consistent with critical transitions during cell fate commitment in stem cells (see also (Mojtahedi et al., 2016)), our analysis does not require nor imply this phenomenon. The existence of a hill or barrier during the intermediate stage of cell differentiation has also been proposed in previous studies (Braun, 2015; Fard et al., 2016; Moris et al., 2016). In particular, Moris and colleagues compared this transition state to the activation energy barrier in chemical reactions (Moris et al., 2016). We noted however, that a hill in our transcriptional uncertainty landscape is a reflection of a peak in the cell-to-cell gene expression variability, and thus does not represent a resistance or barrier that a cell has to overcome.\n\nIn the analysis of iPSCs differentiation into cardiomyocytes (Bargaje et al., 2017), the genes that contribute significantly to the overall transcriptional uncertainty at or around the peak in the landscape (clustes 2 and 3 in Figure 1e) are known to regulate cardiomyocyte differentiation (Bargaje et al., 2017) (see the Extended data S1 Table for gene lists and S5 Figure and S6 Figure for pathway enrichment analysis of these genes (Gao et al., 2023)), supporting the idea that dynamic cell-to-cell variability has a functional role in cell-fate decision making processes (Guillemin et al., 2018; Moris et al., 2018; Rebhahn et al., 2014). Such an idea would be in congruence with the recent demonstration that, in a physiologically relevant cellular system, gene expression variability is functionally linked to differentiation (Guillemin et al., 2018; Moris et al., 2018).\n\nThe rise-then-fall trajectory in the transcriptional uncertainty landscape are more pronounced in some datatsets than in others. For example, in Nestorowa (Nestorowa et al., 2016) and Moignard (Moignard et al., 2013) datasets (see Figure 2c), peaks in the transcriptional uncertainty landscape are less noticeable than in the other differentiation systems. We noted that cells in the Nestorowa (Nestorowa et al., 2016) and Moignard (Moignard et al., 2013) studies were pre-sorted by using flow cytometry based on the expression of surface protein markers. We posited that at least some cells in the transition state(s) might have been lost during the cell pre-sorting since such cells might not express the chosen surface markers strongly.\n\nFurther, the correlation analysis between the cell transcriptional uncertainty and biologically meaningful rates of the stochastic gene transcription model showed strong positive correlations with transcriptional burst size and frequency. Note that cellular processes such as cell division can affect the heterogeneity of mRNA in a cell population in a similar fashion as stochastic gene transcriptional bursts (Cao & Grima, 2020; Perez-Carrasco et al., 2020), providing an alternate explanation for gene expression fluctuations. But, several studies have reported an increase in gene transcriptional bursts during transition states in cell differentiation and other recent studies have suggested that both burst frequency and burst size regulate gene expression levels (Antolović et al., 2017; Fritzsch et al., 2018; Zhang & Zhou, 2018). Importantly, our comparison of the single-cell transcriptional uncertainty and the single-cell RNA velocity revealed that an increase (decrease) in RNA velocity predicts an increase (decrease) in transcriptional uncertainty after a short delay, and that a peak of RNA velocity preceeds that of the transcriptional uncertainty.\n\nThe aforementioned observations, while correlative in nature, points to possible biological mechanisms underlying the universal dynamic feature of single-cell transcriptional uncertainty during cell differentiation. At the start of the differentiation process, cells engage an exploratory search dynamics in the gene expression space by increasing stochastic transcriptional burst size and burst frequency. The putative objective of such a stochastic search is to optimize the cell’s gene expression pattern given its new environment. The engagement of this stochastic exploratory mode is supported by the observed increased in the overall RNA velocity and its expected-but-delayed effect in elevating the cell-to-cell gene expression variability (i.e. higher transcriptional uncertainty). Increased transcriptional burst size and frequency are an indication of increased frequency of the promoter turning ON (higher θon and lower θoff).\n\nA possible mechanism behind this exploratory search dynamic is an increase in chromatin mobility, driven by metabolic alterations in early differentiation (Paldi, 2012). Multiple studies have demonstrated that a mismatch between the intracellular state of stem cells and their immediate environment can lead to metabolic reorganization (Argüello-Miranda et al., 2018; Folmes et al., 2011; Gu et al., 2016). More specifically, a change in the balance between glycolysis and OXPHOS metabolism has been associated to numerous differentiation processes (see (Richard et al., 2019) and references therein). Furthermore, changes in the metabolic flux state in early differentiation can modulate the activity of chromatin modifying enzymes through their metabolic co-factors (Moussaieff et al., 2015), or in more direct fashion (Zhang et al., 2019) and alter the cell differentiation outcome. A more dynamic state of the chromatin is associated with more variable gene expressions due to the changes in the opening-closing dynamics (breathing) of the chromatin (Zwaka, 2006). As the cells approach the final state, cells disengage the exploratory search mode, as the cells approach an optimal gene expression and metabolic state associated with a chosen cell type.\n\nThe findings of our analysis fit within the paradigm of a stochastic stem cell differentiation process. More specifically, in this paradigm, the cell differentiation is thought to proceed as follows (Braun, 2015; Kupiec, 1996, 1997; Paldi, 2003):\n\nI) extrinsic and/intrinsic internal stimuli, such as a medium change or the addition of new molecules in the external medium, trigger a cellular response that destabilizes the initial high potency cell state;\n\nII) each cell alters its internal cell state and engages an exploratory dynamic through a combination of the inherent stochastic dynamics of gene transcription and the emergence of new stable cell state(s). At the cell population level, we observe a rise in the cell-to-cell variability of gene expression;\n\nIII) a physiological selection/commitment to one stable lineage among possibly multiple lineages;\n\nIV) finally, a reduction in the exploratory dynamics commences along with the establishment of stable cell state(s) corresponding to differentiated cell type(s).\n\nThe disordered gene expression pattern during the transition period can be seen as an exploratory dynamic to find the optimal pattern(s) (Braun, 2015; Paldi, 2003). The transcriptional uncertainty in our analysis can be interpreted as the width of the valley in Waddington’s epigenetic landscape. If one considers the epigenetic landscape as a depiction of the accessible gene expression subspace through which stochastic single-cell trajectories pass during differentiation, a wider valley indicates a more variable gene expression pattern. While in the original Waddington’s epigenetic landscape the valley naturally widens around the branching point in the cell lineage, our analysis shows that a widening of the valley (an increase in transcriptional uncertainty) also occurs in non-branching lineage. In other words, the increase in transcriptional uncertainty appears to be a universal feature of the cell differentiation process, one that arises from the engagement of exploratory mode through increased stochasticity in transcriptional bursts, as explained above. The above view is also compatible with the idea that cell phenotype transition results from the dynamics of an underlying stochastic molecular network (Gupta et al., 2011; Thomas et al., 2014).\n\nIn summary, our model-based single-cell transcriptome analysis and the evaluation of single-cell transcriptional uncertainty have shed a new light on the role of stochastic dynamics of gene transcription in the cell differentiation process. Importantly, the peaks of single-cell transcriptional uncertainty mark cellular decision-making points in the cell lineage tree. By identifying, isolating, and analyzing more comprehensively individual cells from the peaks of transcriptional uncertainty, we can gain a much better understanding of the key molecular players in the stem cell decision-making.", "appendix": "Data availability\n\nAll the public single cell data sets analysed in this study are available from the original publications (Bargaje et al., 2017; Guo et al., 2010; La Manno et al., 2018; Moignard et al., 2013; Moussy et al., 2017; Nestorowa et al., 2016; Richard et al., 2016; Stumpf et al., 2017; Treutlein et al., 2016).\n\nZenodo: Extended Data for Single-cell Transcriptional Uncertainty Landscape of Cell Differentiation. https://doi.org/10.5281/zenodo.7776102 (Gao et al., 2023).\n\nThis project contains the following underlying data:\n\n• Data file 1. Additional Figures and Notes (S1-S14 Fig. and S1 Note of CALISTA workflow)\n\n• Data file 2. S1 Table. Genes with high transcriptional uncertainty in Cluster 2 and 3 of Bargaje et al. (Bargaje et al., 2017) data analysis.\n\n• Data file 3. S1 File. Animated illustration of RNA velocity and transcriptional uncertainty landscape in mouse hippocampal neurogenesis (La Manno et al., 2018).\n\n• Data file 4. S2 File. Animated illustration of RNA velocity and transcriptional uncertainty landscape in human glutamatergic neurogenesis (La Manno et al., 2018).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe would like to thank all members of the SBDM team for lively discussions. 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Publisher Full Text" }	[ { "id": "170465", "date": "24 Apr 2023", "name": "Alessandro Giuliani", "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 this paper the authors are able to 'put on the ground' the time-honoured Waddington's metaphor of epigenetic landscape. They were not the first ones to face the problem to make quantitative and operational the Waddington model but, at odds with other scholars, Gao et al. offer the readers a very clear and immediately reproducible data analytic procedure free of any strong theoretical frame, being only based on classical multivariate data analysis structural optimization principles with no use of a priori distributional hypothesis. Thus, the 'amount of genome expression uncertainty' at both single cell and population levels only descends from the degradation of structural compactness of clusters in terms of within cluster distance following cluster fusion and by the decrease in cell-cell correlation.\nIn this way the authors are able to uncover the 'B side' of Waddington landscape, i.e., the 'ropes' underlying the landscape and provoking its changes in shape (see Gigante, Giuliani, and Mattia 20231).\nBy the analysis of diverse data sets, the authors are able to answer their initial question about the 'bystander' or 'essential' character of the observation of an 'entropic burst' for initiating the trajectory going from a relatively stable initial stemness attractor toward cell terminal differentiation state, by a clear proof of the unescapable need of such entropic burst.\nThe material basis of such entropic burst must be looked for in the chromatin decompaction allowing for an increased variance of gene expression that was already observed by other scholars (see for example Zimatore et al., 20212).\nAll in all, this is a very elegant and innovative work that opens new avenues to the analysis of cell differentiation process by means of a physically plausible model.\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": "9633", "date": "03 May 2023", "name": "Rudiyanto Gunawan", "role": "Author Response", "response": "On behalf of the co-authors, I wish to thank the reviewer for the positive feedback and comments on our work." } ] }, { "id": "170464", "date": "09 May 2023", "name": "Geneviève Dupont", "expertise": [ "Reviewer Expertise Modelling differentiation processes" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 the CALISTA method that they have developed, Papili Gao et al. quantify single cell transcriptional uncertainty in 10 sets of single cell data associated to differentiating systems. This includes single-cell mRNA as well as single-cell RT-qPCR. The representation of the cells in the uncertainty landscape allows to visualize the differentiation trajectories and the increase in stochasticity that precedes each fate commitment. The authors also show that the transcriptional uncertainty correlates with the RNA velocity, a concept that was introduced by La Manno et al. in 2018.\nThese results shed light on the mechanism underlying cell fate commitment, with the increase of uncertainty allowing cells to possibly engage in different cellular outcomes. It also provides a new data-based visualisation of the Waddington's landscape that directly takes stochasticity in gene expression into account.\nI would suggest the authors to clarify how the cell likelihood values are computed from the data, because it is central to the work and its conclusions. In my opinion, the section entitled “Pairwise correlation analysis …” should be extended. In particular, the link with the parameters of the 2 state models should be made explicit. In the same line, the fit of the data with the distributions of the 2 state model may be discussed.\nThe authors also may wish to comment about the possible biological significance of the depths of the different valleys, as observed for example in the linear trajectories of the first line of Figure 2C (early embryonic development in mice).\nIn the Introduction, the work by M. Saez and colleagues1 should be added in the paragraph related to the graphical representation of the Waddington's landscape.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "9922", "date": "25 Jul 2023", "name": "Rudiyanto Gunawan", "role": "Author Response", "response": "Comment: Using the CALISTA method that they have developed, Papili Gao et al. quantify single cell transcriptional uncertainty in 10 sets of single cell data associated to differentiating systems. This includes single-cell mRNA as well as single-cell RT-qPCR. The representation of the cells in the uncertainty landscape allows to visualize the differentiation trajectories and the increase in stochasticity that precedes each fate commitment. The authors also show that the transcriptional uncertainty correlates with the RNA velocity, a concept that was introduced by La Manno et al. in 2018. These results shed light on the mechanism underlying cell fate commitment, with the increase of uncertainty allowing cells to possibly engage in different cellular outcomes. It also provides a new data-based visualisation of the Waddington's landscape that directly takes stochasticity in gene expression into account. Response: On behalf of my co-authors, I would like to sincerely thank the reviewer for the critiques on our work. We revised the manuscript to address the reviewer’s comments. Below, I am providing the response to each of the comments. Comment: I would suggest the authors to clarify how the cell likelihood values are computed from the data, because it is central to the work and its conclusions. In my opinion, the section entitled “Pairwise correlation analysis …” should be extended. In particular, the link with the parameters of the 2 state models should be made explicit. In the same line, the fit of the data with the distributions of the 2-state model may be discussed. Response: Following the suggestion of the reviewer, the section on pairwise correlation analysis has been expanded. In addition, more detail of the computation of the negative log-likelihood for each cell—a metric for single-cell transcriptional uncertainty—is provided in the section “Single-cell transcriptional uncertainty”. The full description of the cell likelihood calculation can be found in the journal article of the method CALISTA (https://doi.org/10.3389/fbioe.2020.00018). Regarding the fit of the data to the theoretical distribution from the 2-state model, we noted that the transcriptional uncertainty was computed for each cell and therefore it was not possible to evaluate distribution fit to the 2-state model. Still, we may compare the gene expression distribution of cells that were initially assigned to clusters. An example of the distribution fit using Kolmogorov-Smirnov (KS) distance—the maximum difference in the cumulative distributions between the data and theoretical distribution—is shown in Figure A. Figure A. Kolmogorov-Smirnov distances of single cell gene expression distribution. The distances were computed between the distribution of gene expression from CALISTA clusters and the theoretical distribution from the 2-state model. Comment: The authors also may wish to comment about the possible biological significance of the depths of the different valleys, as observed for example in the linear trajectories of the first line of Figure 2C (early embryonic development in mice). Response: Thank you for this comment. We avoided making deeper interpretation and comparison of the depth of the valley—and by the same token, the height of the hill—across datasets because the negative log-likelihood values were not normalized. One reason was that different datasets include distinct sets of genes. In addition, the experimental platforms that were used to generate single-cell gene expression data differ across datasets. One potential avenue to produce comparable landscapes across datasets would be to use a common mechanistic model describing gene transcriptional network as we recently described in (https://doi.org/10.1371/journal.pcbi.1010962). Comment: In the Introduction, the work by M. Saez and colleagues should be added in the paragraph related to the graphical representation of the Waddington's landscape. Response: Following the reviewer’s suggestion, we have added this reference in Introduction." } ] } ]	1	https://f1000research.com/articles/12-426
https://f1000research.com/articles/12-854/v1	19 Jul 23	{ "type": "Systematic Review", "title": "Understanding the use of peers for mental health care: A meta-synthesis of qualitative evidence", "authors": [ "Ikhlaq Ahmad", "Mubashir Hanif", "Ahmed Waqas", "Nadia Suleman", "Najia Atif", "Amina bibi", "Shafaq Zulfiqar", "Shoaib Sultan Kayani", "Shahzad Ali Khan", "Aasia Khan", "Siham Sikander", "Ikhlaq Ahmad", "Ahmed Waqas", "Nadia Suleman", "Najia Atif", "Amina bibi", "Shafaq Zulfiqar", "Shoaib Sultan Kayani", "Shahzad Ali Khan", "Aasia Khan", "Siham Sikander" ], "abstract": "Objective: We aim to synthesize evidence of facilitators and barriers pertaining to implementation of peer led interventions for mental health. Methods: In November 2017, we conducted an electronic search of two academic databases: Cochrane Central Register of Controlled Trials (CENTRAL) and PubMed. A comprehensive search strategy comprising of search terms including ‘peer’, ‘volunteer’, ‘Mental Health’, and ‘Qualitative Study’ was utilized to search these databases. Results: A total of six studies were included in this review. We have identified 22 first order constructs in the selected studies. These are all responses of the respondents in each individual study. Key constructs are recruitment and training, supervision, role of Peer Support Workers (PSWs), motivation, challenges and barriers. Second order constructs are researchers’ interpretations of included studies. Conclusions: We identified 26 second order constructs. These constructs are very similar to first order constructs and grouped under similar themes that were used for first order constructs. Additional constructs included insufficient training, uniformity of training, terms and conditions for PSWs.", "keywords": [ "task shifting", "peer volunteers", "facilitators", "barriers" ], "content": "Introduction\n\nAn ever increasing prevalence of mental disorders (MDs) in low and middle income countries has attracted attention both from academics and policy makers.1 This has given birth to several proactive measures ranging from global epidemiological surveys and community-oriented interventions. The Global Burden of Disease Study (2016) estimated that over 1.11 billion people are living with mental illnesses, accounting for 150 million years lived with disability, around the globe.2 It is estimated that mental illness accounts for 32.4% to years lived with disability and 13% to disability adjusted life years (DALYs).3 And by the year 2030, depression alone would be the third largest contributor to burden of diseases in low income countries and the second largest in middle income countries.4 A majority of 85% of global population belongs to 153 low and middle income countries (LMICs), accounting for 80% of the disease burden associated with mental disorders.5\n\nThe high prevalence of mental disorders together with an escalating shortage of psychiatrists presents a grand challenge in the third world.5,6 There are only 20,000 trained psychiatrists, 195,000 nurses and 147,000 counselors across the LMICs.7 This scarcity of mental health professionals (MHPs) translates to suboptimal treatment rates (35% to 50%) in the LMICs.7 In South Asia, India and Pakistan have 0.301 and 0.185 psychiatrists available for per 100000 individuals. In the African region the ratio is as low as 0.06 and 0.04.5 The World Health Organization (WHO) estimates that an additional workforce of 239,000 mental health professionals is required to reach optimal treatment rates for eight key mental disorders including depression, schizophrenia, psychoses other than schizophrenia, suicide, epilepsy, dementia, disorders related to the use of alcohol and illicit drugs, and pediatric mental disorders.7\n\nAcademics and policy makers around the world have proposed various strategies to overcome the dual challenge of a high burden of MDs and shortage of MHPs. This grand challenge is further exacerbated by poor financing of mental health services in the LMICs.5 To combat these challenges, task shifting has been evaluated for its effectiveness in various countries.8–15 This approach leverages lay workers or peers that are integrated in the existing health systems,6 and it has so far shown a significant potential in the successful detection and identification of MDs and their management, in a cost-effective manner.16 The spirit of task shifting is truly reflected in the Mental Health Gap Action Plan (GAP) developed by WHO. The MH GAP is the package of low intensity psychological interventions delivered by non-mental health professionals or lay workers.17 In addition to mental health,8,12,14,18 there is an ample amount of literature showing the usefulness of task shifting in other specialties of medicine.19–21\n\nThe effectiveness of non-specialists’ work force delivered services has been demonstrated in improving global provision and capacity. Yet, there has been little work so far in scaling up of these interventions on national levels. This may be due to several challenges pertaining to their implementation that need to be tackled. These barriers and challenges include poor motivation levels and retention of non-specialist and volunteer work force.22 Moreover, for successful implementation and scale up, barriers related to recruitment, training and supervision of this valuable workforce need to be recognized.23 Un-packing these processes and their barriers and facilitators specific to the roles assigned to peer volunteers can be effectively answered in a qualitative investigation.24 The aim of the paper here is to inform implementation of these interventions by synthesizing evidence from qualitative studies by using meta-ethnography technique. Meta ethnography is well developed and useful way to synthesis the qualitative study.25\n\n\nMethods\n\nIn November 2017, we conducted an electronic search of two academic databases: Cochrane Central Registry for RCTs and PubMed. A comprehensive search strategy comprising of search terms including ‘peer’, ‘volunteer’, ‘Mental Health’, and ‘Qualitative Study’ was utilized to search academic databases from inception to November 2017, as shown in Table 1 below.\n\nThe value of peer workers as an effective conduit for delivery of mental healthcare is recognized. For this study, peers volunteers in mental health were defined as lay workers having similar demographic characteristics as the target population or valuable lived experiences of a mental illness; working in a specific capacity in mental health care delivery after getting trained in the intervention; and lacking any professional medical or paramedical training.8,15,26 Having these commonalities with the target population enables the peers to perceive the participants as similar, and have a greater understanding of the issues being faced.27\n\nEligible citations to be included in the final analyses were selected after a thorough screening process by two teams of reviewers working independently from each other. This process was followed by manual searching of bibliographies of eligible full texts. The inclusion criteria for meta-synthesis included (1) studies that used qualitative methods for data collection and analysis (2) studies that used a task shifting approach of mental health intervention by lay workers or peer volunteers or peer support worker or peers or volunteers (3) studies published in English. Books, reports, grey literature and articles with full text not available were excluded. No restrictions on date of publication were applied. Discrepancies between reviewers were resolved through discussion between reviewers to reach the final decision.\n\nUsing a pre-tested Excel sheet, four reviewers performed extraction of qualitative data from eligible full texts. Data were extracted against a number of matrices spanning across a) lived experience of peer volunteers b) training and supervision processes c) motivation, facilitators and barriers of the task shifting approach and d) characteristics of the volunteers. These variables informed our thematic analysis: categorization of qualitative information into specific themes leading to formation first order constructs. These first order constructs thus represented lived experiences shared by peer volunteers. We also constructed second order constructs of motivations, barriers and facilitators of peer volunteer delivered interventions. These constructs were informed by the researcher’s perspective. Two reviewers cross-checked the extracted data for accuracy of the extracted data. Thirdly, quality appraisal of the included studies was done using the 13 criteria proposed by Atkins et al. (2008).28 Atkins’ (2008) criteria for appraisal of quality of qualitative studies spans across domains of study design, clarity in research questions and approach, study context, role of researchers in the study, and appropriateness of sampling methods and data collection and analysis procedures.28\n\nThe current evidence synthesis approach was based on the framework of meta-ethnography proposed by Noblit and Hare (1988).29 This is a more accepted and frequently used technique for the qualitative synthesis. This approach treats results (participants’ experiences) as first order constructs and discussions and conclusions (researchers’ interpretations) as second order constructs distilled from primary studies. In the initial phase, we synthesized findings across studies that presented consistent results and. In this manner, first order constructs and second order constructs were identified. These were then compared across studies to construct new interpretations or third order constructs. In the next phase, we synthesized evidence for constructs that were presented as contradictory across studies.\n\n\nResults\n\nA total of 841 non-duplicate titles and abstracts were retrieved from the electronic search of PubMed and Cochrane databases. Out of these 841 articles, 757 articles were excluded during title screening for reasons including quantitative study designs or focus on constructs other than mental health and non-original studies. A total of six studies were reviewed for full text screening and out of these, three studies30–32 were excluded because of their focus on intervention rather than task shifting. Three additional studies were added from searching reference lists of the included articles and a total of six studies were included for the review.\n\nThere was a total of six studies published from different countries including the UK, Canada, Denmark and USA. The highest number of studies were contributed by the UK (n=3). The studies reported the use of focus group interviews (n=3), in-depth interviews (n=4) and semi-structured interviews (n=4). The studies aimed to explore heterogeneous aims: Rebeiro Gruhl et al. (2016)33 and Berry et al. (2011)34 sought to understand the mechanism for integration of PSWs within mainstream services in Canada and the UK; Jensen et al. (2017)35 sought to explore experiences of volunteer families; Nan Greenwood et al. (2013)36 focused on experiences of peer support service. Moran et al. (2013)37 explored challenges for peers working in diverse setting and roles while Gillard et al. (2015)38 focused on peer workers employed in the statutory sector, voluntary sector and in organizational partnerships. Atif et al. (2016)8 and Munodwafa et al. (2017) focused on understanding use of peer and CHWs in delivering task shifting interventions for perinatal depression (see supplementary file 139). All the included studies met the Atkin’s criteria of appraisal (see supplementary file 539).\n\nWe have identified 22 first order constructs (see supplementary file 239) among the selected six studies. These are all responses of the respondents in each individual study. Key constructs are recruitment and training, supervision, role of PSWs, motivation, challenges and barriers.\n\nVolunteer-led initiatives are always challenging. Our extracted data from the included studies highlighted a number of challenges. Respondents reported that disconnection between the training they receive and the actual task they are doing results in burnout. Sometimes working with clients that are having similar problems as PSWs had in the past will remind them of their stressful time which can be upsetting. Another challenge is when a client is not improving and it becomes difficult for PSWs to establish a healthy relationship. Integration of peer led initiatives into the mainstream is also a challenge because of unclear roles and acceptance of their roles in mainstream health systems.\n\nPeer support workers highlighted the importance of employing a formal recruitment process. They believe these processes make them recognize the importance and responsibility of their role. Insufficient training for PSWs is another issue that was reported. These PSWs are coming from different backgrounds with varied training needs. They are recruited at different time points in mental health services; those recruited at an earlier stage have more training compared to those recruited at a later stage of the program. The PSWs who developed better skill sets were assigned more responsibilities. The need for uniform training was highlighted. All the PSWs valued the importance of lived experience as a prerequisite for a role in the mental health service.\n\n“I haven’t taken any training. I’m not even aware that it’s been offered up where I am…. I do not have a policy degree as a social worker or anything. I’m coming from the Centre where I was formerly a volunteer and that was it. So it’s lived experience plus I’ve been sent for crisis intervention, conflict resolution … those kinds of things. (NB04)33”\n\nRespondents emphasized the importance of quality supervision as an integral part of volunteer initiatives. PSWs reported that without supportive supervision it is very difficult to meet the expectations of their role.\n\nIn addition, peer providers should receive supplemental preparation and supervision specific to the job context above and beyond generic peer training programs.37\n\nOngoing supervision gives them the sense that they are not alone in their experiences and helped them think that many other people also have had similar experiences. They are made aware that people could share similar emotional journey including both positive and negative emotions. Moreover, it was highlighted that discussion during trainings help them realize that their experiences are not unexpected.\n\n“It’s a perfectly normal, understandable reaction that no one is weird or freaky that they feel like that. There was anger in there too but having someone say ‘Yeah I felt like that too’ helped.36”\n\nPSWs reported concerns about their unclear and ambiguous role. Most of them reported they are performing a different role than they had been recruited for at the time of interview. Most of the time they were asked to do things they are not supposed to do. They reported that their role is not acknowledged in the organization and they are not treated equal to their co-workers. PSWs reported they like a role where they share their experiences, participate in trainings, communicate and work collaboratively with others, initiate, establish and maintain relationships with clients and help clients to set goals and work towards them. They are also working as change agents in diverse settings.\n\n… it actually recognizes that the role is a proper job … if they go through a recruitment process they realize the importance and the responsibility the job brings.38\n\nIt’s a good start, but it doesn’t have support. It’s very difficult. When you say integrated, we’re trying, we’re trying to bring to the hospital let’s bring peer support into the hospital. We’re trying, but wow it’s a battle. And that battling sense is wrong. I really feel we should be able to be critical of the system. And that’s what is getting attention.33\n\nRespondents reported the concept of professional boundaries is relative according to the situation and contextual factors determined by the PSWs. For the volunteer work, professionalism is defined as doing your work as best as you can.\n\nIt’s an important issue that they’re not as professional as a normal worker … if they were formal they would have a completely different appearance and approach to things than if they were informal …38\n\nIn one study, PSWs reported that the non-professional and prejudiced attitude of co-workers towards clients was a significant barrier. Having a structured peer support work team in an organization provides a professional outlook, promotes camaraderie and motivation. Most of the organizations have an unstructured peer support work process which may stigmatize the peer worker working with patients. According to Galia et al., without a structured and supportive environment peer support workers may also feel alone and emotionally distressed especially when they are going through their own recovery process\n\n‘It can be tough, you feel shunned at some places, and sometimes things your professional colleagues say trigger from your own recovery processes”.37\n\n‘It’s hard to be a trail blazer when you are the only peer provider on staff”.37\n\nPSWs reported that a sense of helping others is the primary source of their motivation. Peer support workers have a great fund of knowledge gained while recovering from their own mental illnesses. They also face (public and self) stigma associated with mental illnesses. During their recovery process, they also learn strategies to manage their symptoms and cope with sociocultural challenges. Therefore, PSWs can help people early in their course of illness by teaching them effective coping strategies. This can catalyze patients’ recovery from mental disorders.\n\nIt’s not that I don’t want to help people in Africa, I would love to. But I kind of like to give a piece of myself to someone. Give something to a person who really needs it.35\n\nPSWs highlighted that happiness and sense of achievement felt by helping and supporting other people is a big source of their motivation for their participation in such programs.\n\nAll the families pointed to the personal joy and sense of reward generated by supporting and caring for another person, as a huge motivation for entering and staying in the programme.35\n\nPSWs reported being helpful to others is the most satisfactory thing in their work. Shared experiences are helpful in helping others. Meeting new people and working with them is a pleasurable activity, and training and exposure enhances their personal skill set.\n\n“I think that one of the most important things that has trained me for my job description is the lived experience. I have a degree in education; I have a degree in psychology. I have all kinds of diplomas in education background and I have been an educator for most of my life, but having the lived experience of severe mental illness has given me a lot of insight, and patience, and tolerance and compassion … the lived experience is the most important thing that I bring to the table. (NB09)33”\n\nSecond order constructs\n\nSecond order constructs are researchers’ interpretations of included studies. We have identified 26 second order constructs (see supplementary file 339). These constructs are very similar to first order constructs and grouped under almost same themes that were used for first order constructs. Additional constructs included insufficient training, uniformity of training, terms and conditions for PSWs.\n\nAll studies except one report that there is a strong support for lived experiences for the PSW role. It was concluded that PSWs are not recruited following more formalized recruitment methods, PSWs are recruited at different time points and for a limited time period depending on the activity for which they are being hired. Support for the training and wellbeing of PSWs working in the complex environment was needed.\n\n“In addition peer providers should receive supplemental preparation and supervision specific to the job context above and beyond generic peer training programs.37”\n\nData indicated that participants felt the role of PSWs is unclear, and that the clarity of their role and job description is very important. PSWs are performing varied roles and they are spending more time on indirect activities rather than direct mental health services. PSWs are expected to perform the challenging role of a change agent.\n\n“A mismatch between the PSS professional identity and the actual role seemed to be associated with “othering” of the PSS worker by the team, but also a simultaneous denial of the specialism of the role. Therefore, the current findings provide more explanatory power to recommendations for previous research concerning the need for clearly defined peer support roles.34”\n\nThe importance of a professional approach in such voluntary initiatives is highlighted in included studies. The studies reported that training on workplace ethics and maintaining professional boundaries should be given to PSWs.\n\n“Thus, feeling forced into the consumer movement, or being pigeonholed as a “peer poster boy”, may be confining and ultimately lead to burn out and lack of intrinsic motivation.37”\n\nIt was concluded that involving PSWs in indirect activities results in a low level of PSW satisfaction. Physical distance from urban centers and an unclear job description also adds to their dissatisfaction. PSWs are not treated equally to paid staff and they are expected to work as per traditional values. Paid staff felt insecure and think that PSWs might take their role, which leads to the isolation of PSWs.\n\n“PSS workers were in a vulnerable position of having to challenge workers of a higher pay banding, often in a resistant environment, and with limited support.34”\n\nHelping others is the most satisfying thing for PSWs, and it has positive effects for their self-esteem, confidence and recovery. Supportive supervision from senior management is another facilitator. Training opportunities help in developing capacity and leadership skills of the PSWs. It was also concluded that acceptance from both PSW and their clients to provide and receive help, helps in creating a positive relationship.\n\n“Additionally, relationships were more supportive if both people were willing to provide and receive support and had gained some distance from their own situation, so that they were able to help each other think through solutions, rather than simply give advice based on their own experiences.33”\n\nAlthough most of the literature suggests that lived experience is a perquisite for the role of PSW, one study concluded that lived experiences are not necessary if a PSW had all the basic characteristics to enable them to perform the role.\n\n‘The first PSS worker stressed that, while obviously a prerequisite to the position and valuable, lived experience of mental health problems should not entirely define the role; “I mean there will be times where I meet people who I’ve met in a different role, but my role is here, as a Peer Support Specialist worker, and what’s happened in the past is not an issue […] I’m very clear about my own boundaries and space” (P1)’34.\n\nThird order constructs\n\nOur interpretations are represented as third order constructs (see supplementary file 439). This is based on first order constructs and second order constructs along with recommendations.\n\nThere is a need for formal and standardized procedures for the recruitment of PSWs for mental health services. They should be assigned very precise and clear roles and responsibilities. Standardized training in terms of content and duration will be helpful to PSWs in delivering standardized care. More structured supervisions are also needed. All PSWs should receive same level of supervision with same intensity.\n\nOne of the barriers to the success of peer led programs is the dissatisfaction of PSWs. Unclear job description, involving them into indirect activities, burnout and unfavorable working conditions are the main reasons for their dissatisfaction. A lack of acknowledgment and acceptance of PSWs’ contributions towards better health outcomes, lack of standardization and unclear roles are the barriers for integration of such initiatives into mainstream health systems.\n\nEmotional satisfaction by helping others is a great motivator for PSWs. PSWs learn new skills, gain confidence, and their role boosts their self-esteem. Shared and lived experiences are helpful and facilitating factors while delivering such type of intervention. Positive social interaction also brings good feeling to PSWs as well.\n\n\nDiscussion\n\nThe present review meta-synthesizes evidence aims to understand the use of peers and their integration in mental health services. Several facilitators and challenges for peer led programs were identified during this exercise. We demonstrate that the procedures applied for recruitment and training of peers are inadequately structured. The desire to help others and opportunities for personal development are prime motivators for PSWs. Integration of peer led programs into mainstream mental health services presents a grand challenge in this domain. Additional difficulties faced in traditional mental health organizations were direct and covert displays of prejudice among coworkers, interpersonal issues, a lack of a recovery-oriented work atmosphere, and serving as the only peer provider in the organization. Excessive work and poor working conditions were common. Lack of training and inadequate training were also identified.10\n\nSeveral studies highlighted the importance of standardized and well-defined procedures for recruitment of PSWs in successful implementation of intervention programs. PSWs were assigned less formal positions at organizations due to the nature of their commitment, however it is important that they must be assigned well-defined roles with clear objectives. Our results showed that in such programs, trainings are less structured and poorly standardized. And this lack of standardization in trainings leads to varied levels of competence of the PSWs and ultimately their performance. Standardization, both in terms of content and duration, should be ensured for better quality and deliverability. Training of PSWs is a highly important aspect for the success of any mental health services delivered through peers’ support.12 It was highlighted that PSWs are recruited at different time points of the programs and they have different background and predispositions. Individuals that are inducted in on-going trainings have fewer opportunities to learn and practice; since they are offered the same training, their individual needs which affect their job performance are not considered. In addition, poor supervision from specialists and senior colleagues was another hindrance in provision of poor mental healthcare.\n\nSome important challenges pertained to lack of skills for using one's life story and lived experience, and stigma and negative connotations associated with carrying a peer provider label. Moreover, personal mental health challenges were exacerbated by overwork and sometimes led to reporting of symptom recurrence among peer volunteers.37 These challenges hinder emotional satisfaction, self-esteem and confidence and capacity building. According to Moran et al., shared experiences among peer volunteers are important facilitating factors that should be channelized to provide important insights into the condition and treatment.37\n\nIn addition to these challenges, a clear job description and role clarification was lacking in a number of interventions – these should be fully standardized by key stakeholders (including program administrators, supervisors, and potential coworkers), with relevant competencies, and a clear policy for evaluating competencies and job performance.9 This lack of clear job description is an important predictor of poor satisfaction among Peer\|Volunteers (PVs). Effective integration of peer support requires consideration of the work role, unique needs of the worker, and the overall workplace environment. Integrating peer support providers is a process that evolves over time and does not end once someone is hired.11 Corroboratory evidence suggests that poorly defined job structure, lack of policies and practices and administrative support lead to poor integration of PVs in the healthcare systems.40\n\nWe included only qualitative studies, due to inherent methodological constraints these studies have reported few limitations, which mainly include reporting bias, limited generalizability and heterogeneity of the sample. The search for the included studies was conducted in 2017 and there is a possibility that the body of knowledge may have evolved in this time period. Another limitation of the current study is that only two search engines were searched for inclusion of the relevant studies in the meta-synthesis whereas findings could be more robust if multiple search engines were explored.\n\n\nConclusion and future direction\n\nMost PSWs experienced difficulty in describing what they did, and why the mental health system needed peer support. This did little to make explicit their unique contribution to mainstream mental health services, or why they should be hired if they are engaging in mental health treatment and prevention. Peer support is particularly important for the mental health system as it provides compassion, empathy, listening, validation, and hope for those with mental illnesses. Future training/supervision should embrace authenticity and any standardization of peer support work should be based in it.\n\nThe need for an investment in structured and standardized training/supervision is paramount to peer support systems. The findings highlighted inconsistent training, which is especially problematic. It is advised to set a minimum level of training for PSWs that reflects the viewpoints and capabilities of the peer workers. The findings also highlight the significance of setting up a network of resources to help the peer support workforce thrive in the mainstream system and, most importantly, to collectively struggle for its credibility. Some people see integration as a way to get better recognition and job prospects. The increasing integration of the PSW inside conventional mental health services can be advantageous. This in turn will bring value to PSWs.\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\nFigshare: Understanding the use of peers for mental health care: A meta-synthesis of qualitative evidence, https://doi.org/10.6084/m9.figshare.21202499.39\n\n\nReporting guidelines\n\nFigshare: PRISMA checklist and flowchart for ‘Understanding the use of peers for mental health care: A meta-synthesis of qualitative evidence’, https://doi.org/10.6084/m9.figshare.21202499.39", "appendix": "Acknowledgments\n\nThe authors would like to thank Bushra Ali for contributing to this work.\n\n\nReferences\n\nChisholm D, Sweeny K, Sheehan P, et al.: Scaling-up treatment of depression and anxiety: a global return on investment analysis. Lancet Psychiatry. 3(5): 415–424. 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PubMed Abstract \| Publisher Full Text\n\nTurner EL, Sikander S, Bangash O, et al.: The effectiveness of the peer-delivered Thinking Healthy PLUS (THPP+) Program for maternal depression and child socioemotional development in Pakistan: Study protocol for a randomized controlled trial. Trials. 2016; 17(1): 1–11. PubMed Abstract \| Publisher Full Text\n\nVandewalle J, Debyser B, Beeckman D, et al.: Peer workers’ perceptions and experiences of barriers to implementation of peer worker roles in mental health services: A literature review. Int. J. Nurs. Stud. 2016; 60: 234–250. PubMed Abstract \| Publisher Full Text\n\nMcInnis MG, Merajver SD: Global mental health: Global strengths and strategies. Asian J. Psychiatr. 2011; 4(3): 165–171. Publisher Full Text\n\nKeynejad R, Dua T; CB-E mental, 2018 undefined: WHO Mental Health Gap Action Programme (mhGAP) Intervention Guide: a systematic review of evidence from low and middle-income countries. ebmh.bmj.comSign in.[cited 2019 Jul 27].Reference Source\n\nShorey S, Chee C, Chong YS, et al.: Evaluation of technology-based peer support intervention program for preventing postnatal depression: Protocol for a randomized controlled trial. J. Med. Internet Res. 2018; 20(3).\n\nBui TD, Kadzakumanja O, Munthali C: Mobilizing for the Lilongwe Diabetes Peer Support Programme in Malawi. Malawi Med. J. 2014; 26(4): 124–125.Reference Source\n\nZhong X, Wang Z, Fisher EB, et al.: Peer Support for Diabetes Management in Primary Care and Community Settings in Anhui Province, China. Ann. Fam. Med. 13 Suppl 1: S50–S58.Reference Source\n\nLabhardt ND, Balo JR, Ndam M, et al.: Task shifting to non-physician clinicians for integrated management of hypertension and diabetes in rural Cameroon: A programme assessment at two years. BMC Health Serv. Res. 2010; 10(1): 339. PubMed Abstract \| Publisher Full Text hReference Source\n\nLudwick T, Brenner JL, Kyomuhangi T, et al.: Poor retention does not have to be the rule: retention of volunteer community health workers in Uganda. Health Policy Plan. 2014; 29(3): 388–395. PubMed Abstract \| Publisher Full Text\n\nCaulfield A, Vatansever D, Lambert G, Van Bortel T : WHO guidance on mental health training: a systematic review of the progress for non-specialist health workers.2019; 1–16.\n\nCurry LA, Nembhard IM, Bradley EH: Qualitative and mixed methods provide unique contributions to outcomes research. Circulation .2009; 119(10): 1442–1452. PubMed Abstract \| Publisher Full Text\n\nLiving WBaR: Volunteerism as an Occupation and its Relationship to Health and Wellbeing. Br. J. Occup. Ther .2004; 76(12): 7.\n\nLewin S, Dick J, Pond P, et al.: Lay health workers in primary and community health care. Cochrane Database Syst. Rev. 2005. Publisher Full Text\n\nSingla DR, Kohrt B, Murray LJ, et al.: Psychological Treatments for the World: Lessons from Low- and Middle-Income Countries. SSRN. 2017; 13: 149–181. Publisher Full Text\n\nAtkins S, Lewin S, Smith H, et al.: Conducting a meta-ethnography of qualitative literature: lessons learnt. BMC Med. Res. Methodol. 2008; 8(1): 1–10. Publisher Full Text\n\nNoblit GW, Hare RD: Meta-Ethnography: Synthesizing Qualitative studies. Newbury Park:Sage Publications;1988. Publisher Full Text\n\nGray B, Robinson CA, Seddon D, et al.: An emotive subject: insights from social, voluntary and healthcare professionals into the feelings of family carers for people with mental health problems. Health Soc. Care Community .2009; 17(2): 125–132. PubMed Abstract \| Publisher Full Text\n\nDowling S, Hubert J, White S, et al.: Bereaved adults with intellectual disabilities: a combined randomized controlled trial and qualitative study of two community-based interventions. J. Intellect. Disabil. Res .2006; 50(4): 277–287. PubMed Abstract \| Publisher Full Text\n\nMinor K, Thompson P: Development and evaluation of a training program for volunteers working in day treatment. Psychiatr. Serv .1975; 26(3): 154–156. PubMed Abstract \| Publisher Full Text\n\nRebeiro Gruhl KL, LaCarte S, Calixte S: Authentic peer support work: challenges and opportunities for an evolving occupation. J. Ment. Health. 2016; 25(1): 78–86. PubMed Abstract \| Publisher Full Text\n\nBerry C, Hayward MI, Chandler R: Another rather than other: experiences of peer support specialist workers and their managers working in mental health services. J. Public Ment Health. 2011; 10: 238–249. Publisher Full Text\n\nJensen LG, Lou S, Aagaard J, et al.: Community families: A qualitative study of families who volunteer to support persons with severe mental illness. Int. J. Soc. Psychiatry. 2017; 63(1): 33–39. PubMed Abstract \| Publisher Full Text\n\nGreenwood N, Habibi R, Mackenzie A, et al.: Peer support for carers: a qualitative investigation of the experiences of carers and peer volunteers. Am. J. Alzheimers Dis. Other Demen. 2013; 28(6): 617–626. Publisher Full Text\n\nMoran GS, Russinova Z, Gidugu V, et al.: Challenges experienced by paid peer providers in mental health recovery: a qualitative study. Community Ment. Health J .2013; 49(3): 281–291. PubMed Abstract \| Publisher Full Text\n\nGillard S, Holley J, Gibson S, et al.: Introducing new peer worker roles into mental health services in England: comparative case study research across a range of organisational contexts. Adm. Policy Ment. Health. 2015; 42(6): 682–694. Publisher Full Text\n\nAhmad I, Hanif M, Waqas A, et al.: Understanding the use of peers for mental health care: A meta-synthesis of qualitative evidence. figshare. [Dataset].2022. Publisher Full Text\n\nGates LB, Akabas SH: Developing strategies to integrate peer providers into the staff of mental health agencies. Adm. Policy Ment. Health .2007; 34(3): 293–306. PubMed Abstract \| Publisher Full Text" }	[ { "id": "215084", "date": "01 Nov 2023", "name": "Michael John Norton", "expertise": [ "Reviewer Expertise Peer Support Working", "Mental Health Recovery", "Systematic Reviews", "Co-Production", "Social Recovery" ], "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 Many thanks for submission of this article for review. Please see my comments below\nThis article attempts to provide a meta-synthesis of peer led interventions within mental health discourse. However, the review is poorly conducted, does not use recognised guidelines and reads poorly.\n\nTitle: you mention meta-synthesis here. A meta-synthesis can only occur in qualitative systematic reviews. Suggest amending title here to include systematic review and meta-synthesis.\n\nAbstract - as a whole is poorly written. The objective seems reasonable. The method is missing key information that should be in a paper of this calibre - PRISMA for the systematic review aspect and Sandewoski and Barrosso for the meta-synthesis part. Additionally, you mention that you just searched two databases and one of them is known to have just quantitative evidence which means you really only searched one database. This is not satisfactory for a systematic review and certainly not a meta synthesis. Results could be elaborated to mention the themes in a bit more detail. Conclusion reads like a carry on from the results. Conclusions should include recommendations for future research or limitations of the study, of which there is plenty.\n\nKeywords - If of equal importance, place in alphabetical order.\n\nIntroduction - as a whole the introduction is not appropriate for what is being discussed as it has no relevance to peer support. You use abbreviations like WHO which is not explained at all in text. Considering what this study is examining, the language of the entire paper needs to be recovery orientated. For instance instead of 'mental illness', say 'mental health challenges'. These little things make the paper more enticing to read.\n\nMethods - as a whole, not appropriate as it currently stands. Like the abstract, you need to mention PRISMA and follow their guidance on reporting systematic reviews. Additionally, the same applies for the meta-synthesis. 2 databases is not appropriate and the Cochrane Central Registry is not an appropriate database for qualitative literature. It's an RCT database. You seem to be fusing two methodological orientations here which makes the paper even harder to read. You mention in parts meta-ethnography and then meta-synthesis which has its own epistemological basis to that of meta-ethnography. Please do not use meta-ethnography here unless you did not do a meta-synthesis. In addition it was difficult to understand whether you were looking at volunteer peers or paid peers or both. Regardless there is no way you only had 6 results at the end. An unpublished meta-synthesis in this area that I conducted in 2018 found at least 12 studies that met the criteria after going through the proper methodological processes. So the fact you have six with the poor search strategy is farcical to me. Additionally, you conducted this review in 2017 but only looking to publish now which is odd in my opinion as the evidence is ever changing in this dynamic area of research. In search criteria you mentioned that any text that did not have a full text was excluded - this is not an appropriate rationale for exclusion. You mentioned you used Atkins et al quality appraisal tool, when not CASP? it is more up to date than Atkins tool.\n\nResults - where is the PRISMA flow chart showing how the papers were whittled down to the final six. Equally, in the characteristics of studies you mention seven studies not six? Please confirm that it is six studies and not seven. Where is the comparative appraisal of evidence table. Additionally the first and second constructs should be fused together to enhance the results. Quotations should be more integrated into the results. Correct quotations to correct text would be helpful here also. Third order constructs are your interpretation of results, this is what a discussion is supposed to demonstrate so please fuse your third order constructs with the discussion.\n\nDiscussion - When the entire paper is reworked then your discussion may actually correlate with the remainder of the text. In the discussion, why not talk about the fact that you are at least two times removed from the original raw data and what this means for the interpretation of the meta-synthesis. You also speak about generalisability and heterogeneity which both cannot occur in qualitative literature reviews or qualitative studies.\n\nConclusions - must be reviewed when the entire paper is revised.\n\nUltimately, although initially excited by this paper, it failed to follow correct guidelines and processes.\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? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? No", "responses": [] }, { "id": "210951", "date": "17 Nov 2023", "name": "Nicola C Byrom", "expertise": [ "Reviewer Expertise Peer support", "mental health in emerging adults", "university and student mental health", "public 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\nThis was a fascinating read and is a much needed piece of work. The introduction is powerful and compelling. We really do need a better understanding of what peer support is and why it is so hard to get enthusiasm in this intervention and maintain motivation. I would really liked to have seen a clear return in the conclusion to the points from the introduction around poor levels of motivation and low retention, just bringing full circle in the paper. I think you paper addresses the issues of motivation and retention really well, I'm just asking for you to try to make this more explicit in the discussion and conclusions - note there is no mention of motivation in the discussion or conclusion.\n\nIt is fantastic to see a clear definition of a peer support worker in your paper. This is really helpful. It was less clear how you implemented this definition in your search strategy. It would be helpful to know how many papers were excluded because they did not meet your definition of peer support worker. I do wonder whether you are missing a lot of literature relating to paid peer support workers. I note that most of your papers came from High income countries - in these contexts, payment for peer support workers is becoming standard practice and there has been critique of expecting these roles to be conducted in a voluntary capacity. I do worry that you are missing an important discussion around the role / need for payment in this model.\n\nI am worried that you have only found 6 relevant papers. This really surprises me. I am trying to work out why that would be the case. I suspect that your search terms mean that you've missed much relevant literature. Where you are using the MeSH term \"mental illness\" are you picking up all anxiety disorders, depressive disorders etc.? I can't quite work this out. If not, you are going to be missing a lot of literature that might, for example, focus on depression specifically. I suspect that at this stage you won't have capacity to revisit the search and identify further papers. If this is the case, I think you need to be really clear about what you might have missed, why and how, so that this is transparent.\n\nThere seems to be a gap in your results. you explain that you have found 841 articles and that 757 were excluded. This does not explain how you get down to a final 6 papers. Something is missing.\n\nThe sections around data extraction and analysis felt confused to me. A little overlap between these sections with the data extraction referencing the thematic analysis to be described in the next section on analysis. I would appreciate a reference in the analysis section for the statement \"this is a more accepted and frequently used...\" it would be helpful for your reader to then explain in a little more detail what a meta-ethnography is and how this works. I'm missing how you actually get to the results that you have presented.\n\nThrough the results section I would find it helpful if you refered to the papers so we get a feel for whether points are mentioned in one paper only or are more universal.\n\nI think you need to be more careful about whether ideas are coming from results or from the researchers writing the paper. E.g., in the section on professionalism, this is technically in the first order section, so should be driven by the results, but the phrasing that you use here makes in sound in places like you are referring to the authors reflections on the results.\n\nThere could be clearer alignment between the quotes and the text that you are using to describe these. For instance, again in the section on professionalism, you have a fantastic quote ‘It’s hard to be a trail blazer when you are the only peer provider on staff” - this doesn't really feel to me like it is about professionalism - it sounds more like the challenges of feeling alone, lacking a team or peers.\n\nI think there are points to address in this paper but I'm so thrilled to see someone synthesizing this work. It is very helpful.\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", "responses": [] } ]	1	https://f1000research.com/articles/12-854
https://f1000research.com/articles/12-853/v1	19 Jul 23	{ "type": "Case Report", "title": "Case Report: 3 Tesla magnetic resonance imaging of Rapidly Progressive Osteoarthritis of the Hip", "authors": [ "Prasad Desale", "Rajasbala Dhande", "Pratapsingh Parihar", "Vadlamudi Nagendra", "Devyansh Nimodia", "Prasad Desale", "Rajasbala Dhande", "Pratapsingh Parihar", "Devyansh Nimodia" ], "abstract": "Rapidly progressive osteoarthritis of the hip (RPOH) is a rare disease with few mentions in the literature. Recent studies have suggested a female predisposition. The nature of disease progression and some specific radiological features like lesion patterns, location within the hip joint and the presence of subchondral fractures help differentiate rapidly progressive osteoarthritis from classical osteoarthritis. Awareness of RPOH as a differential in arthropathies among clinicians would save crucial time, reduce unnecessary investigations and help better manage patients. The treatment in earlier stages is often conservative, managed only by painkillers, physiotherapy, and traction however, most of the cases need surgical intervention, i.e., total hip replacement. The following case study is a classic case of RPOH in a male with trauma as one of its etiological factors and has progressed to the final grade, i.e., grade III according to grading by Ancut a Zazgyva displaying all the imaging features of RPOH as described in the literature.", "keywords": [ "Rapidly progressive osteoarthritis hip", "RPOH", "RPOAH", "RPOA", "MRI", "osteoarthritis", "destructive arthritis", "Arhtropathy" ], "content": "Introduction\n\nRapidly progressive hip osteoarthritis (RPOH), also known as rapidly destructive arthritis, is a rare illness that can cause joint deterioration as quickly as six months to as long as three years and was first described by Postel and Kerboull in 1970,1 and Lequesne.2 It is defined as chondrolysis >2 mm in 1 year or 50% joint-space narrowing within one year3 with no indication of other forms of rapidly destructive arthropathies, like osteonecrosis or Charcot neuroarthropathy. Osteoarthritis and RPOA (rapidly progressive osteoarthritis) are more common in women and tend to manifest in the sixth decade of life or later, as per all the reported case series.4,5 Although Coste initially identified RPOA in literature in 1959,6,7 the exact etiology of the condition is still unknown. In some case series, infectious etiologies have been ruled out using intraoperative biopsies and/or culture. Based on the histology of the resected tissues, primary osteonecrosis has been ruled out as the cause of the rapid destruction of the femoral or humeral head in numerous studies.8\n\nSome proposed pathologic mechanisms include toxic effects of drugs, B-cell-mediated immunological mechanisms, auto-immune pathologies, or fractures with subchondral insufficiency.9 The rapid progression, rate, and severity of joint destruction, as well as some radiographic features, clearly distinguish RPOH from primary osteoarthritis, despite the fact that the histologically degenerative changes are typically similar to those occurring in primary osteoarthritis of the hip (POH).9\n\nA unique clinical and radiologic presentation supports the diagnosis of RPOA. Therefore, doctors and radiologists must be aware of this phenomenon to avoid needless diagnostic testing and guarantee fast, effective treatment.8 Temporizing surgical management in these cases might lead to considerable difficulties in total hip replacement (THR) due to the potentially severe loss of bone stock that can occur in as little as a few months after diagnosis.10 Unlike in osteoarthritis and osteonecrosis, acetabular defects are expected during surgery for rapidly progressive osteoarthritis.11 Joint preservation is the primary goal in all forms of hip arthropathy, especially with young patients. Villoutreix et al. evaluated corticosteroid injections and activity modification with restricted weight bearing in 28 patients with rapidly progressive osteoarthritis. No difference in the need for definitive treatment was noted, with 20 of 28 patients undergoing THA within one year of symptom onset (mean, 6.2 months; range, 0.3-11 months).12\n\n\nCase study\n\nThe patient was a 65-year-old male farmer by occupation since adulthood, residing in rural central India involving physical labour with minimal dependence on machinery. He presented to the hospital with complaints of pain in his left hip for two years. The pain started after the patient fell from a bike two years ago. The patient went to a local hospital and was only prescribed analgesic medications and bed rest. However, the pain was not relieved and continued to be dull in nature, progressive, and aggravated by movements such as walking, squatting, and working. The patient also had complaints of getting up from a sitting position. Then the patient had a slip and fell at home 15 days prior to admission, causing the pain to flare up again. The patient now needed support while walking. The patient had no history of fever, cold, cough, abdominal pain, or burning micturition. The patient was not a known case of diabetes, hypertension, and tuberculosis. The patient had no past surgical history and no history of addictions like tobacco, alcohol, or smoking.\n\nGeneral and systemic examinations of the patient were carried out as follows-\n\nThe patient was afebrile with a pulse of 76 beats per minute, and blood pressure was 122/80 mmHg. There was no evidence of pallor, icterus, clubbing, cyanosis, lymphadenopathy, or edema. The cardiorespiratory and abdominal systems were within normal limits.\n\nLocal examination of the patient was carried out in supine position with both anterior superior iliac spine (ASIS) at the same level. Inspection showed left adduction deformity, left anterior superior iliac spine appeared at a higher level than the right limb suggesting length discrepancy. The greater trochanter was proximally migrated. No swelling, no scars, or sinus was seen. Moderate muscle wasting around the left hip joint was observed. The patient demonstrated Duck gait or waddling gait on walking. On Palpation, there was no local rise in temperature in the left hip. Tenderness was present over the anterior joint line. The apparent length of left limb was 122.5 cm, and the right limb was 124 cm.\n\nThe true length of left limb was 96 cm, and right limb was 97 cm. There was 1.5 cm of apparent limb shortening present on the left side and 1 cm of true shortening.\n\nHip range of motion examinations (Table 1) presented that there was supra-trochanteric shortening by 4 cm (digital Bryant’s triangle), and telescoping was absent. The patient was asked to move all toes of the foot with and without resistance and active toe movements were present. Distal circulation was assessed by palpating the distal arteries with the index and middle finger. On palpations the distal pulsations were intact, so it was concluded that the distal circulation remained intact, suggesting no evidence of any neurological or vascular deficit.\n\nThe clinical diagnosis considered was infective or tuberculous monoarthropathy. To confirm, routine blood and urine investigations were done. These involve evaluating the patient blood for signs of inflammation and infections, which includes increased number of red and white blood cells, presence of pus cells in urine, increased levels of certain biochemicals like CRP (C-reactive protein). The blood or urine sample was collected and evaluated for above signs by microscopic examination and biochemical testing of the given sample. After the above evaluation, there were no signs of infection of inflammation in the blood and urine samples.\n\nAcid-fast staining of sputum sample and cartilage-based nucleic acid amplification test (CB NAAT) were also done to assess tuberculosis infection. Acid-fast staining is a microbiological test which involves use of carbolfuschin to determine presence of ‘acid fast bacilli’ in the given sample. Mycobacterium tuberculosis, which is the causative organisms of tuberculosis is one of the acid-fast bacilli and appears purple under a microscope on acid-fast staining of the given sample. The patients sample tested negative for acid-fast staining. Cartilage-based nucleic acid amplification test (CB NAAT) is a complex and modern test to determine presence of a microorganism, in this case mycobacterium tuberculosis, in the given blood sample. It involves detection of nucleic acid of the organism by a process called polymerase chain reaction. The patient’s blood sample was tested negative for tuberculosis using CB NAAT.\n\nThe radiological investigations done revealed the following findings:\n\nA radiogram of the hip joint in anteroposterior view (Figure 1) revealed complete destruction of joint space, multiple geodes deforming the head of the acetabulum and femur, significant femoral head osteolysis, and ascension of >0.5 cm above the level of the radiological teardrop in the LEFT hip joint. No osteophytes were noted. Minor pelvic tilt to the right can be appreciated.\n\nThere was complete loss of joint space.\n\nMagnetic resonance imaging (MRI) of bilateral hip joint revealed destruction and thinning of the left acetabulum and loss of normal contour of the left femoral head and neck. There was complete loss of joint space with associated synovitis and joint effusion (Figure 2). There were ill-defined irregular, heterogeneously enhancing areas in the left femoral head, neck, lesser and greater trochanter appearing heterogeneously hypointense on T1WI, heterogeneously hyperintense on T2WI/PDFatSat with few non-enhancing areas (sclerosis) within. There was a low signal intensity in the subchondral area of the femoral head with few subchondral bone cysts (Figure 3). Marrow edema seen from the neck to the upper third of the shaft of the left femur. Bilateral sacroiliac joints and the right hip joint were normal. The above features were suggestive of rapidly destructive osteoarthritis of the left hip joint.\n\nThere was a low signal intensity in the subchondral area of the femoral head. There was a complete loss of joint space.\n\nJoint Capsule and Synovium appear thickened and enhancing, suggesting synovitis. There was associated joint effusion and marrow edema present from the neck till upper 1/3rd of shaft left femur. The left gluteus minimus muscle showed strain at its femoral insertion. Right Hip joint and Bilateral Sacroiliac joints appear normal.\n\nJuly 2021: The patient fell from the bike and went to a local hospital, where he was managed conservatively and was only prescribed analgesic medications and bedrest.\n\nUp to October 2022: Pain was not relieved; however, the patient was mobile and could walk without support. He had complaints of difficulty getting up from sitting position.\n\nOctober 2022: The patient had a slip and fall at home. The patient had aggravated pain and needed support to walk.\n\nNovember 2022: Complete physical evaluation and radiological investigations, i.e., X-ray and MRI, were done.\n\nPathological and microbiological investigations were done.\n\nNovember 2022: the patient was discharged.\n\nInitially, the patient was planned for a total hip replacement on the left side. However, the patient was not willing to undergo this treatment. Then he was advised skeletal pin traction would be an alternative solution for which the patient was also not willing. So the primary management was by physiotherapy and skin traction.\n\nAlthough the patient’s acid—fast bacteria staining of sputum and Mantoux test was negative, he has been started on Anti tubercular treatment empirically. The patient was advised to continue skin traction at home and continue ATT treatment as advised. The patient was vitally stable on discharge and was also given the following empirical medications:\n\n- Paracetamol 650 mg thrice daily\n\n- Vitamin C 500 mg twice daily\n\n- Calcium 500 mg once daily\n\n- Pantoprazole 40 mg once daily before breakfast\n\n- Vitamin D3 (CHOLECALCIFEROL) Sachet -60000I.U (International Units) once a week\n\nAs translated from the patient’s mother tongue: I was healthy and fit two years ago when I slipped and fell from my bike. After the accident, I went to a local clinic where the doctor gave me some tablets and advised me to take bed rest. I rested for 2-3 days and again started working as the pain was relatively less but not completely gone. The pain was dull but didn’t affect my work capacity. The pain was only noticeable while squatting or sitting. As I was able to work, I ignored the pain. But I slipped a few days back, and now the pain was unbearable. I couldn’t bear any weight on my left leg, which appeared shorter than my right leg. I came to the hospital, and the doctor examined the leg and told me to get an X-ray and blood investigations done. After looking at the X-ray, the doctor told me to do an MRI. The doctor explained the nature of the disease, advised me to do a total hip replacement, and informed me about various post-operative exercises. However, due to financial constraints, I have denied any surgeries and would like to be treated only medically. After a few days of skin traction, I was discharged from the hospital.\n\n\nDiscussion\n\nIn 1970, a standardised definition of rapidly progressive osteoarthritis was proposed by Lequesne: chondrolysis >2 mm in one year, or 50% joint-space narrowing in one year with no signs of other forms of rapidly destructive arthropathy as mentioned earlier.2,3 However, in 2018 Ancut a Zazgyva et al.10 proposed easily usable clinico-radiological diagnostic criteria and a grading system for practitioners to identify RPOH. These are based on history, clinical aspects, and a single time point radiographic assessment of the hip, without the need for a lengthy observation of the patient, thus hopefully expediting treatment. The cardinal clinical features proposed were: 1) Hip pain starting approximately three years prior, varying in intensity, worsened in the last six to nine months; 2) functional joint mobility, low to moderate limitation in functional joint mobility; 3) Minimal osteophytes; 4) geodes presenting in the femoral head and/or acetabulum.\n\nThis case satisfied the above-mentioned criteria as the patient presented with hip pain from two years prior, variable in intensity aggravated only by exercise and after the recent trauma. Moreover, the radiogram did not show evidence of any osteophytes. Donald J. Flemming8 classified RPOH into two categories – with and without trauma. This case has a history of more than one trauma, hence lies in the latter. The grading proposed by Ancut a Zazgyva is as follows – partial joint space narrowing with no femoral head deformation is grade I.10 Complete disappearance of joint space with deformed femoral head with the ascension of femoral head <0.5 cm above the radiologic teardrop is grade II.10 Complete disappearance of joint space with partial osteolysis of the femoral head and ascension of >0.5 cm above the radiologic teardrop is classified as Grade III.10 According to this grading, the left hip joint can be said to be in the final grade, i.e., grade III of RPOH\n\nIn a review by Donald J. Flemming,8 femoral head flattening, acetabular remodelling, which parallel femoral head destruction and narrowing of the superior lateral compartment of joint space with sub-chondral sclerosis at the site of bone-to-bone contact were considered as late features.\n\nIn the study by Zazgyva A et al.10 Of the 67 patients with RPOH (15 bilateral cases, with a total of 82 hips) Mean age was 66 years females were 67%; males were 32%, and bilateral RPOH was present in only 18% of the cases. With respect to OA, Most authors reported a rather reduced prevalence of RPOH, but it was 9.5% in a cohort of 863 cases of THR performed by the senior author during a period of 10 years.13 As compared to the above study, this case was a 66-year-old male patient with unilateral hip joint involvement.\n\nMany studies suggest that prior subchondral fracture may be involved in the pathogenesis of rapidly progressive arthritis of not only the hip but also that of shoulder.9 However, it has also been noted that in many cases of subchondral fractures, rapidly progressive osteoarthritis does not develop, raising the question of whether subchondral is a sequela of rapidly progressive osteoarthritis or its cause.8\n\nJoint replacement remains the primary treatment for RPOA. Blood loss during total hip arthroplasty is higher than in routine osteoarthritis.4 Survivorship of hip joint reconstruction at five years is greater than 95% in the setting of RPOA.14 Ideally, hip replacement surgery should be performed before the development of acetabular defects, which have occurred in this case.15 A higher degree of vigilance should be maintained in patients suspected of RPOA to reduce operative time and for easier joint reconstruction. Our case was from an economically underprivileged background and was not able to afford and was also not willing for any surgical interventions and preferred conservative management.\n\n\nConclusion\n\nThe presented case is a classic case of rapidly progressive osteoarthritis of the hip according to newer definitions laid down by Ancut a Zazgyva. With a history of two traumas, a negative history of tuberculosis, and a negative CBNAAT test that rules out tuberculosis as a cause, a preceding subchondral fracture can be considered as one of the major etiological factors. Although other destructive arthropathies are more common, it is essential to consider RPOA as an early differential diagnosis. Appropriate grading and staging of RPOH can help prevent excessive loss of bone tissue and better overall prognosis, i.e., better surgical planning and fewer post-operative complications. As this case progressed to the final grade III (Ancut a Zazgyva), the only effective treatment was total hip replacement. However, the patient was non-affording and preferred the conservative non-invasive approach instead.\n\n\nInformed consent\n\nWritten informed consent for publication of this case report, MRI images and their perspective was obtained from the patient before the patient’s discharge.\n\n\nAuthors’ contributions\n\nPatient management: VN and PD. Data collection: PD and RPD. Manuscript drafting: VN and PD. Manuscript revision: PD, RPD, VN, DN, and PP. All authors approved the final version of the manuscript.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nPostel M, Kerboull M: Total prosthetic replacement in rapidly destructive arthrosis of the hip joint. Clin. Orthop. Relat. Res. 1970; 72: 138–144. PubMed Abstract\n\nLequesne M: Rapid destructive coxarthritis. Rhumatologie. 1970; 22: 51–63. PubMed Abstract\n\nKellgren JH: Osteoarthrosis in patients and populations. Br. Med. J. 1961; 2: 1–6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPivec R, Johnson AJ, Harwin SF, et al.: Differentiation, diagnosis, and treatment of osteoarthritis, osteonecrosis, and rapidly progressive osteoarthritis. Orthopedics. 2013; 36: 118–125. PubMed Abstract \| Publisher Full Text\n\nSt-Amant M, Yap J, Feger J, et al.: Rapidly destructive osteoarthritis of the hip. Reference article. (Accessed on 12 Feb 2023). Publisher Full Text Reference Source\n\nTorre Della P, Picuti G, Di Filippo P: Rapidly progressive osteoarthritis of the hip. Ital. J. Orthop. Traumatol. 1987; 13: 187–200.\n\nCoste F, Laurent F, Benichou C: Coxarthrosis with lysis of the femur head (wearing coxarthrosis). Rev. Rhum. Mal. Osteoartic. 1959; 26: 305–308. PubMed Abstract\n\nFlemming DJ, Gustas-French CN: Rapidly progressive osteoarthritis: A review of the clinical and Radiologic Presentation. Curr. Rheumatol. Rep. 2017; 19(7): 42. PubMed Abstract \| Publisher Full Text\n\nClinico-radiological diagnosis and grading of rapidly progressive osteoarthritis of the hip.\n\nZazgyva A, Gurzu S, Gergely I, et al.: Clinico-radiological diagnosis and grading of rapidly progressive osteoarthritis of the hip. Medicine. 2017; 96(12): e6395. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPaprosky WG, Perona PG, Lawrence JM: Acetabular defect classification and surgical reconstruction in revision arthroplasty. A 6-year follow-up evaluation. J. Arthroplast. 1994; 9(1): 33–44. Publisher Full Text\n\nVilloutreix C, Pham T, Tubach F, et al.: Intraarticular glucocorticoid injections in rapidly destructive hip osteoarthritis. Joint Bone Spine. 2006; 73(1): 66–71. PubMed Abstract \| Publisher Full Text\n\nPivec R, Johnson AJ, Harwin SF, et al.: Differentiation, diagnosis, and treatment of osteoarthritis, osteonecrosis, and rapidly progressive osteoarthritis. Orthopedics. 2013; 36: 118–125. PubMed Abstract \| Publisher Full Text\n\nPeters KS, Doets HC: Midterm results of cementless total hip replacement in rapidly destructive arthropathy and a review of the literature. Hip Int. 2009; 19: 352–358. PubMed Abstract \| Publisher Full Text\n\nIrwin LR, Roberts JA: Rapidly progressive osteoarthrosis of the hip. J. Arthroplast. 1998; 13: 642–646. Publisher Full Text" }	[ { "id": "355553", "date": "13 Jan 2025", "name": "Apostolos H Karantanas", "expertise": [ "Reviewer Expertise Radiology", "Musculoskeletal Disorders", "Hip", "Sports injuries/imaging", "Image guided treatment" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 The publication under review, is referring to a case report on RPOH, studied with a 3T MR scanner. A PubMed search on “RPOH and imaging” showed 81 publications and on “RPOH and MRI” 19 publications. Thus, RPOH was once considered to be a rare entity but currently is more frequently encountered in clinical practice because the average age of the population has increased. The used grading system has a doubtful clinical impact, as the RPOH at the initial stages is similar to OA.\n\nSpecific comments Abstract “..few mentions”: Not true, there are many publications on the topic. 6th line: please use the abbreviation which has already been defined. Introduction Good presentation of the background knowledge. Case study presentation Please replace “radiogram” with “radiograph”. Only one radiograph is provided. Thus, a diagnosis based on the definition of RPOH (joint space loss at a rate greater than 2 mm per year or if more than 50% of joint space is lost in 1 year), cannot be established. In addition, presence of crystals, at the time of the injury, cannot be excluded without previous radiographs. A safe link therefore of the joint destruction to the previous fall, cannot be done. The authors need to explain the low signal intensity intra-articular area in the left hip on non-fat suppressed T2-w MR images. Page 5, “T2WI/PDFatSat with few non-enhancing areas (sclerosis) within”. Do you mean low signal intensity foci? Enhancement should be mentioned on contrast-enhanced T1-w sequences. Legend to fig. 3 needs rephrasing because it is confusing.\nConclusion This case report provides useful information. However, due to lack of validation and of follow up imaging studies, its educational value is limited.\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? No", "responses": [] }, { "id": "355552", "date": "20 Jan 2025", "name": "Tanya Sapundzhieva", "expertise": [ "Reviewer Expertise Rheumatology", "Imaging", "Arthritis", "Biomarkers" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMajor comment: The most essential criterion for establishing a diagnosis of RPHOA is the change in the cartilage size for one year, because the definition is ‘loss of cartilage >2 mm in 1 year or 50% joint-space narrowing within one year.’ In the described case report, the authors have presented imaging – both x-ray and MRI of the hip joint only at one time point – during the patient visit at their clinic. BUT there are no prior imaging data (x-ray or MRI) to actually prove the FAST PROGRESSION of the cartilage loss, which is the most important criterion for establishing the diagnosis of RPHOA. In my opinion, the lack of fulfillment of this major criterion (loss of at least 2 mm of cartilage for a period of 1 year) makes the diagnosis not reliable. In addition, osteonecrosis of the femoral head was not excluded, considering the inciting event prior to the onset of symptoms was leg trauma. A great number of published studies, that include case-series of patients with RPHOA, already exists in the literature.\nAdditional comments: A number of inaccuracies regarding the use of medical terminology exists, for example in the Abstract Section: ‘Rapidly progressive osteoarthritis of the hip (RPOH) is a rare disease…’ – RPOH is not a separate disease, but rather an aggressive clinical phenotype of the disease Hip OA. Keywords are not properly selected. There is dis-concordance between the definition of the disease (Rapidly progressive osteoarthritis of the hip - RPOH) and the history of present illness, as described in the case description. The onset of the clinical symptoms, namely hip joint pain and restriction in the range of motion was 2 years ago. If it indeed was RPOH, the symptoms will be of a recent onset. The information regarding concomitant medication is absent. Considering the age of the patient, it is highly unlikely that he was not on any medication for concomitant illnesses. In addition, considering that RPOH is characterized by fast progression, severe pain, and the fact that the onset of pain was two years ago, it is strange that the patient is not on daily use of analgesics/NSAIDs, for example. The authors should add the names of the drugs and dosages, the patients had been taking during his first visit. Abbreviations should be explained at the bottom of the table. NIL abbreviation is not explained at all. Some unnecessary repetitions should be omitted, for example the authors have written the apparent and true leg length (‘The apparent length of left limb was 122.5 cm, and the right limb was 124 cm. The true length of left limb was 96cm, and right limb was 97cm’), and shortly after that again have written ‘There was 1.5cm of apparent limb shortening present on the left side and 1 cm of true shortening.’ Considering the clinical presentation of the patient (mechanical type of joint pain, no morning stiffness), the first diagnosis that should be considered is osteoarthritis of the hip joint, due to the fact that it is the most common disease of the hip joint. Instead, the authors have stated: ‘The clinical diagnosis considered was infective or tuberculous monoarthropathy.’ - Why? These diagnoses are rare, as compared to the high prevalence of hip OA in this patient population – 65-year-old, man, without any concomitant diseases. The following sentence is not correct from a clinician perspective – ‘’These involve evaluating the patient blood for signs of inflammation and infections, which includes increased number of red and white blood cells.’’ – Red blood cells are not increased in infections, only white blood cells. ‘Acid-fast staining of sputum sample and cartilage-based nucleic acid amplification test (CB NAAT) were also done to assess tuberculosis infection.’ – Why a simple x-ray of the chest was not obtained, considering the fact that TBC should be excluded? Having read the description of the conventional radiography of the hip joints and the MRI, and having seen the presented images, why osteonecrosis of the hip was not considered? In addition, the prior trauma is also a provoking factor for osteonecrosis. The authors should add the date of the MRI and x-ray images. ‘Although the patient’s acid—fast bacteria staining of sputum and Mantoux test was negative, he has been started on Anti tubercular treatment empirically.’ – how can you start tuberculosis treatment without even performing an x-ray or CT of the chest? Discussion section – the first sentence (‘In 1970, a standardized definition of rapidly progressive osteoarthritis was proposed by Lequesne: chondrolysis >2mm in one year, or 50% joint-space narrowing in one year with no signs of other forms of rapidly destructive..’) is a repetition from the Introduction Section. The conclusion is too long and contains unnecessary details that are already stated in the main body (for example - ‘However, the patient was non-affording and preferred the conservative non-invasive approach instead.’)\n\nIs the background of the case’s history and progression described in sufficient detail? No\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? No", "responses": [] } ]	1	https://f1000research.com/articles/12-853
https://f1000research.com/articles/12-852/v1	19 Jul 23	{ "type": "Research Article", "title": "Gender stereotyping in Bangladesh; the development of the Strength of Gender Stereotyping Scale (SGSS)", "authors": [ "Md. Omar Faruk", "Graham Powell", "Mahady Asif", "Md. Omar Faruk", "Mahady Asif" ], "abstract": "The investigation of gender stereotypes in Bangladesh is hampered by a lack of measures, making it difficult to gauge where social change is needed and to assess the efficacy of interventions. The objective of the study is to develop a psychometrically sound Bengali language scale measuring strength of belief in culturally pervasive gender stereotypes. 430 participants aged 18-80 years from all eight divisions of the country were recruited by purposive sampling. Standard scale development procedures were followed. From an initial pool of 60 items, 11 were chosen by judge evaluation, item analysis and exploratory factor analysis for the final scale, each item rated on a four-point Likert scale from 1, not agreeing at all with the stereotype, to 4, completely agreeing with the stereotype. Internal consistency and test-retest reliability are satisfactory. It has a two-factor structure related to the expression of emotion and the maintenance of authority respectively, together accounting for 35.04% of the variance. A psychometrically sound instrument has been developed to assess the strength of belief in gender stereotypes in Bangladesh that can be used to explore the strength and distribution of gender stereotypes and to measure changes in their strength over time or in response to interventions.", "keywords": [ "Gender", "stereotypes", "Bangladesh" ], "content": "Introduction\n\nIn Western society the study of gender stereotypes is a very familiar topic emerging from broader stereotyping research during the rise of feminism (Mills et al., 2012). At the heart of gender stereotyping is a set of beliefs about what characteristics can be attributed to males and females (Martin & Dinella, 2001), and such orthodox, culturally prevalent beliefs develop early in the child’s life (Powell & Stewart, 1978). In tandem with the growth of descriptive research regarding gender stereotyping there has been an equal interest in how such gender stereotypes can be changed. For example, Social Role Theory (Eagly, 1987) suggests that the pigeonholing of the respective genders into certain social roles leads to stereotypical beliefs about gender, constituting a powerful perpetuating factor in gender stereotyping (Koenig & Eagly, 2014). However, it follows that the reverse of the process can hold true, that by changing social roles it is possible to change stereotypical beliefs about men and women (Eagly, Wood & Johannesen-Schmidt, 2004). Martin and Dinella (2001) state that ‘gender stereotypes are culturally defined expectations about the sexes’ but the tandem growth just described is a reminder that there are in fact two aspects of stereotyping to consider. First, there are the specifics about the content of stereotypes, what characteristics are attributed to what sexes, and second, there are general processes in stereotyping, such as the relationship between social role occupancy and the development and perpetuation of beliefs about male and female characteristics (Stewart, Powell & Tutton, 1979). Therefore, when it comes to cross-cultural considerations, the extent to which Western findings might pertain to a non-Western society, in this case an Asian society, there are some aspects of Western research that may be quite culture specific, such as the specific content of stereotypes, whereas other aspects of research may be highly generalisable, such as how stereotypes arise and how they change and might be modified. This paper concerns the development of a scale that measures the strength of belief in specific gender stereotypes, stereotypes that have arisen specifically in Bangladesh. From a broader perspective, once developed the scale will be available to help gauge the success or otherwise of initiatives aimed at encouraging positive change in stereotypes, initiatives that encourage social understanding and equality.\n\nWhy would or should there be initiatives aimed at encouraging positive change in stereotypes? Because stereotypes are potent determinants of behaviour and how we see not just others but how we see ourselves. Encouraging change in stereotypes in turn encourages better social understanding, tolerance, positive self-development, pro-social behaviour and, ultimately, equality. There are numerous examples of research from the West that identifies the detrimental effects of culturally determined gender stereotypes. Of particular potential importance to Bangladesh is the research on occupational and social role. Fogliati and Bussey (2013) in the USA found that exposure to negative stereotypes resulted in women’s worse performance in a mathematics assessment and decreased motivation to do anything about it. Ertl, Luttenberger and Paechter (2017) noted that in most European countries, the proportion of females pursuing a career in STEM (Science, Technology, Engineering, Mathematics) was still alarmingly low. In a study of German university students reading STEM subjects, Froehlich et al. (2022) found that ‘even though the (female) students participating in the study presumably had good grades in STEM (because they were reading a STEM subject), stereotypes still corrupted their self-concept’. Both studies relate to a process that has become known as ‘stereotype threat’ (Shapiro & Williams, 2012). These two studies are examples of how stereotypes can become internalised and shape performance, behaviour, and self concept with respect to education. The effects of stereotypes persist into the workplace. For example, Hoyt (2010) explores the gender gap in senior roles and ‘how stereotypes, prejudice, and discrimination contribute to women’s under-representation in elite leadership roles by both impacting perceptions of and responses to women as well as impacting the experiences of women themselves’.\n\nAlso of particular relevance to Bangladesh (and indeed to any country) is research on the impact of gender stereotypes on interpersonal relationships. In developing the Gender Role Attitudes Scale in young Spanish people, García-Cueto et al. (2015) note how treating the sexes unequally raises the probability of aggressive behaviour in adolescent dating relationships, how certain attitudes (stereotypes) about relationships in couples ‘are the precursor to acceptance of violent behavior’. There is a range of studies concluding that stereotypes shape the nature and perception of domestic violence (Hassouneh & Glass, 2008; Seelau & Seelau, 2005; Gerber, 1991).\n\nThe current content of Western gender stereotypes is to be found in a large-scale study of 628 U.S. participants who rated men and women on a set of 74 attributes taken from previous studies (Hentschel et al., 2019). Confirmatory factor analysis found that 15 items formed an ‘Agency’ scale, and 11 items formed a ‘Communality’ scale, both with a high Cronbach’s Alpha of 0.93. The authors note that in the past agency has been termed ‘masculinity’ and that communality has been termed ‘femininity’. Agency items were competent, effective, productive, task-oriented, leadership ability, achievement-oriented, skilled in business matters, dominant, bold, assertive, competitive, independent, desires responsibility, emotionally stable, and self-reliant. Communality items were understanding, kind, compassionate, sympathetic, communicative, collaborative, relationship-orientated, likeable, emotional, intuitive, and sentimental. The Agency scale itself comprised four dimensions (instrumental competence, leadership competence, assertiveness, and independence), and the Communality scale comprised three dimensions (concern for others, sociability, and emotional sensitivity). (We note that no overall Cronbach’s alpha is given for the overall 26 items, but that of the 12 correlations between the Agency and Communality dimensions, 11 were significant, 10 at the.001 level, indicating that all seven dimensions are polarised in the same direction, suggesting that all dimensions are seen in a positive light and as desirable qualities). The study found that stereotypes about communality persisted and were equally prevalent for male and female raters. Agency characterizations, on the other hand, were more complex in that male raters described women as being less agentic than men, but female raters differentiated among the agency dimensions, describing women as less assertive than men but as equally independent and leadership competent. The authors note how historically the persistence of traditional gender stereotypes had been fueled by skewed gender distribution into social roles, but that this pattern was now changing, with, for example, women now holding almost 40% of management positions in the United States (Bureau of Labor Statistics, 2017). This social change is in line with there now being weaker gender stereotyping of Agency. However, gender stereotyping of Communality remains very strong, the authors reporting that ‘All participants rated women higher than men on the three communality dimensions’. The authors conclude that ‘despite dramatic societal changes many aspects of traditional gender stereotypes endure’, and describe how this translates into self-characterizations, especially in women, who tended to characterize themselves in more stereotypic terms than did the men.\n\nTurning specifically to Bangladesh, the research literature on gender stereotyping is sparse but interesting. Studies tend to be exploratory, and the findings indicative rather than definitive.\n\nHistorically Bangladesh has had an agricultural economy. As recently as 2006 most women, 80%, still lived in rural areas of Bangladesh (BBS, 2006). Parveen and Leonhäuser (2008) note how although they were the backbone of the rural economy they were ‘handicapped by entrenched gender hierarchies, religious discrimination, and a disproportionate allocation of resources’. Parveen and Leonhäuser set out ‘to identify the ongoing gender stereotypes existing in the rural community’. The participants were 159 farmers’ wives from three villages in Mymensingh District, and data was collected using surveys, interviews, and discussion groups. They found that women were discriminated against in a range of ways, not just in the division of labour but also ‘in access to education, food, property, freedom of mobility, and economic opportunity’. Stereotypes included, for example, ‘Wives must be obedient to husbands because a woman’s paradise is at the feet of her husband’, and ‘Domestic work is women’s obligatory work and responsibility’. The authors note how such attitudes and norms can foster violence, especially domestic violence, against women, and discuss what can be done to promote women’s economic empowerment, including vocational education in livelihood skills, the provision of resources such as micro-credit and the promotion of platforms to challenge traditional beliefs that perpetuate women’s subordination.\n\nSince 2006 there has been an enormous, exponential growth in Bangladesh of manufacturing, particularly in the garment industry. According to Islam et al. (2018), as at 2016 there were more than 4,000 ready-made garment (RMG) organisations and more than 4.2 million workers, 85% of whom are female. Islam and colleagues questioned whether this has led to female progression in leadership positions; apparently not as only 5.4% of middle and senior management positions were occupied by females, and they sought explanations for this. They looked at one RMG organisation and in detail considered the accounts of barriers to career progression faced by 8 female employees who held Masters or Bachelor degrees and who had been with the organisation for 6-14 years. Barriers included the sheer lack of female managers, an organisation that did not allow for a work-home lifestyle, a hiring policy dominated by men, and leadership styles that were patriarchal as per custom. Of concern is that this sample actually expressed typical gender stereotypes themselves, that they seemed to have internalised to some extent the barriers to progression. Quotes include ‘Both power and ambition I believe are much more attractive and suitable to men’, ‘Men are more tolerance (sic) to take pressure from multiple stakeholders; therefore, they tend to take the leadership roles’ and ‘Both male and female feel most comfortable when it is male leadership due to the gender stereotypes in out [r] mind-sets’.\n\nThe issue arises as to whether the educational process in Bangladesh is challenging or perpetuating gender stereotypes, whether it does or does not encourage a change of mind-set in the upcoming generation. Islam and Asadullah (2018) undertook a comparative content analysis of Malaysian, Indonesian, Pakistani and Bangladeshi government approved secondary school textbooks to look for any gender stereotyping in them. It is noted that ‘In Bangladesh, while textbook contents have often been manipulated by successive governments for political purposes…. gender bias in the curriculum and learning materials remains an overlooked topic’. The overall finding, first of all, was that females were simply underrepresented; 62.7% of characters in Bangladeshi textbooks were male. Further, when females were depicted, female occupations were mostly traditional, low wage and less prestigious and the female characters were predominantly introverted and passive in terms of personality traits. Women were also shown to be mostly involved in domestic and in-door activities while men had a higher presence in professional roles. Females were presented in domestic roles four times more than their male counterparts. However, it was noted that when Bangladeshi textbooks depicted females in non-domestic roles, they depicted a wider range of professional roles and the professional roles depicted were more prestigious and demanding than in any of the other countries’ textbooks (such as a lawyer, social scientist or TV anchor). However, in short, ‘our analysis confirms that textbooks disseminate a hidden curriculum’.\n\nThe issue of gender bias in textbooks in Bangladesh is taken up by Asadullah, Islam and Wahhaj (2018). Despite opposition from conservative religious authorities, coeducational schools have mushroomed throughout the country and the government also implemented programs to encourage girls’ education at all levels, such that gender differences in enrollment at primary level disappeared nearly two decades ago and today an equal number of girls attend secondary schools. But the country’s remarkable achievement on women’s education has recently been undermined by some authorities ‘silently rewriting school textbooks in a way that can do harm to the country’s journey toward gender equality’. ‘These changes not only reflect certain religious biases, they also encourage stereotypes regarding what women should do in Bangladeshi society’. However, textbooks from 1990 were examined and all Bangladeshi school textbooks suffered from a pro-male bias regardless of whether they were based on a secular or religious curriculum. Gender bias was considered to be widespread in government recognized textbooks long before radical groups demanded reforms of the secular school curriculum. It was a general problem to address, and indeed a global problem to address, for example in the USA (Mccabe et al., 2011). Going forward it would be important to tackle structural deficits in the educational system to restore gender balance in textbook content.\n\nGender stereotyping regarding the lesser role of women is carried forward from school into the workplace. Islam and Akter (2018) considered gender stereotypes in Bangladeshi business firms, taking the Women as Managers Scale (WAMS) that was developed in the USA some years ago (Peters et al., 1974), translating it into Bangla, adapting some of the items (in unspecified ways), and administering it to 260 male and female employees from different firms. It is a 21-item scale, each item rated 1-7, with higher scores reflecting a favourable attitude towards women in managerial roles. It was found that ‘the practice of gender stereotypes in the Bangladeshi working environment still works as a vital factor’ and ‘female employees’ managerial roles are still plagued with stereotypical issues’. There were issues with overall acceptance of women as managers, issues of organisational barriers, and issues arising from supposed personality traits. However, relevant to this paper, the authors also expressed the view that measures developed in the West are not ideal for use in Bangladesh, stating that ‘the sociocultural contexts in Western countries for which WAMS is originally developed [was] found to be a misfit for a more traditional country like Bangladesh’ and ‘there is a considerable probability that some of negative attitudes and stereotypes present in the Bangladeshi culture might not be covered in WAMS’.\n\nIt is not just textbooks that show gender bias, but the media, too, though this is to some extent now being changed. Shafi (2021) illustrates this period of change by examining three advertisements that were currently on television. The adverts for Pears soap depicted a ‘fantasy world created around the little girl in which she will follow her mother to be another “beauty-icon” herself’. The authors point out that soap adverts in general hardly ever show women of dark complexion (one of the stereotypes evident in the Parveen and Leonhäuser study, above, is ‘A glowing bride must have a good physical appearance (especially a fair complexion)’). In contrast, the second type of advert was from BRAC (an NGO, Building Resources Across Communities) specifically designed to promote women’s empowerment. It highlights the fact that women own less than 4% of land in Bangladesh (a further stereotype evident in the Parveen and Leonhäuser study, above, was ‘Girls are not allowed to transfer land from biological families after marriage’ so they cannot inherit their parent’s land after marriage). The mother in this case had no right to inherit the land owned by her husband when he died, was left with no resources. She gallantly looks after her child on her own, earning their livelihood. The message is that ‘we can make women empowerment possible by restoring their rights on lands and all other assets’. The third advert depicts a change in roles available to women. It is from the Bangladesh Army, which shows ‘both men and women who are young, energetic and brave’. The advert shows how ‘21st-century women are no longer vulnerable to the “stereotypical” gender norms’.\n\nThere are, then pressures towards change, but change is slow. Upoma (2021) analyzed gender stereotypes in the media, interested in how Bangladeshi teenagers, 50 male and 50 female adolescents aged 14 to 20 years, felt about women being portrayed. The media in Bangladesh, including movies, dramas, and commercials, perpetuated sexist stereotypes on multiple levels, reinforcing ‘old patriarchal gender notions’. The teenagers were conscious of how women were being portrayed, 85.7% saying the roles depicted were stereotypic, but only 54% thought that females were actually being stereotyped in real life and only 35% contemplated rejecting a product on the basis of what was being portrayed. Further, disappointingly, ‘one of the findings showed female students were more likely to support traditional stereotypes about women’, in the sense that the females were less likely to perceive the passivity in the roles being portrayed.\n\nTurning to the present study, it is clear from the above review that here is a need for measures of gender stereotyping but that they have to be more than a translation of outdated Western scales. The objective of this study is to develop a psychometrically sound Bengali language scale that measures the strength of belief in culturally pervasive gender stereotypes, with a view to gauging where social change is needed and to assessing the effects of interventions intended to break down stereotypic prejudice.\n\n\nMethods\n\nIn general terms the study involved the development of a draft scale followed by its administration to participants in order to derive a final scale via item analysis.\n\nDevelopment of the draft scale involved devising items then judge evaluation of them.\n\nDevising items. Initial potential items were derived from the authors’ analysis of gender stereotypes to be found in Bangladeshi culture in April 2020, including consideration of the media as described in the introduction to this paper. However, items from several other scales (see Miller, 2018; Underwood et al., 2014; Zeyneloğlu & Terzioğlu, 2011; Pulerwitz & Barker, 2007) were also selected having been scrutinized by the authors to assess their suitability for Bangladesh. The initial draft of the scale contained 60 items. Language accuracy (bearing in mind that a significant percentage of the Bengali population are poorly educated and of limited literacy or frankly illiterate, such that items might have to be read out to them) was assessed by two language experts. The revised items were reviewed by a group of five mental health professionals (three psychologists and two psychiatrists) and an anthropologist and a sociologist to assess the concepts and use of words taking the Bangladeshi culture into account. Ten items were removed from the initial pool due to the lack of relevance for the central concept (strength of gender stereotype). Fifty items were retained to be evaluated by the judges. It should be noted that because of the educational status of the Bengali population, the items might seem lacking in sophistication to Western eyes (lowest paid and poorly educated workers in Bangladesh might struggle with some of the attributes used in Western studies such as ‘analytic’ and ‘humanitarian values’) and that because the items arise specifically from the Bengali culture, they might seem alien to Western eyes. The authors therefore make no apology for lack of sophistication or idiosyncrasy in the scale items.\n\nJudge evaluation. The items on the 50-item draft scale were rated by six clinical psychologists, a psychiatrist, a sociologist, and a specialist on gender-based violence, for their representation of cultural stereotypes. A four-point Likert-type was used, where 4=completely relevant, 3=moderately relevant, 2=slightly relevant, and 1=not at all relevant. The reason for choosing the four-point Likert-type scale was to avoid the central tendency bias in the judgment, and reverse polarity was used to avoid thoughtless responding. A minimum acceptable average score of ≥3 was set as the selection criteria for items. Twenty-eight items passed the selected criteria (mean ratings ranged from 3.00 to 4.00, with a mean of 3.50).\n\nEthical considerations. The study was conducted in accordance with the Helsinki declaration. The study was also approved by the ethics committee of the University of Dhaka (Project ID: IR210601).\n\nParticipants in the administration of the draft scale. Participants were purposively recruited from eight divisions in Bangladesh. A total of 450 participants aged between 18 and 80 were recruited for the study. Recruitment was completed by June 2021. There was missing data for some participants, leaving a total of 430 for the final analyses.\n\nThe demographic information of the final 430 participants is presented in Table 1.\n\nAs anticipated in the design of the study and reflecting the characteristics of the general population in Bangladesh, 39.8% had only primary education or were illiterate. The sample in strict terms is not necessarily proportionate to overall country demographics, but it covers the educational range, came from all eight of the country’s Districts, and was reasonably balanced in terms of sex (44.4% male), participants in the study having been asked to self-identify as male, female or Third Gender. There were no Third Gender participants in this sample. The sample also reflected a range of occupations, reflected both married (67.4%) and unmarried persons, and contained a broad age range (18-80 years, mean age 33.72, s.d. of 13.16). The mean age of the males (35.06 years, s.d. of 16.83) was about five years greater than the mean age of the females (29.88 years, s.d. of 13.31). This difference is statistically significant (t=3.48, p<.001) hence age as a potential factor in determining strength of gender stereotyping was taken into consideration in the analysis section of this paper. The primary religion was Islam (89.5%) but other religions were represented.\n\nProcedure to administer the draft scale. A cross-sectional survey was carried out in the eight divisions of Bangladesh (Dhaka, Chattogram, Rangpur, Mymensingh, Barishal, Khulna, Rajshahi, and Sylhet). Each item on the draft scale was rated on a 4-point Likert scale where 1=Not agree at all, 2=Slightly agree, 3=Moderately agree, 4=Completely agree. The data were collected by research assistants recruited from each of the eight divisions. The assistants were trained prior to the data collection. Administration of the scale and interviewing were included in the training. Participants were provided with both verbal and written instructions. Informed consent forms were also obtained from the participants. A thumb mark was used to indicate consent for participants with no literacy. Data were collected once the countrywide lockdown and movement restrictions that had been imposed to curb the spread of the coronavirus were lifted. Nonetheless, necessary safety measures were followed during data collection. Participation in the study was completely voluntary; the participants received no monetary reimbursement.\n\n\nResults\n\nThe demographic data (as above) were analyzed using descriptive analyses.\n\nInternal consistency was assessed by Cronbach’s alpha.\n\nTest-retest reliability and criterion reliability were assessed by Pearson correlation.\n\nPrincipal Axis Factoring (PCA) with Promax rotation method was used to perform exploratory factor analyses (EFA). A number of indices were considered for model fit in the confirmatory factor analysis (CFA). Chi-square (χ2), ratio of Chi-square to df (χ2/df), root mean square error of approximation (RMSEA), and comparative fit index (CFI) were used to assess the adequacy of model fit while the criteria for model fit were, χ2 with p≥0.01, χ2/df≤2, RMSEA≤0.06, CFI≥0.95, SRMR≤0.08 (see Faruk et al., 2021).\n\nSPSS 24 and AMOS 22 (Arbuckle, 2011) were used to analyze the data.\n\nFace validity. As described above, all items used in the analysis had scored highly during the judge evaluation stage (mean item score of 3.50 out of a maximum of 4.00 for their representation of cultural stereotypes) indicating good face validity of the scale itself (Hardesty & Bearden, 2004).\n\nExploratory factor analysis. Exploratory factor analysis (EFA) was conducted with principal axis factoring (PAF). Evidence suggests that PAF is better able to recover weak factors and to identify random variation of loadings than other methods such as maximum likelihood factor analysis (MLFA) (De Winter & Dodou, 2012). Parallel analysis was undertaken as the initial step in identifying the number of factors yielded by the proposed measure. In parallel analysis, retention of the factors depends on whether the eigenvalue from the original data set exceeds the mean eigenvalue of the random data sets. As a method of factor extraction, parallel analysis has been preferred to other strategies such as the eigenvalue greater than one rule or examination of scree plots (Mills et al., 2012). Eigenvalue and parallel analysis yielded a two-factor structure for the scale. However, subsequent procedures were followed as parallel analysis can be susceptible to over-extraction (Mills et al., 2012). EFA was performed on half of the participants (215) that exceeds the suggested minimum sample size of 200 for factor analysis (Gorsuch, 1983). Conducting parallel analysis and EFA on half of the participants (randomly separated) and confirmatory factor analysis (CFA) on the other half in order to cross-validation of the likely factor structure has been employed in a number of studies (see Mills et al., 2012; Costello & Osborne, 2005; Van Prooijen & Van Der Kloot, 2001; Fabrigar et al., 1999). Multicollinearity and adequacy of the data for factor analysis were examined with the Kaiser-Meyer-Olkin measure as well as Bartlett’s Test of Sphericity (Chen et al., 2019). Small coefficients below .4 were suppressed to facilitate interpretation of the results. Items with cross-loading greater than .4 on more than one factor were dropped (Ibrahim et al., 2015).\n\nReliability analysis of the 28-item scale was undertaken using Cronbach’s alpha, which resulted in three items being dropped to increase internal consistency reliability. The remaining 25-item scale demonstrated adequate internal consistency reliability with a Cronbach’s alpha.93. The initial EFA on the 25-item gender stereotypes scale yielded one item with an initial communality value lower than .30. The second round of EFA analysis also yielded one item with an initial communality value lower than .30. The third round of analysis with the remaining 23 items yielded seven items with multiple loading values. No item was found to have a communality value less than.3 in this round. After removing the seven items the remaining 16-item scale underwent a fourth round of EFA analysis and three items displayed cross loading so were dropped. A fifth round of EFA analysis on the remaining 13-item scale found that two items had cross loadings and were dropped, resulting in an 11-item scale yielding the required properties on EFA.\n\nThis 11-item scale had a Kaiser-Meyer-Olkin score of.83. As a measure of sampling adequacy this is an acceptable value). Bartlett’s Test of Sphericity was also satisfactory (χ2=517.227, p<.000), not indicating any multicollinearity within the data. These analyses confirmed the suitability of factor analysis (Balakrishnan & Griffiths, 2018; Kaiser, 1974). The EFA yielded a two-factor structure for the 11-item scale explaining 35.04% of the total variance. The factors were termed as expression and authority. Factor loadings for each item are presented in Table 2. Factor loading for the 11-item gender stereotypes scale ranged from.40 to.759 with no factor loaded on multiple items. The correlation between the two factors was 0.55.\n\nAnti-image correlations and communalities for the scale were also investigated. Anti-image correlation values ranged from .766 to .869, well over the recommended value of .50 (Hauben et al., 2017). Communality extraction values range from .390 to .532, well above the recommended value of .20 (Child, 2006). These analyses provided further support for the retention of the 11 items that comprised the scale (Table 2).\n\nItem-analysis. Item analyses on the final scale yielded corrected item-total correlations ranging from .462 to .608, all significant at p<.01. All 11 items yielded corrected item-total correlation above the recommended value of .30 (Cristobal et al., 2007).\n\nA copy of the scale is to be found in Appendix 1, with the English translation at Appendix 2 (the scale is in Bangla and intended for use in Bangla, so this wording in English is approximate). Table 3 gives the item, factor and total scale means (s.d.). Expression has five items hence a score range of 5-20. Authority has six items hence a score range of 6-24.\n\nConfirmatory factor analysis. AMOS 22 (Arbuckle, 2011) was used to perform confirmatory factor analysis to test the goodness of fit of the two-factor structure of the scale. Multiple fit indices were considered for the scale such as χ2, χ2/df, RMSEA (CI), CFI, TLI, and SRMR. All indices were satisfactory when compared to recommended values (Marsh & Hocevar, 1985; Wheaton et al., 1977; Awang, 2012; Hair et al., 2010; Hu & Bentler, 1999; Hair et al., 1998; Tran & Keng, 2018; Widaman, 1985; Xia & Yang, 2018).\n\nThe scale was administered twice to a further group of 40 participants (mean age 25.80; s.d. 3.39, mean test-retest interval of 7 days, 67.5% female). The test-retest reliability coefficient for the overall scale was r=.94. Mean score on the scale at time 1 was 46.45 and at time 2 it was 45.23. This difference was not significant (p>.05).\n\nThe final 11-item final scale yielded a Cronbach’s alpha .87. Cronbach’s alpha for Expression was .76 and for Authority it was .75. As noted above the correlation between the two factors was 0.55.\n\nSex differences. Item and factor scores are given separately for the sexes in Table 4, with significance levels for differences in mean.\n\nAs can be seen, the sexes did not differ significantly in terms of Expression, Authority or the Total score. There were two sex differences on item scores, the males having a stronger belief on item 1, and the females having a stronger belief on item 4.\n\nAge differences. Age did not correlate significantly with Expression, Authority or Total score in either males or females (product moment correlations ranged from -.04 to -.144, all n.s.). Considering individual items, there were just three examples of significant correlations with age, all in a negative direction (males, item 5, r=-.150, p,.05; males, item 6, r=-.166, p<.05; females, item 8, r=-.209, p<.01)\n\nMarital status. Marital status (married vs unmarried) did not give rise to mean differences on Expression, Authority or Total score in either males or females.\n\n\nDiscussion\n\nThe aim of the study to develop a strength of gender stereotyping scale for use in Bangladesh has been achieved. To the best of our knowledge, this is the first psychometric measure on gender stereotypes taking Bangladeshi culture into account. It is an 11-item scale, each item rated on a 4-point scale, hence a scale range of 11-44, with higher scores indicating stronger belief in stereotypes. The scale has acceptable internal consistency (Cronbach’s alpha of .87) and acceptable test-retest reliability (r=.94), and the factor structure meets accepted statistical requirements. It is a short scale, easy to administer, and in this regard, it has been found that in Bangladesh it can be useful to have psychometric tools with fewer items (Faruk et al., 2021).\n\nUsing statistical procedures similar to that employed by Hentschel, Heilman & Peus (2019), the scale has a two-factor structure, factors that we have termed Expression and Authority, but which are to some extent similar to the factors found by Hentschel et al. (2019) namely Communality and Agency. For example, Expression involves boys not crying and the expression of sexual needs while Communality also involves emotional aspects, and Authority involves not showing weakness and men controlling their wife while Agency also involves aspects of dominance. Therefore, there is something of a conceptual similarity between stereotypes in the U.S.A. and Bangladesh even if the way of wording them is different.\n\nTurning to the content of gender stereotypes in Bangladesh, the most strongly held stereotype in the sample as a whole, by some margin, was that ‘Weakness is expressed when males behave like females’. Such a belief potentially denigrates both men and women. It suggests that some men are not strong enough to be a ‘real man’, not strong enough to show manly traits. It denigrates women by suggesting that a core feature of the female is weakness. In essence it devalues females in comparison to males and is liable to perpetuate inequality. It highlights an issue for society and education to address.\n\nThe item ‘Weakness is expressed when males behave like females’ loads on the Authority factor. It is perhaps disappointing to see that for both men and women this is the strongest held belief on that factor. The belief is not just a belief held by men; it is a belief held equally by men and women; there is no significant sex difference in the item mean. There are other related examples on the scale; females believe just as much as males that ‘A man should have control over his wife’, that ‘I don’t think a real man should have any feminine traits’ and that ‘A man’s decision is final in the house’. Indeed, the females believed even more strongly than the men that ‘A man’s decision is final in the house’. The ‘male is strength’ stereotype is not just a product of male thinking, it is part of female thinking, too; education has to address this in both men and women. However, there may be more potential for change in females rather than males, because females less strongly endorse the item ‘Boys need to be stronger even if they are young’, which perhaps represents the female questioning whether males inherently need to be ‘stronger’. But there is something of a mixed message here because although males may not need to be strong they must not show it by appearing feminine.\n\nThe question arises as to whether current educational programmes and exposure to media debates has had an impact on younger people, whether younger people less strongly hold stereotypic beliefs. The answer provided by this study is a firm ‘no’. There was no significant correlation with age for Expression or Authority or the Total scale. Indeed if anything the opposite is true, in that correlations with these factors while not significant were negative in direction, and the few significant correlations between item scores and age were also all in a negative direction., i.e. younger people more strongly held stereotypic beliefs.\n\nIn the future the scale will help assess the strength of gender stereotypes held by individuals and groups. The scale is easily understandable with no reverse items and is culturally appropriate. The scale can be used as an outcome indicator for interventions designed to encourage gender friendliness, including reducing incidents of gender-based violence and improving the recruitment or promotion policies of organizations. The scale is developed for the adult population, but its simplicity suggests that in time it may be possible to produce a child version to help understand and address the stereotyping issues evident in the educational system as set out in the introduction to this paper.\n\n\nConclusion\n\nGender stereotypes develop at a very young age and universally, in the West as well as in countries like Bangladesh, they have a wide ranging influence on many aspect of life including academic growth, the formation of personality traits, emotional expression, career progression and the shaping of behaviour in general (Ruble & Martin, 1998; Chaplin & Aldao, 2013; Hutson-Comeaux & Kelly, 2002; Plant et al., 2000; Bonebright et al., 1996). This study contributes to the goal of understanding and changing gender stereotypes in Bangladesh by providing the reliable, valid, and psychometrically sound measure that researchers and policy makers have sought (Mills et al., 2012). The Strength of Gender Stereotyping Scale provides a psychometrically sound, short in length, easy to administer, less time-consuming scale (it takes about four or five minutes to complete even in its oral form) that assesses the strengths of gender stereotypes in the adult population of Bangladesh. The results presented in this paper show that gender stereotypes in Bangladesh of the type that perpetuate inequality in favour of men are strong and above all pervasive, equally held by both males and females and by the young and old. It is a huge challenge for the educational system and for programmes aimed at encouraging social change.", "appendix": "Data availability\n\nFigshare. SGSS Dataset. DOI: https://doi.org/10.6084/m9.figshare.22776563.v1 (Faruk et al., 2023a).\n\nFigshare. Materials used for the study. DOI: https://doi.org/10.6084/m9.figshare.22776578.v1 (Faruk et al., 2023b).\n\nThese projects contain the following data:\n\n- Dataset for the current study (Faruk et al., 2023a)\n\n- Materials used for the study (Faruk 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\nReferences\n\nArbuckle JL: IBM SPSS Amos 20 user’s guide. Amos Development Corporation, SPSS Inc.; 2011.\n\nAsadullah MN, Islam KMM, Wahhaj Z: Gender Bias in Bangladeshi School Textbooks: Not Just a Matter of Politics or Growing Influence of Islamists. Rev. Faith Int. Aff. 2018; 16(2): 84–89. 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Reference Source" }	[ { "id": "209342", "date": "19 Oct 2023", "name": "Brian Heilman", "expertise": [ "Reviewer Expertise I have 15 years experience in survey research on gender attitudes", "and full professional abilities in Bangla." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article is a thorough testing of survey items related to gender stereotypes, with an outcome of a validated 11-item scale for measuring an individual's \"strength of gender stereotype\" in Bangladesh.\n\nThe work is an important contribution to the field of gender-related survey research in Bangladesh and provides a nice starting point for future researchers seeking to use gender stereotypes or attitudes as a factor or main focus in a quantitative study.\n\nFor me, the writing style is a little bit more complicated than necessary, and I would have liked to see an edit of the text for more clarity. Even specialized readers from within this field may have trouble with the writing style, which is very dense.\nI also have questions about the use of individual \"judges\" to eliminate several possible scale items at the outset of the study. The examples of which items were removed were not provided, so it isn't possible for the reader to validate and make their own judgment about those items not being relevant for Bangladesh. Certainly, it is important to remove any items that could cause extreme discomfort to the respondents or danger for the interviewers. These kinds of decisions could have been explained in more detail, with specific examples provided.\n\nThe final 11 item scale in Bangla seems very useful in many ways. The items are clear and easy to understand in Bangla. The English translations are not perfect, however, so non-Bangla reading audiences may question the precision of the items.\n\nIn the first item, for instance, the word \"stronger\" is incorrectly used. The English reader will think, \"stronger than what?\" But the Bangla version does not say \"stronger\", it says \"onek shaktishali\" meaning \"very strong.\" Another clear example is the phrase \"smile out loud\" which does not make sense in English. The Bangla \"jore hasha\" should be translated \"laugh loudly\". A new English translation which tries to replicate the Bangla more closely instead of making shortcuts to create shorter English sentences would be helpful.\n\nIt's also very noticeable that some scale items begin with the phrase \"aami mone kori\" meaning \"I think\", whereas others don't. I don't understand why this wouldn't have been standardized throughout. All of the items are assessing what the respondent thinks. So it seems imprecise that some items say \"I think\" or \"I don't think\" right within the item text while others don't. This shouldn't be changed after the fact but it's notable.\n\nMy personal reaction is also that the authors have made a bit too much of the two-factor result as well. It might have been enough to note that the final scale settled on two factors, and leave it at that. The step of theorizing that one factor stands for \"Expression\" and one stands for \"Authority\" seems a step too far. I note this especially when items categorized in one category seem to fit better in the other. The aforementioned, \"Women should not laugh loudly\" seems related to expression, but falls on the authority factor.\n\nOne might wonder what a one-factor final scale would have looked like, had the factor analysis kept going.\n\nRegardless of these observations and suggestions, I do think that such a rigorous factor analysis of a new scale of gender attitude items in Bangla is tremendously valuable, and I suspect that I may have my own opportunities to apply this scale in coming years. I thank the authors for their work and for considering my ideas.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "249886", "date": "29 Mar 2024", "name": "Silia Vitoratou", "expertise": [ "Reviewer Expertise psychometrics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn my opinion this is an important work and very well conducted.\nFirst things first, I would like to say that I found the introduction absolutely captivating. I very much enjoyed reading it and I learnt a lot from it.\n\nOn the psychometric side of things, which is my field, all steps of the psychometric procedure, including but not limited to the analysis, are well conducted and reported, assuming that one agrees that the data should be treated as continuous. My main concern is that the rating scale was of a four point scale and was analysed using models suitable for continuous data (as SPSS and AMOS do not have estimators for ordinal data such as the WLSMV estimator). Many authors strongly advise against using 4-point ordinal data as continuous especially in the presence of ceiling or floor effects (was the case in your data?). Could the authors comment on that or run ordinal factor analysis instead? As second point that i think would be incredibly interesting in this application is to test for measurement invariance in relation to gender (perhaps adjusted for age via MIMIC?). Finally, i would like to comment that in test retest reliability is best to use agreement coefficients rather than correlation in my opinion (for the total scores the intraclass correlation coefficient, mixed effects, absolute agreement, or the Psi coefficient for ordinal data per item).\n\nI hope these comments will help to improve an already interesting manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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/12-852
https://f1000research.com/articles/12-848/v1	19 Jul 23	{ "type": "Research Article", "title": "Effect of airway masks on physiological parameters of healthcare workers: a clinical trial", "authors": [ "Rahmad Rahmad", "Muhammad Barlian Nugroho", "Mochammad Ridwan", "Shabrina Narasati", "Cholid Tri Tjahjono", "Holipah Holipah", "Mohammad Saifur Rohman", "Rahmad Rahmad", "Mochammad Ridwan", "Shabrina Narasati", "Cholid Tri Tjahjono", "Holipah Holipah", "Mohammad Saifur Rohman" ], "abstract": "Background: Airway masks helps protect the wearer’s respiratory environment. There are many types of airway masks which differ in materials and effectiveness. This study aims to evaluate the effect of a surgical mask, the N95 mask, and an elastomeric respirator mask on cardiopulmonary, metabolic, and subjective parameters on healthcare workers. Methods: We conducted a controlled clinical trial on healthcare workers aged between 17-35 years old. Each subject performed a treadmill test (speed 5.6 km/hour) for 30 minutes while their physiological variables were monitored (pulse rate, respiratory rate, oxygen saturation, end-tidal CO2, body temperature, Borg scale, talk test, blood lactate, intermittent blood sugar, and subjective indicators). Each healthcare workers will be tested for four treatments, namely without using a mask, surgical mask, N95 mask, and elastomeric respirator. Results: All healthcare workers (age 25.10 ± 2.2 years old; 5 males and 5 females) completed the protocol with no adverse event. Pair-wise comparison using two-way ANOVA reported no significant difference within the mask condition for pulse rate (p=0.6497), respiratory rate (p=0.6772), oxygen saturation, (p=0.2587), end-tidal CO2 (p=0.0191), body temperature (p=0.7425), Borg scale (p=0.0930), blood lactate (p=0.6537) and glucose (p=0.8755). A statistically significant difference was reported in talk test (p=0.0129) with elastomeric respirator group showing highest result compared to control. Similarly, statistical significance was reported in subjective indicator of tightness (p=0.0017) with highest mean rank seen in N95 mask condition. However, these differences were clinically insignificant. Conclusions: The effect of surgical mask, N95 mask, and elastomeric respirator on the cardiopulmonary parameters, metabolic parameters, and subjective indicators during 30 minutes of low-moderate intensity exercise is negligible and generally well tolerated by healthcare workers. Registration: TCTR20230630001", "keywords": [ "personal protective equipment", "filtering facepiece respirator", "cardiopulmonary", "metabolic", "subjective sensation", "healthcare workers" ], "content": "Introduction\n\nSince the COVID-19 pandemic occurred in February 2020, the World Health Organization has recommended the use of face masks as one of the preventative measures to reduce COVID-19 transmission. Face masks help protect the wearer’s respiratory environment from droplets that contains the virus, thus reducing the virus’s transmission. Face masks come in several types, such as cloth masks, surgical masks, N95 masks, respirator masks, etc. These masks differ in materials and effectiveness on reducing viral transmission. Masks with more condensed layers have a more protective barrier, thus are more effective in preventing viral transmission. Several types of masks, e.g. the N95 and elastomeric respirator masks, are able to give protection toward airborne agents as well as droplets.1\n\nAlthough it can help reduce the spread of COVID-19, wearing a face mask for a relatively long period of time can be uncomfortable. Prolonged use of face masks has been associated with exertion, breathing difficulties, headaches, and even light-headedness. A previous study by Scheid et al.2 showed that wearing mask for more than four hours triggers several subjective discomforts.2 Furthermore, the study also reported that people with a history of troublesome headaches were more likely to also experience headaches while using a mask for a long period of time.2 In addition, Ipek et al.3 showed that the causes of dizziness and headache while using respirators were associated with respiratory alkalosis and hypercarbia.3 Heart rate is expected to increase during physical exertion. Hence, perceived exertion and difficulty in breathing often felt by mask users suggests that it might stimulate an increase in heart rate.\n\nDiscomfort from wearing a mask has also been associated with the increased facial skin temperature and humidity inside the mask. However, a previous study using thermal imagery and an infrared thermometer found that while wearing a filtering facepiece respirator (N95 mask), facial skin temperature increased in a manner that was not clinically significant.2,4 Subjective thermal comfort measured using a visual analog numerical scale while using a respirator also revealed a statistically insignificant difference compared to control.5 The increased discomfort caused by prolonged face mask use can potentially reduce the optimal working condition of healthcare workers. Moreover, that discomfort might ultimately cause non-compliance on wearing face mask. This will increase the spread of COVID-19 in healthcare workers and their environment.\n\nIn this study, we aimed to evaluate the effect of a surgical mask, N95 mask, and elastomeric respirator on physiological variables including pulse rate, respiratory rate, oxygen saturation, end-tidal CO2, body temperature, Borg scale, talk test, blood lactate, intermittent blood sugar, and subjective indicators in healthcare workers. Everyday workload was reflected in this study by low intensity treadmill test (5.6 km/h). The result of this research can aid in the future regulations regarding mask use for the public.\n\n\nMethods\n\nThis study received approval from Dr. Saiful Anwar Hospital’s Ethics Commission on July 28th, 2020 (ethical approval number: 400/159/K.3/302/2020). Written and verbal informed consent were received from the participants prior to starting the procedures.\n\nThis study was registered retrospectively to Thai Clinical Trials Registration (TCTR) because the authors initially did not consider that this study could not be categorized as a clinical trial. The trial identification number is TCTR20230630001 (https://www.thaiclinicaltrials.org/show/TCTR20230630001).\n\nWe conducted a non-randomized trial in which every participant underwent the same treatment (no mask, surgical mask, N95 mask, and elastomeric mask). The study trial went accordingly, hence no changes were made to the study procedure and population. Although a cloth mask condition was originally included, this has been excluded from analysis as it is no longer recommended by the Ministry of Health. This study took place in Dr. Saiful Anwar Hospital’s Malang, Indonesia.\n\nThe study population includes healthcare workers aged between 17-35 years old without cardiopulmonary, neuromuscular, and musculoskeletal disorders, with a body mass index (BMI) between 18.5-24.99kg/m2, and who are willing to take part in a series of tests and are able to sign their informed consent. Pregnant participants were also excluded. The healthcare workers participated under their own personal willingness. Prior to the start of the study, authors had distributed the announcement of this research project as to recruit potential participants. The information was relayed through broadcast message and banners in front of the physical rehabilitation and medicine department in Dr. Saiful Anwar Hospital.\n\nParticipants who did not complete the research protocol and had to terminate their involvement while performing the tests were categorized as dropouts. Dropouts were not included in our final analysis. The absolute indications for test termination were as follows: a) participant’s request, b) systolic pressure drops > 10 mmHg below systolic pressure at rest while standing with evidence of ischemia, or > 20 mmHg after a previous systolic increase, and c) technical problems with equipment. The relative indications for termination were as follow; a) severe chest pain, b) tightness, fatigue, leg cramps, or claudication, c) systolic blood pressure ≥ 230 mmHg, diastolic ≥ 115 mmHg, and d) evidence of arrhythmia. The minimum number of participants was calculated using Federer’s formula. Sampling was carried out using consecutive sampling. Participants who fit the study criteria were included as the study population.\n\nAfter receiving approval from Dr. Saiful Anwar Hospital’s Ethics Commission, this research was carried out. Prior to recruitment, all participants were screened by an author (medical doctor) for illnesses. The form for this screening is available in the extended data.28 The study procedures were demonstrated to the healthcare workers after they passed the health screening. All 10 of the participants passed the health screening, so no one was excluded from the study. All participants provided written and verbal informed consent.\n\nFor 30 minutes, each healthcare worker ran on a treadmill (Berwyn) at a low-moderate intensity (5.6 km/h). Four separate treatments were prepared for each healthcare worker. First, they carried out the exercise without a mask. Second, while wearing a surgical mask. Third, they wore an N95 or similar respirator. Lastly, the healthcare workers used a reusable elastomeric respirator. Each treatment was conducted 7-14 days apart (Figure 1). To keep the healthcare workers from falling, the treadmill speed was progressively decreased to zero at the end of each workout. The patients were then instructed to cool down by walking until their pulse rate dropped below 100 beats per minute. All the participants were asked to bring athletic clothing and shoes to be worn during the study.\n\nTiming of the parameters is shown in Figure 2. Each test was conducted once by each participant. Pulse rate and oxygen saturation was measured using a Withleof® handheld pulse oximeter. Capnography was used to measure respiratory rate and end-tidal CO2. Meanwhile, body temperature was measured using an infrared thermometer (Omron). Borg rating of perceived exertion (Borg Scale) was used to measure the physical sensations experienced by the healthcare workers.6 The scale starts from 6 indicating no exertion at all to 20 indicating maximal exertion. These measurements were obtained before exercise, 3 minutes, 10 minutes, 20 minutes, and 30 minutes into the exercise, and then 3 minutes and 30 minutes after resting (Figure 2). A talk test was conducted according to previous studies.7,8 The healthcare workers joined in a conversation with the examiner, then the examiner determined how the subject talked. The range of talk test measurement is shown in Figure 3. For the purpose of statistical analysis, the intensity of the exercise (light, moderate, and vigorous) was represented by 1, 2, and 3, respectively. If the participant could easily carry the conversation with the examiner, the physical activity then classified into light activity, etc. Blood lactate was measured by taking the participants’ capillary blood while running, using a blood lancet, which was then inserted to Accutrend® Plus Lactate. Blood glucose levels were also measured by taking the capillary blood and inserted to Accutrend® Plus Glucose.\n\nAll participants were given a form that contains a subjective indicators scale. They were asked to rate each subjective indicator from 0 (not at all) to 10 (strongly) before exercise and then after they finished the exercise. The subjective indicators scale (Figure 4) was adopted from a previous study by Li et al.4\n\nA master table was used to record data that were gathered in this study. SPSS version 23.0 and GraphPad version 9.1.0 were used to analyze the data. The Saphiro-Wilk test was used to determine the normality of numerical data, after which homogeneous or normally distributed data (p > 0.05) were presented with mean and standard deviation (SD), while data that were not normally distributed (p > 0.05) were presented with the median (minimum value; maximum value). Pairwise comparison using the two-way ANOVA non-parametric test was used to examine the relationship between variables with non-homogeneous results. A statistically significant correlation is shown by a p-value of less than 0.05 (95% significance). If a significant value was obtained, a post-hoc multiple comparison analysis was performed with Dunn’s test. The relationship between the ordinal data was analyzed using a non-parametric pairwise comparative with Friedman’s two-way ANOVA test. A p-value below 0.05 indicates a statistically significant correlation (95% significance). If a significant value was obtained, a post hoc pair-wise comparison analysis was performed with Bonferroni’s correction.\n\n\nResults\n\nA total of 10 healthcare workers (consisting of 5 men and 5 women) were recruited in this study.27 All healthcare workers passed the health screening and completed the whole study protocol. The baseline characteristics assessed were gender, age, weight, height, and body mass index. As reported in Table 1, the age range of study healthcare workers was 22-29 years with a mean of 25.10 years old, a mean body weight of 55.90±11.32 kg, height 162.8±8.2 cm, and BMI 20.97±3.0 kg/m2. No statistical difference was reported on these baseline characteristics (Table 2).\n\nThe results of the normality test of all cardiorespiratory parameters, metabolic parameters, and subjective indicators were non-homogenous, hence they are reported in median, minimum and maximum. Table 3 compares the result of pulse rate, respiratory rate, oxygen saturation, end-tidal CO2, body temperature, Borg scale, talk test, blood lactate, and intermittent blood glucose in control, surgical mask, N95 mask, and elastomeric respirator group. Statistical analysis yielded insignificant differences between control, surgical mask, N95 mask, and elastomeric respirator group.\n\n* statistically significant in main effect comparison (p-value <0.05).\n\nThere was no statistically significant difference between all groups in every time for the median of pulse rate, respiratory rate, oxygen saturation, end-tidal CO2, body temperature, and Borg scale (Table 3). Pair-wise comparison using two-way ANOVA (Table 4) also reported no significant difference when analyzed within the mask condition for pulse rate (p=0.6497), respiratory rate (p=0.6772), oxygen saturation, (p=0.2587), end-tidal CO2 (p=0.0191), body temperature (p=0.7425), and Borg scale (p=0.0930). Compared to the control condition, the elastomeric respirator condition had significant differences at 0-minutes (p=0.0045), 3-minutes during exercise (p=0.0353), and 30-minutes after rest (p=0.0243). A statistically significant effect of time (Table 4) was reported for pulse rate (p=<0.0001), respiratory rate (p=<0.0001), oxygen saturation, (p=0.0052), end-tidal CO2 (p=<0.0001), body temperature (p=<0.0001), and Borg scale (p=<0.0001).\n\n* statistically significant in main effect comparison (p-value <0.05).\n\nResults of the talk test revealed a statistically significant difference between control and elastomeric respirator (p=0.0110). Between each time interval, a statistically significant difference compared to control was reported at minute-30 in elastomeric respirator group (p=0.034).\n\nAnalysis of blood lactate and glucose data resulted in no significant statistical difference when compared between mask conditions with p-value of 0.6537 and 0.8755 respectively. As seen in Table 3, blood lactate levels on every group tend to increase during exercise and decrease while resting.\n\nTable 5 describes the result of subjective indicators in surgical mask, N95 mask, and elastomeric respirator group. Pair wise comparison (two-way ANOVA) was reported in Table 6. All subjective indicators’ variables excluding salty and unfit sensations have a statistically significant difference on time effects. Meanwhile, for mask effects, statistical difference was only reported in tight sensation with p-value of 0.0017. Analysis of the mean rank between mask conditions showed that the N95 condition most commonly scores higher in the tight sensation compared to the other mask conditions.\n\n* statistically significant in main effect comparison (p-value <0.05).\n\n* statistically significant in main effect comparison (p-value <0.05).\n\n\nDiscussion\n\nThe increased need for oxygen during physical exercise affects heart rate, which is reflected by the pulse rate in this study. Increased sympathetic response during physical exercise causes an increase in pulse rate.9 This is shown in this study by the result of time effect in pair-wise comparison which means with each time period, the value of pulse rate differs. However, the difference between pulse rate between control and tested mask conditions did not show any statistically significant difference, which was in accordance with the results of several previous studies.5,10–13 Contrary to our findings, there were several studies that showed significant differences in the use of filtering facepiece respirators, where the N95 mask condition showed a statistically significant difference in pulse rate compared to surgical mask condition. However, in that study, the treadmill speed tested was higher compared to this study, which was at 6.4km/h. The higher treadmill speed might have caused the significant difference seen between the two masks.4\n\nThe increase of oxygen demand also affects the respiratory physiology. The physiological impact that occurs while using a mask is hypothesized to be caused by the filter media inside, which blocks the flow of air into the respiratory tract.14 Thus, the more layers a mask has, the higher the resistance it will cause while breathing. Therefore, the respiratory rate is expected to increase as well. In this study, there was no significant difference between the various tested masks compared with controls.\n\nIn this study, treadmill exercise did not cause the healthcare workers to reach a hypoxic state, with the lowest SpO2 median of 96%. Previous studies have shown that physical exercise causes SpO2 to decrease as oxygen demand increases.15 Coupled with the possibility of an increase in respiratory resistance caused by wearing masks, the SpO2 is expected to decrease in the tested mask conditions compared to the control conditoin. However, in this study, the SpO2 values were not significantly different statistically compared to the control condition. The reason behind this might be due to the intensity of exercise carried out in this study (moderate intensity) did not cause an increase in oxygen demand that will significantly reduces SpO2.\n\nThe other parameter of respiratory physiology are end-tidal CO2, capillary oxygen saturation, and the Borg scale. When PtcCO2 value increases, the body will compensate by increasing the respiratory rate.16,17 In this study, there was no statistically significant difference between the tested mask conditions and the control condition during physical exercise. This result is in accordance with previous studies.10,11,13,18\n\nBody temperature is very tightly regulated by thermoreceptors located in the hypothalamus. Physical exercise can trigger vasodilation which causes blood vessels to dilate to allow greater blood flow to the skin and ultimately increases skin temperature.19 In this study, body temperature was described by skin temperature measured using an infrared thermometer placed on the forehead. The moderate intensity exercise in this study was not expected to trigger heat stress which stimulates an increase in skin temperature. This is consistent with the results of this study which showed that until the 30th minute, the control condition did not show an increase in body temperature greater than 37.5 °C. Similar result can be seen in the tested mask conditions, where in the post-hoc analysis there was no significant difference compared with control, which means that the use of masks does not cause heat-stress in moderate-intensity physical exercise. Previous study by Kim et al. obtained similar results where the measurement of rectal temperature (p= 0.519) and overall temperature (p= 0.654) were similar in the FFR (filtering facepiece respirator) mask group and the control condition.20 In the study by Li et al. comparing the skin temperature in the use of N95 masks with surgical masks, there was a significant difference where the skin temperature in the surgical mask group was lower than that of the N95 mask.4 However, in that study the mask was used for longer period of time, namely for 100 minutes, and at a higher treadmill speed at 6.4km/h. This result showed that the FFR mask has the potential to cause greater metabolic stress when used for a longer period of time and at higher workload or exercise intensity.\n\nThe scores for the Borg scale did not differ significantly between the control and the other tested masks. However, the median results of the Borg scale measurement increased with time, and decreased at rest, and this result was statistically significant. This shows that the value of the Borg scale, which describes exertion efforts, was influenced more by the length of time exercising than the use of mask. Several previous studies also found the similar result. A study by Roberge et al. compared Borg scale scores on a treadmill test using a filtering facepiece respirator at two different speeds (2.74 km/h vs. 4.03 km/h). The results of this study showed a significant difference in the scores for exertion (p=0.01).5,11,12,20\n\nThe concentration of serum lactate is a represent of anaerobic metabolism.20,21 The results of this study indicated that lactate concentration increases after 15 minutes of exercise compared to the pre-exercise measurement even though when compared between the test mask groups, there was no significant difference. Thus, it can be concluded that the use of surgical, N95, or elastomeric respirator does not cause an increase or decrease in anaerobic metabolism compared to using no mask during the treadmill test. A study by Lassing et al.23 showed that in exercise using constant load, the concentration of blood lactate in the control and surgical masks group was not significantly different (p= 0.26).23\n\nThe talk test has been used before in several studies to determine exercise intensity.16,24,26 Exercise with moderate intensity will result in the ability of the healthcare workers to speak comfortably without gasping or the need to alter their speed.25 Compared to control, there was a statistically different result in elastomeric respirator group (Table 2). However, this difference was not clinically meaningful since in the mean of every group was in the range of light to moderate. The talk test has been proposed to be comparable with lactate threshold in measuring exercise intensity.16 The findings in this study are in accordance with that, in which the value of blood lactate and talk test represented moderate exercise intensity in all group. This finding showed that using a mask did not increase exercise load, despite the presence of filtering layers.\n\nThe cardiovascular system will respond to the exercise with an increase of cardiac output to deliver the oxygen and glucose to the muscles that play important roles in the metabolic process during physical exercise.21,22 In this study, the results of the blood glucose measurements before exercise compared to 3 minutes after rest showed no significant difference. There are no studies yet that have examined the effects of using various masks on random blood glucose levels. This may be caused by the intensity of physical exercise. In addition, the duration of exercise was 30 minutes. This duration period might be too short for it to cause hypoglycemia. In addition, the ideal measurement of glucose consumption is to measure it directly on muscle cells i.e using nanobiosensor.26\n\nThe results of the subjective indicators values before and after physical exercise showed no significant differences between the various masks, except for the tight sensation (p= 0.0017) with the highest mean rank in the N95 mask group. A previous study by Li et al.4 comparing the use of N95 masks and surgical masks showed significant differences in all subjective sensations with higher scores in the N95 mask group.4 In this study, masks were tested for 100 minutes. Compared to other masks, the wearer of an N95 mask has the highest probability in feeling subjective discomforts. However, with a longer period of mask use, other types of masks also might also cause discomforts. Hence, studies with a longer period of mask use should be conducted in the future.\n\n\nConclusions\n\nThe effect of surgical masks, N95 masks, and elastomeric respirators on the cardiopulmonary and metabolic response during 30 minutes of low-moderate intensity exercise is negligible and generally well tolerated by healthy healthcare workers.", "appendix": "Data availability\n\nfigshare: (Raw data) Effect of Airway Masks on Physiological Parameters of Healthcare Workers. https://doi.org/10.6084/m9.figshare.21981080.v2. 27\n\nThis project contains the raw data file.\n\nfigshare: (Appendix) Effect of Airway Masks on Physiological Parameters of Healthcare Workers. https://doi.org/10.6084/m9.figshare.21981029.v2. 28\n\nThis project contains the consent form and other materials given to participants.\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 was presented in the 6th International Conference and Exhibition on Indonesian Medical Education and Research Institute (6th ICE on IMERI), Faculty of Medicine, Universitas Indonesia. We thank the 6th ICE on IMERI committee, who had supported the peer-review and manuscript preparation before submitting it to the journal. We thank Yan Martha, Universitas Indonesia, for her assistance in editing and revising the final manuscript.\n\n\nReferences\n\nLepelletier D, Grandbastien B, Romano-Bertrand S, et al.: What face mask for what use in the context of the COVID-19 pandemic? the French guidelines. J. Hosp. Infect. 2020; 105(3): 414–418. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nScheid JL, Lupien SP, Ford GS, et al.: Commentary: Physiological and psychological impact of face mask usage during the COVID-19 pandemic. Int. J. Environ. Res. Public Health. 2020; 17(18): 1–12.\n\nİpek S, Yurttutan S, Güllü UU, et al.: Is N95 face mask linked to dizziness and headache? Int. Arch. Occup. Environ. Health. 2021; 94: 1627–1636. 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PubMed Abstract \| Publisher Full Text\n\nGawn J, Clayton M, Makison C, et al.: Evaluating the protection afforded by surgical masks against influenza bioaerosols: gross protection of surgical masks compared to filtering facepiece respirators. Health & Safety Executive. 2008; ((Research report; 619)).\n\nEroğlu H, Okyaz B, Türkçapar Ü: The effect of acute aerobical exercise on arterial blood oxygen saturation of athletes. J. Educ. Train. Stud. 2018 Aug; 6: 74. Publisher Full Text\n\nReed JL, Pipe AL: Practical approaches to prescribing physical activity and monitoring exercise intensity. Can. J. Cardiol. 2016 Apr; 32(4): 514–522. PubMed Abstract \| Publisher Full Text\n\nRestrepo RD, Hirst KR, Wittnebel L, et al.: AARC clinical practice guideline: transcutaneous monitoring of carbon dioxide and oxygen: 2012. Respir. Care. 2012 Nov; 57(11): 1955–1962. Publisher Full Text\n\nKim JH: Results of switching from pro re nata to treat-and-extend regimen in treatment of patients with type 3 neovascularization. Semin. Ophthalmol. 2020 Jan; 35(1): 33–40. PubMed Abstract \| Publisher Full Text\n\nKenny GP, Sigal RJ, McGinn R: Body temperature regulation in diabetes. Temp (Austin, Tex). 2016 Jan; 3(1): 119–145. Publisher Full Text\n\nKim JH, Wu T, Powell JB, et al.: Physiologic and fit factor profiles of N95 and P100 filtering facepiece respirators for use in hot, humid environments. Am. J. Infect. Control. 2020; 44(2): 194–198.\n\nGoodwin ML, Harris JE, Hernández A, et al.: Blood lactate measurements and analysis during exercise: a guide for clinicians. J. Diabetes Sci. Technol. 2007 Jul; 1(4): 558–569. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVucetic V, Mozek M, Rakovac M: Peak blood lactate parameters in athletes of different running events during low-intensity recovery after ramp-type protocol. J. Strength Cond. Res. 2015; 29(4): 1057–1063. PubMed Abstract \| Publisher Full Text\n\nLässing J, Falz R, Pökel C, et al.: Effects of surgical face masks on cardiopulmonary parameters during steady state exercise. Sci. Rep. 2020; 10(1): 22363. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReed JL, Pipe AL: The talk test: A useful tool for prescribing and monitoring exercise intensity. Current Opinion in Cardiology. Lippincott Williams and Wilkins; 2014; Vol. 29. : 475–480. Publisher Full Text\n\nWoltmann ML, Foster C, Porcari JP, et al.: Evidence that the talk test can be used to regulate exercise intensity. J. Strength Cond. Res. 2015 May; 29(5): 1248–1254. PubMed Abstract \| Publisher Full Text\n\nObregón R, Ahadian S, Ramón-Azcón J, et al.: Non-invasive measurement of glucose uptake of skeletal muscle tissue models using a glucose nanobiosensor. Biosens. Bioelectron. 2013 Dec; 50: 194–201. PubMed Abstract \| Publisher Full Text\n\nNarasati S: (Raw data) Effect of Airway Masks on Physiological Parameters of Healthcare Workers. Dataset. figshare. 2023. Publisher Full Text\n\nNarasati S: (Appendix) Effect of Airway Masks on Physiological Parameters of Healthcare Workers. figshare. 2023. Online resource. Publisher Full Text" }	[ { "id": "204105", "date": "19 Sep 2023", "name": "Arin Choudhury", "expertise": [ "Reviewer Expertise Emergency and trauma", "AI" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI have reviewed the article you provided. It seems to be a detailed and comprehensive study on the effects of different types of masks (surgical mask, N95 mask, and elastomeric respirator) on healthcare workers during a low-moderate intensity exercise. Here are some observations:\nStrengths:\nClear Objective: The study's objective, to evaluate the impact of various masks on physiological parameters in healthcare workers during exercise, is well-defined.\n\nEthical Considerations: The study mentions receiving ethical approval and obtaining informed consent from participants, which is essential in research involving human subjects.\n\nStudy Design: The non-randomized controlled trial design is suitable for this research question and is described in detail.\n\nData Collection: The methods for collecting data, including the instruments used for measuring physiological parameters, are clearly explained.\n\nStatistical Analysis: The statistical methods used for data analysis are outlined, including the significance levels and post-hoc tests.\n\nAreas for Improvement:\n\nIntroduction: While the introduction provides some context about the importance of masks during the COVID-19 pandemic, it could benefit from a more thorough review of existing literature related to mask usage during exercise and the associated discomforts.\n\nMethods: While the methods section is detailed, it might be beneficial to include information about the sample size calculation and the rationale behind the chosen treadmill speed and duration.\n\nResults: The results section provides a comprehensive overview of the findings, but it could benefit from visual aids such as tables or graphs to present numerical data and make it easier for readers to interpret the results. Additionally, some of the values mentioned in the text, such as p-values, should be included in tables or figures for clarity.\n\nDiscussion: The discussion section is missing in the provided text. It's essential to include this section to interpret the results, compare them with previous research, discuss the implications of the findings, and highlight the limitations of the study.\n\nPlagiarism: Based on the text you've provided, there are no apparent signs of plagiarism. However, it's crucial to ensure that any information or text borrowed from other sources is properly cited when you complete the full article.\n\nConclusion: The conclusion briefly summarizes the findings but does not provide a comprehensive interpretation or discussion of their significance. It should also highlight the practical implications for healthcare workers and future research directions.\n\nOverall, the article appears to be well-structured and provides valuable insights into the impact of different masks on healthcare workers during exercise. To enhance its quality, consider addressing the areas for improvement mentioned above and completing the discussion and conclusion sections when writing the full 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?\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": "246273", "date": "23 Feb 2024", "name": "Zhipeng Deng", "expertise": [ "Reviewer Expertise indoor airflow", "IAQ", "physiological signals" ], "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\nRegarding the literature review, it seems to overlook several relevant studies. Please consider including additional research on the concentrations of O2 and CO2 inside the face mask.\nHow to determine the fit of wearing a mask? It is best to provide photos of the experiment, including masks, test procedures, measuring instruments and equipment Even though the author mentioned age range 17-35 in Abstract, the actual age range was 22-29. Could you share the reasoning or references behind choosing a low-intensity treadmill test at 5.6 km/h? More specifics about the testing conditions are needed, such as room temperature, the attire of participants, and the external temperature and season during the tests. Were participants required to follow any specific dietary or lifestyle restrictions, such as avoiding smoking or caffeine, before the test? Figure 3 contains too little information and is unnecessary. The choice of only 10 participants, with a narrow age range, raises questions about the study's breadth. Can you justify how this sample size was deemed adequate for the conclusions drawn? Especially conclusions for cardiovascular, respiratory and metabolic parameters. What is the sample size for similar studies? The scale used to measure subjective sensations seems overly simplistic. Consider incorporating established standard questionnaires that cover temperature, humidity, odor, fatigue, and comfort sensations more comprehensively. Incorporating figures to illustrate key findings might offer clearer insights than tables alone. In Discussion section the author mentioned and compared a lot of previous studies. Most state-of-the-art results should be mentioned in literature review in Introduction. Measuring instruments required more information, such as model and accuracy.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-848
https://f1000research.com/articles/12-847/v1	19 Jul 23	{ "type": "Study Protocol", "title": "An epidemiological study of oral tobacco use amongst urban slum inhabitants in a town from central urban India", "authors": [ "Sulochana Kuruwanshi", "Abhishek Joshi", "Abhishek Joshi" ], "abstract": "Background: Smokeless tobacco users receive levels of nicotine known to be addictive, and clinical symptoms of dependency and withdrawal for smokeless tobacco are identical to those for cigarettes. Smokeless tobacco usage patterns share significant parallels with patterns of use of other addictive drugs. Because everyone spits after using oral tobacco, there are more persons who spit in public due toits use. Use of smokeless tobacco during pregnancy increases the chance of low-birth-weight babies by two to three times and is linked to stillbirths. Other negative health implications of smokeless tobacco use include dental decay, gum recession, high blood pressure, oral sub-mucous fibrosis (OSF), a crippling disorder, and mouth and food pipe malignancies. This warrants the study of patterns of oral tobacco use and its determinants in urban slum areas. Objective: To estimate the prevalence and patterns of oral tobacco use and assess the motivating and demotivating factors associated with it amongst urban slum inhabitants. Methods: A community-based cross-sectional study will be conducted in the urban field practice area of a tertiary care hospital. A semi-structured questionnaire assessing the socio-demographic profile, prevalence and pattern associated factors for oral tobacco use among the study participants will be implemented. Study implications: This study will help to determine the prevalence and pattern of oral tobacco use, as well as the motivating and demotivating factors that contribute to oral tobacco use. Insights gained shall be useful to implement focussed prevention strategies.", "keywords": [ "Tobacco use", "Oral tobacco", "Urban slum", "Epidemiological study." ], "content": "Introduction\n\nThe United Nations' World Health Organization (WHO) oversees global public health. The primary goal of the WHO, according to its constitution, is to ensure that everyone has the best possible level of health. Smokeless tobacco users receive levels of nicotine known to be addictive, and clinical symptoms of dependency and withdrawal for smokeless tobacco are identical to those for cigarettes. Smokeless tobacco usage patterns share significant parallels with patterns of use of other addictive drugs. The mandate of the WHO calls for global collaboration to enhance health, uphold world peace and harmony, and assist the vulnerable. It encourages a billion more people to participate in monitoring public health risks, coordinating emergency medical response efforts, promoting health and wellness, and implementing universal health care.\n\nPan is frequently taken with chewed smokeless tobacco products like Mishri and Pan masala (a chewable tobacco made with areca nuts). Smokeless tobacco use, particularly in the eastern, northern, and north-eastern regions of the country, is a socially accepted addiction. Most prior studies on the prevalence of tobacco use were either based on small-scale research surveys with an urban bias, small sample numbers, and poorly known sociodemographic correlates of tobacco use. Additionally, earlier prevalence estimations made in India are still extremely speculative and non-representative.1 Use of oral tobacco increases the frequency of people spitting in public because everyone spits after using it. In developing nations, it raises the risk of airborne infectious diseases, among which tuberculosis (TB) dissemination is one. Our primary goal in this study is to evaluate the pattern, prevalence, and sociodemographic characteristics associated with smokeless tobacco use in urban slum dwellers. To prepare tobacco for these uses, tobacco leaves are harvested when they turn yellow and brownish stains begin to develop. The leaves are then uniformly dried in the field, tied into bundles with water or molasses to keep them moist, and then stored for a few weeks to ferment. There are several issues with South Asians using smokeless tobacco. It is widely used and becoming more so, especially with the introduction of new smokeless tobacco varieties in recent years that have attracted more consumers.2\n\nTransport employees who are under stress are more likely to abuse alcohol and other drugs, with cigarettes being the most popular. There has been research on a connection between smoking and job stress. It is often believed that a substantial percentage of bus drivers and other employees smoke cigarettes. The second leading cause of death worldwide and the leading contributor to morbidity and mortality that may be prevented is tobacco smoking. Oral malignancies and possibly malignant lesions, the degree and depth of periodontal disease, and poor wound healing are the most harmful impacts of tobacco use on the oral cavity.3 Although its use varies around the world, betel quid (pan), the most popular type of smokeless tobacco, quickly adopted tobacco as a new ingredient after its introduction. However, the legal gaps are being effectively used. For instance, replacements like “supari mix” packets are offered for sale with a free packet of Zarda or Khaini chewing tobacco. Except for a few limited geographic locations, both men and women regularly chew betel nut, but smoking tobacco is far more prevalent among men in Bangladesh, India, Pakistan, and Sri Lanka than among women.4 To enable the creation and implementation of efficient intervention plans, this knowledge is necessary. The goal of the current report is to analyse in depth the smoking habits of a community in northern India and how they relate to the three different living strata, namely urban, urban-slum, and rural. However, the amount of substance being consumed, and the age of commencement are frequently not mentioned in these questionnaires. Studies on the epidemiology of coronary heart disease and its risk factors have either concentrated on urban or rural settings. studied the incidence of tobacco usage in northern Indian villages, towns, and cities.5 But it is crucial to emphasize a few points that are crucial for comprehending how addicted smokeless tobacco is. The use of smokeless tobacco rapidly increased, the products were found to be carcinogenic, and the demographics of users abruptly changed, all of which led to the development of smokeless tobacco addiction as a public health issue in the United States in the middle of the 1980s. Older folks were the main consumers of its products, and when they died off there were no new consumers to take their place. The smokeless tobacco business turned this trend around by creating new products, notably moist snuff products, and employing strong marketing techniques.6\n\nIndia is a diverse nation that is home to numerous cultures, faiths, and languages in addition to various socioeconomic classes. Community health is a concern for all swaths of society, including the poor, the wealthy, children, adults, the elderly, men, and women. The Tobacco Control Team for the India Region works to reduce the burden of illness, mortality, and the financial costs associated with tobacco use and passive smoking. Tobacco use is currently the leading cause of death that may be prevented worldwide. Depending on the metastasis's location and features, other structures including the internal jugular vein, sternocleidomastoid muscle, or spinal auxiliary nerve may need to be sacrificed.7\n\nA significant portion of the nation's gross domestic product (GDP) and export earnings come from the production of tobacco, which is exported in 98 percent of cases. Typically, the crop accounts for roughly 10% of GDP, 30% of overall exports, and more than 50% of agricultural exports. The Tobacco Control team works to reduce the burden of illness, mortality, and the financial costs associated with tobacco use and exposure to passive smoking. Currently, smoking is the leading preventable cause of mortality in the world. For smokeless tobacco control, various strategies are required, including media campaigns and related programmes. Variable tobacco industry marketing tactics, lax enforcement of tobacco control laws, persistent affordability, and incomplete knowledge of the health hazards of tobacco use are all contributing reasons that are raising the use of smokeless tobacco.8\n\nPrimary objective\n\nTo study the prevalence of oral tobacco usage amongst residents from an urban slum in central urban India\n\nSecondary objectives\n\n1. To study the pattern of oral tobacco usage amongst residents from an urban slum in central urban India.\n\n2. To assess the motivating and demotivating factors associated with usage of oral tobacco in our study settings.\n\n\nProtocol\n\nA cross-sectional study will be conducted in Wardha district from June 2023 to Nov 2023.\n\nThe present study will be conducted in the urban slums of Wardha District.\n\nBoth male and female adult inhabitants of urban slums from the field practice area of the urban health training center of institute will be approached by door-to-door household surveying using the systematic random sampling method.\n\nInclusion criteria: Study participants (>18 years) who are willing to participate.\n\nExclusion criteria: Study participants (>18 years) who do not consent to take part in the research study.\n\nSampling method: The personal interview method will be used to visit the households to reach the sample size.\n\n\n\n1) Oral tobacco use\n\n2) Types of oral tobacco used\n\n3) Motivating & demotivating factors\n\nInformation on the participants' knowledge, attitudes, and perceptions of tobacco use gathered used a questionnaire that modified from the Global Youth Tobacco Survey and the Global Adults Tobacco Survey (Table 1). This questionnaire is designed to obtain data on tobacco usage, including the type of tobacco used, how long used, when people first started chewing tobacco etc.\n\n\n\n• Age\n\n• Education\n\n• Occupation\n\n• Economic status\n\n\n\n• Early initiation\n\n• Oral tobacco duration\n\n• First time chewing tobacco\n\nThe data collected will be entered into a Microsoft Excel spreadsheet.\n\nDescriptive statistics like mean, frequency and percentages of various parameters will calculated, the Open Epi version 3.01 Epi Info software (https://www.openepi.com/Menu/OE_Menu.htm) and data will be presented using tables and graphs.\n\nBias: There may be information bias and selection bias and social desirability bias in this study.\n\nSelection bias will be addressed using systemic random sampling, and information and social disability bias will be minimizes as much as possible by building good rapport with study participants and making the beneficiaries understand the importance and objective of the study.\n\nStudy size: The average population is around 28,000. Using formula n= pq/L2 and precision 10% sample size comes to be around 384 using prevalence 51% as per previous studies.\n\nQuantitative variables\n\n1. Data analysis on the quantitative variables\n\nDescriptive Statistics like mean, frequency and percentages of various parameters will calculated, via the Open EPI Software and data will be presented using tables and graphs. Inferential statistics like chi square tests will be used.\n\n2. Different types of households in urban city areas use these tobacco products in different ways, so such households in field practice areas will be selected using systematic random sampling\n\nStatistical method: Data will be entered using Microsoft Excel. All the responses will be tabulated, and graphical representation will be made wherever necessary. Data will be analysed by using the Open Epi Info software which is freely available in the public domain.\n\nThrough our study we expect to assess the prevalence and pattern of oral tobacco use and its determinants in urban slum area and plan preventive strategies accordingly.\n\nEthical approval for this study (DMIHER (DU) IEC/2023/643) was provided by the Ethical committee of Data Meghe Institute of Higher Education and Research (Deemed to be University) on 11/02/2023.\n\n\nDiscussion\n\nSquamous cell carcinomas of the oral cavity (OSCC) make up a large percentage of cancer cases in India. The two most dangerous forms of oral cancer, with a higher incidence in India, are buccal mucosa and tongue OSCC.9 Patients with oral cancer are always expected to require an intubation or a difficult airway. The safest way to perform nasotracheal intubation in these circumstances is with FOB assistance.10 By autocrine and paracrine production of different growth factors, cytokines, and multiple proteolytic enzymes, the cancer-associated fibroblast would have the capacity to create an aggressive tumour phenotype. Invasive behaviour, local recurrence, and survival of carcinoma are all predicted by the expression of -SMA.11 The main imaging modalities for loco-regional staging of head and neck squamous cell carcinoma continue to be CT and MRI. Both techniques aid in the evaluation of the primary tumour and the identification of non-palpable lymph nodes. Nevertheless, to distinguish between benign and malignant lymph nodes, both techniques rely on size-related and morphological parameters.12 This choice justifies a trustworthy and economical strategy in patients with early-stage oral cancer. For minor to severe oral cavity deformities, inferiorly based islanded nasolabial flaps offer a one-stage procedure that is safer, quicker, and more dependable.13\n\nThe study will provide knowledge and awareness regarding the initiation of oral tobacco use amongst urban slum inhabitants in both male and female.\n\nThe information gathered in the study can further help decide what lifestyles and setting is responsible for oral tobacco problems in male and female. Moreover, the need to promote healthy lifestyle and proper assigning of lifestyles to avoid oral tobacco problems. Women with conditions where oral tobacco is contraindicated i.e., untreated active oral Cancer.\n\nAs the study is a cross sectional study being conducted at urban slums in catchment area of urban health training centre of a tertiary care hospital only so external validity of study shall be limited as prevalence and pattern and determinants of oral tobacco use may vary between geographical locations and prevailing socio-economic-cultural context.\n\nAs the study relies on participant’s response to oral tobacco use and perceptions, determinants there is chance of social desirability bias being introduced in the study.\n\nIn this study, the early initiation of oral tobacco use amongst urban slum inhabitants, exclusive tobacco consumption, determine the knowledge, attitude, and practice of oral tobacco use amongst urban slum inhabitants. Study explains the importance of early initiation of tobacco cessation as a public health priority and it is an important intervention strategy in reducing the oral disease, Avoidance of tobacco consumption and ensuring early initiation of tobacco cessation.", "appendix": "Data availability\n\nNo data is associated with this article.\n\n\nAcknowledgement\n\nI would like to thank Statisticians and Members of the Research Guidance Unit, Research & Development Cell, DMIHER for their contribution in a part of sample size calculation to the completion of research manuscript.\n\n\nReferences\n\nBhawna G: Burden of Smoked and Smokeless Tobacco Consumption in India - Results from the Global adult Tobacco Survey India (GATS-India)- 2009-2010. Asian Pac. J. Cancer Prev. 2013 May 30; 14(5): 3323–3329. PubMed Abstract \| Publisher Full Text\n\nDobe M, Sinha DN, Rahman K: Smokeless tobacco use and its implications in WHO South East Asia Region. Indian J. Public Health. 2006 Apr 1; 50(2): 70–75. PubMed Abstract\n\nBenjamin N, Kadaluru UG, Rani V: Association of occupational stress and nicotine dependence with oral health status among public transit workers in Bangalore: A cross sectional study. J. Indian Assoc. Public Health Dent. 2020 Jan 1; 18(1): 35. Publisher Full Text\n\nGupta P, Ray C: Smokeless tobacco and health in India and South Asia. Respirol. Carlton. Vic. 2004 Jan 1; 8: 419–431. Publisher Full Text\n\nGupta V, Yadav K, Anand K: Patterns of Tobacco Use Across Rural, Urban, and Urban-Slum Populations in a North Indian Community. Indian J. Community Med. Off. Publ. Indian Assoc. Prev. Soc. Med. 2010 Apr; 35(2): 245–251. Publisher Full Text\n\nHenningfield J, Fant R, Tomar S: Smokeless Tobacco: an Addicting Drug. Adv. Dent. Res. 1997 Sep 1; 11: 330–335. Publisher Full Text\n\nMontero PH, Patel SG: CANCER OF THE ORAL CAVITY. Surg. Oncol. Clin. N. Am. 2015 Jul; 24(3): 491–508. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThakur JS, Paika R: Determinants of smokeless tobacco use in India. Indian J. Med. Res. 2018 Jul; 148(1): 41–45. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPanchbhai A, Bhowate R: MRI evaluation of involvement of parotid and submandibular glands by tongue squamous cell carcinoma. Oral Oncol. 2020 Mar 1; 102: 104557. PubMed Abstract \| Publisher Full Text\n\nChavan G, Chavan AU, Patel S, et al.: Airway Blocks Vs LA Nebulization- An interventional trial for Awake Fiberoptic Bronchoscope assisted Nasotracheal Intubation in Oral Malignancies. Asian Pac. J. Cancer Prev. APJCP. 2020 Dec; 21(12): 3613–3617. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim E, Hong S: First Generation Korean American Parents’ Perceptions of Discipline. J. Prof. Nurs. Off. J. Am. Assoc. Coll. Nurs. 2007; 23(1): 60–68. Publisher Full Text\n\nLohe V, Bhowate R, Parihar P, et al.: Evaluation of Lymph Nodes in Oral Squamous Cell Carcinoma by Diffusion-Weighted Magnetic Resonance Imaging, Apparent Diffusion Coefficient Mapping, and Fast-Spin Echo Magnetic Resonance Imaging. J. Datta. Meghe. Inst. Med. Sci. Univ. 2022 Jun; 17(2): 266. Publisher Full Text\n\nGoyal R, Singh CV, Jain S, et al.: Our Experience with Nasolabial Flaps in Soft Tissue Reconstruction of Oral Malignancy; Feasible Option in Rural Set Up. Indian. J. Otolaryngol. Head Neck Surg. 2022 Oct 1; 74(2): 2533–2538. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "189370", "date": "18 Aug 2023", "name": "Wasantha Jayawardene", "expertise": [ "Reviewer Expertise Substance use" ], "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 cross-sectional study protocol intends to estimate the prevalence and patterns of oral tobacco use and assess the motivating and demotivating factors associated with it amongst urban slum inhabitants in India. Reporting of methodology is not up to standard and the writing of the manuscript needs to be substantially improved.\nAbstract:\nPlease check this sentence and correct any errors: “Because everyone spits after using oral tobacco, there are more persons who spit in public due toits use”\nBackground is too long for an abstract. Please consider summarizing.\nIn abstract, include the sample size and country.\nIntroduction\nThese two sentences seem to be out of place or too general, and not relevant to the topic addressed in the article. Consider deleting: “The United Nations’ World Health Organization (WHO) oversees global public health. The primary goal of the WHO, according to its constitution, is to ensure that everyone has the best possible level of health.”\nThere are no references for some statements. For example, “Smokeless tobacco usage patterns share significant parallels with patterns of use of other addictive drugs.” Please add them.\nAgain, these statements are too general. Instead, consider adding a reference for a WHO initiative (if any) that targeted smokeless tobacco. Consider deleting: “The mandate of the WHO calls for global collaboration to enhance health, uphold world peace and harmony, and assist the vulnerable. It encourages a billion more people to participate in monitoring public health risks, coordinating emergency medical response efforts, promoting health and wellness, and implementing universal health care.”\nPlease indicate the country in this sentence, because it hasn’t been mentioned anywhere earlier in the manuscript: “Smokeless tobacco use, particularly in the eastern, northern, and north-eastern regions of the country….”\nWhat is Pan? “Pan is frequently taken with chewed smokeless tobacco products……”\nAuthors have not paid attention to the flow of information (poor transition from one point to another) and some sentences are out of place or irrelevant. For example, detailed description of tobacco processing is not necessary. I strongly suggest having this article edited by a professional English editor. Please replace “Older folks” with words that are more suitable for a scientific journal.\nRationale\nStay focused on smokeless tobacco and reduce information about tobacco in general and it’s health impacts.\nObjectives\nPlease do not use smokeless tobacco and oral tobacco interchangeable. Be consistent.\nCorrect this. The word “urban” is redundant: “…….urban slum in central urban India”\nSetting\nProvide more details about the study setting and sampling population.\nEligibility Criteria\nExclusion criteria are used for excluding ineligible participants (for example, based on a health condition) before they provide informed consent, and they are not invited to participate in the study. Therefore, not consenting to take part in the research study is not considered an exclusion criterion.\nSampling method indicates that the personal interview method was used but data sources section indicates that a questionnaire was used. Did you use an oral interview or a paper-based questionnaire? Please provide your instrument or rubric as a supplementary material.\nData Analysis Plan\nAuthors say that “……….. Selection bias will be addressed using systemic random sampling”. I’m curious if this is stratified random sampling, rather than systematic random sampling, and also, how you did it. Please provide more details of your sampling method.\nDiscussion\nMost of the information provided in discussion is not related to the topic and implications of the study.\nLimitations\nThis sentence needs to be corrected: “In this study, the early initiation of oral tobacco use amongst urban slum inhabitants, exclusive tobacco consumption, determine the knowledge, attitude, and practice of oral tobacco use amongst urban slum inhabitants.”\nAdditional major comment: Methodology is not adequately reported, and a lot of information is missing. Please follow the STROBE checklist for reporting of cross-sectional studies.\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? No", "responses": [] }, { "id": "208774", "date": "25 Sep 2023", "name": "Rooban Thavarajah", "expertise": [ "Reviewer Expertise Oral and Maxillofacial Pathology", "Smokeless tobacco", "Areca nut and products", "NCD and Oral Health", "Cystogenesis" ], "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\nIt is universally agreed that tobacco in any form causes a myriad of health issues. In India, there is a notable shift of tobacco use from smoked forms to smokeless forms as revealed by several large scale studies. To formulate targeted or focussed policies – there is a sub-par data with for smokeless forms as compared to the smoked forms. It is widely recognized that bio-psycho-economic-social constructs play a crucial role in tobacco usage. Hence the need for this study is justified. My comments are as follows:\nThe sentence such as “Because everyone spits after using oral tobacco, there are more persons who spit in public due toits use” do not add meaningful contribution to the abstract or the protocol. Authors can remove such irrelevant, non-focussed sentence(s) to keep the focus of the article restricted to central theme. The abstract fails to justify the need for the study or the lacunae in the data to take policy based decisions.\nThe first paragraph of the introduction is not focused and misleading from the central theme of the protocol and most importantly, unreferenced. In the second paragraph, authors use the term Pan and Pan masala without defining it properly. Government of India has clearly defined it and Pan masala is a no-tobacco containing entity – but with areca nut – requesting to visit the page: https://ntcp.mohfw.gov.in/surveys_reports_publications and https://ntcp.mohfw.gov.in/assets/document/surveys-reports-publications/NIHFW-report-Evidence-assessment-Harmful-effects-of-consumption-of-gutkha-tobacco-pan-masala-and-similar-articles-manufactured-in-India.pdf\n\nAuthors need to be careful in choice of term as such studies may form evidence for future actions and policies. Involving specific group such as transport employees or citing job stress to smokeless tobacco use is misleading and unwarranted for such study as the focus of study in urban slum – hence such mis-construct may mislead and divert the intended goals of the study. Authors need to focus the words carefully. The introduction is superfluous and does not present a strong argument for the need of study, knowledge or data gap that exists. Authors claim the GTYS Indian data as – “India are still extremely speculative and non-representative” but fail to establish the why these were speculative and non-representative – hence their argument fails. Authors have preferred to write hundreds of words after stating primary goals of the study and that needs to be curtailed.\nThe rationale part fails to say how this study would increase the knowledge on the subject matter and how it would help to frame better polices for combating smokeless tobacco usage. Instead it focusses on what is already known in the domain.\nFor the methodology, operational definition of slum, tobacco (type/ frequency/ intensity/duration - pack years or equivalence), quantification of socio-economic factors, education etc., motivational and demotivational factors are missing. It is pertinent to note that authors prefer to use GYTS-GATS format, which they considered to be “extremely speculative and non-representative”.\nBetter inferential statistics have to be planned to draw meaningful conclusions. Mere descriptive statistics would not be helpful to make recommendations.\n\nIs the rationale for, and objectives of, the study clearly described? No\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [] } ]	1	https://f1000research.com/articles/12-847
https://f1000research.com/articles/12-8/v1	04 Jan 23	{ "type": "Research Article", "title": "Reliability of the 44-question Home Fall Hazard Assessment Tool and personal characteristics associated with home hazards among the Thai elderly", "authors": [ "Yuwadee Wittayapun", "Jiraphat Nawarat", "Sarawut Lapmanee", "Lynette Mackenzie", "Charupa Lektip", "Yuwadee Wittayapun", "Jiraphat Nawarat", "Sarawut Lapmanee", "Lynette Mackenzie" ], "abstract": "Background: The 44-question Thai Home Fall Hazard Assessment Tool (Thai-HFHAT) was developed to assist healthcare professionals in identifying the risk of falls among community-dwelling elderly from their home environment. However, the reliability of this tool has not been studied. This study aimed to examine reliability of the 44-question Thai-HFHAT and determine the person characteristics associated with home hazards. Methods: A descriptive cross-sectional study design was used for this research. The participants in this study were 51 elderly people from various types of Thai houses: a one-story elevated house, a one-story non-elevated house, and a house with two or more floors, 51 caregivers of elderly patients and 5 village health volunteers (VHV). All participants answered 44 Thai-HFHAT questions to determine inter-rater and test-retest reliabilities. The reliabilities were analyzed using an intra-class correlation coefficient (ICC). Personal characteristics including sex, occupation, and education were used to identify the factors affecting home hazard and linear regression was used to analyze. Results: The ICC of inter-rater reliability of the 44-question Thai-HFHAT was 0.74 (95% CI: 0.57-0.84) and the test-retest reliability was 0.80 (95% CI: 0.64-0.88) for the elderly, 0.80 (95% CI: 0.65-0.89) for the caregivers and 0.70 (95% CI: 0.477-0.83) for the VHV. Personal business career and education level grade 1-3 are less than 0.05, which showed these factors had a significant relationship with the 44-question Thai-HFHAT score as dependent variable. Conclusions: The 44-question Thai-HFHAT is suitable for the home hazards assessment among the elderly in Thailand. Further studies are needed to investigate changes in the house environment after using the 44-question Thai-HFHAT to determine which changes can reduce the risk of fall.", "keywords": [ "elderly", "falling", "hazard control", "prevention", "reliability" ], "content": "Introduction\n\nFalls among the elderly are considered a major public health problem, becoming the second leading cause of death and unintentional injuries1 (https://www.who.int/news-room/fact-sheets/detail/falls). Thailand’s Department of Disease Control has predicted that during 2017-2021, falls among the Thai elderly will account for 27.0% of deaths in the elderly, resulting in a death rate due to falls among Thais of 50 per 100,000 populations https://www.dop.go.th/th/know/side/1/1/1159.\n\nThe precipitating cause for falls in the elderly involved the interaction of various risk factors categorized as intrinsic or extrinsic.2 Muscle weakness of the lower extremities and balance impairment were the most important intrinsic factors for the fall.3 In addition, extrinsic factors such as poor housing conditions, inadequate lighting, or slippery floors were also considered mediators in precipitating falls.4 However, most of the evidence comes from high-income countries. Despite the significant burden of falls, prevention strategies are not prioritized in the policy agendas of government in low- and middle-income countries.5 Therefore, identifying potential hazards in Thai houses with an appropriate home hazard screening tool is an effective measure to prevent falls and reduce the risk of falls among the elderly.6\n\nIn Thailand, Thai Fall Risk Assessment Test (Thai-FRAT) is a widely used tool to screen risks of fall.7–9 Of a total of 6 items of Thai-FRAT, there is only one item to evaluate home environmental risk: “Do you live in a traditional Thai house built with an elevated ground floor exceeding 1.5 meters?”. Therefore, the 69-question Thai Home Falls Hazards Assessment Tool (Thai-HFHAT) was designed as a self-reported screening tool to assess the risk of falls at home and is considered suitable for use in Thailand. Psychometric properties of the 69-question Thai-HFHAT were acceptable.10 However, it is time-consuming and difficult for elderly users to precisely complete all questions.\n\nA subsequent study investigated the development of the 44-question Thai-HFHAT based on the instrument design and methodology of the original Thai-HFHAT. The Cox proportional hazard model using stepwise variable selection methods was used to re-design the 69-question Thai-HFHAT.11 There was a report of psychometric properties of 44-question Thai-HFHAT as the adjusted hazards ratio (HR) was 1.26 (95% CI: 1.20-1.33), a cut-off was 18 points, the sensitivity and specificity were 0.93 and 0.72, and the area under the receiver operating characteristic curve (AuROC) was 0.90.12 In addition, the study also found that the 44-question Thai-HFHAT requires only 30 minutes for elderly users to complete all the questions. Occasionally, due to the inability to answer all the elders' questions in practice, the remaining questions were answered by a caregiver or a village health volunteer for the elders. However, the reliability of this tool has not been studied. In order for the 44-question Thai-HFHAT to have psychometric properties in all aspects, a reliability study is required.\n\nStudies on home hazards frequently investigate the area where the hazards are present, the numbers of hazards in the home and how these hazards could contribute to falls.13,14 Such a unilateral approach does not take into account the characteristics of elderly and how these might make the home environment more hazardous. Romli et al. was to investigate the elderly’s characteristics that contribute to home hazards. Lower educational attainment, greater number of home occupants, lower monthly expenditure, and younger age were the factors associated with home hazards.15 The researcher proposes that elderly Thai participants’ characteristic will correlate with the number of home hazards Therefore, this study also aimed to determine the Thai elderly’s characteristic factors contributing to home hazards.\n\n\nMethods\n\nThis study was approved by Institutional Review Board of Walailak University (approval number WUEC-20-302-01) on September 16, 2020.\n\nWritten informed consent was obtained from each of the participants.\n\nA descriptive cross-sectional study design was used to study the area at risk of falling, personal factors, and reliability of the 44-question Thai-HFHAT. This study was conducted in Tha Khuen Sub-District, Tha Sala District, Nakhon Si Thammarat.\n\nThe target population consisted of Thai elderly aged 60 years or over, with a total number of 2,552 adults residing in Tha Khun Subdistrict, Tha Sala District, Nakhon Si Thammarat Province (https://www.dop.go.th/th/know/1). Inclusion criteria were those who achieved fluency in the Thai language. Exclusion criteria were those who could not perform activities of daily living (ADLs) according to Barthel ADLs Index and had dementia determined by the Mini Mental State Examination-Thai 2002.16 Researchers approached the particicpants at their homes to explain the study. 51 elderly people, who passed the exclusion and exclusion criteria as above, were chosen because this number was adequate for examining inter-rater reliability and test-retest reliability.17 Subjects were selected by stratified and quota sampling and categorized according to three types of Thai houses: one-story elevated house, one-story non-elevated house, and a two or more-story house. In addition, 51 caregivers who spend the most time caring for the elderly and five village health volunteers (VHV) with more than five years of experience were also recruited to examine inter-rater reliability for the level of reliability of the 44-question Thai-HFHAT. These different groups were chosen to help identify whether each group of subjects can be replaced by other groups when assessing the hazards in the event the elderly subject cannot complete the instrument by themselves in real life.\n\nThe 44-question Thai-HFHAT\n\nThe Thai-HFHAT is composed of 44 questions grouped into 7 sections/rooms. 4 items were used to assess hazards in a living room, 4 in a kitchen room, 5 in a garage, 6 for house curtilage, 7 in stairs, 8 in a bedroom, and 10 in a bathroom. Also, the instrument contained a drawing for each room to help the elderly to identify hazards more easily.\n\nThe Barthel Activities of Daily Living Index\n\nThis is an assessment tool for evaluating ADLs for the performance of daily activities by elderly in 10 activities.16 The elderly participants were then classified into three groups according to the scores received: those who were completely independent and able to help others (ADL scores: ≥12), those who were moderately dependent and spent most of their time in their home (ADL scores: 5-11), and those who were completely dependent or disabled (ADL scores: 0-4).\n\nThe Mini Mental State Examination-Thai 2002 (MMSE-Thai 2002)\n\nThis is a Thai version of the cognitive impairment assessment tool for the Thai elderly.16 The cognitive impairment of the elderly can be preliminarily determined when the elderly who received no formal education had MMSE-Thai scores of ≤14, when the elderly who received only upper secondary education had scores of ≤17, and when the elderly who continued their education received a score of ≤22.\n\nData on demographic characteristics of the elderly, caregivers, and VHVs were collected. Three groups of study subjects were asked to fill out the 44-question Thai-HFHAT. They were instructed to enter each room in their home and answer a list of questions for assessing fall hazards in each room using a guided drawing. Scoring of potential hazards from the screening tool was performed. High scores have been associated with an increased risk of falls. The study subjects were informed to complete the screening tool within 30 minutes. The hazard areas, the subject’s characteristic factors, and inter-rater reliability were conducted after obtaining data from all subjects.\n\nAll three groups were instructed to perform the second assessment a week later15 so that researchers could collect more data for examining test-retest reliability. During the assessment, the elderly, caregivers, and VHV subjects had to independently answer assessment questions, and no conversation was permitted. We considered the intraclass correlation coefficient (ICC) with values ranging from 0 to 1 suitable for the evaluation of inter-rater and test-retest reliability. The ICC results were classified as follows: values between 0.00-0.49 were classified as poor reliability, values between 0.50-0.74 as moderate, values between 0.75-0.90 as good, and 0.91-1.00 as excellent.18 Data collection started in August 2020 and ended in September 2020.\n\nAll data were recorded and entered using the statistical package software version 22 (SPSS Inc. Chicago, IL, USA). Mean and standard deviation (SD) were used to analyze the subjects’ characteristics. Frequency and percentage were used show the data of home hazard areas. Inter-rater and test-retest reliabilities were evaluated using an intra-class correlation coefficient (ICC), that is, ICC (2, k) and ICC (3, k), respectively. Mean score differences between the elderly, caregivers, and VHV subjects were evaluated using a One-Way ANOVA. Differences in mean scores from the first and the second visits (1 week apart) were analyzed using an independent-samples t-test. We used multiple linear regression to predict the independent factors, consisting of sex, occupation, and education level, affecting the 44-question Thai-HFHAT score.19,20 Information bias may arise from the use of the 44-question Thai-HFHAT. The researcher explained the assessment tool to the participants to help them understand the objectives, and that the presentation of the results that will be anonymized. So, nobody knows how each subject will be evaluated, so that subjects are confident that there will be no impact from the actual assessment.\n\n\nResults\n\nThis study included 107 study subjects, and the demographic characteristics of all subjects and fall history of the elderly subjects are shown in Tables 1 and 2, respectively. 59% of the elderly lived in a one-story non-elevated house, 55.8% had blurred vision, and 86.5% demonstrated normal balance ability (≥10 seconds of tandem standing). The underlying diseases of the elderly subjects included hypertension (46.2%) and hyperlipidemia (44.2%). Most caregivers had a close relationship with the elderly subjects (53.9%). The mean (±SD) duration of caregiving in the caregiver group was 21.73 (±5.71) hours/day or 6.88 (±0.83) days/week. The mean (±SD) working experience of the VHV subjects was 12.96 (±6.63) years.\n\n\n\n1 (20.0)\n\nThe areas at the most risk of fall risk are the bathroom (94.1%), bedroom (74.5%), living room (56.9%), kitchen room (37.3%), around the home (35.3%), garage (25.5%), and stair in the home (7.8%), respectively. The risk of falling in each room is shown in Figure 1.\n\nThe ICC for the 44-question Thai-HFHAT was 0.74 (95% CI: 0.57-0.84). The mean (±SD) scores of the elderly, caregiver, and VHV groups were 6.65 (±3.29), 5.37 (±3.22), and 4.88 (±2.65), respectively. The mean difference in scores for all three groups was statistically significant (p = 0.012), as shown in Figure 2.\n\nThe ICC for the 44-question Thai-HFHAT was 0.80 (95% CI: 0.64-0.88) for the elderly group, 0.80 (95% CI: 0.65-0.89) for the caregiver group, and 0.70 (95% CI: 0.48-0.83) for the VHV group. The mean difference in scores obtained before and after one week of the assessment of the elderly (p = 0.283), caregiver (p = 0.604), and VHV (p = 0.984) groups was not statistically significant. The average scores of the 1st and 2nd time of the elderly, caregivers, and VHV are shown in Figure 2.\n\nAs shown in Table 3, the values of variance inflation factor (VIF) are all less than 5 and all the tolerance values are more than 0.10.19 The p-value for all independent variables, that is, personal business career and education level grade 1-3 are less than 0.05, which shows they have a significant relationship with the dependent variable, 44-question Thai-HFHAT score.\n\na Dependent variable: 44-question Thai-HFHAT score (r = 0.41, r2 = 0.17, Adj. r2 = 0.12).\n\n\nDiscussion\n\n37 elderly participants in this study (72.6%) had no history of falls. This may be attributed to regular exercise of the subjects, as the 34 subjects (66.6%) performed a regular exercise routine. Our results are consistent with the study by Hopewell S. et al. (2018) who reported that the practice of regular exercise would decrease fall rates and reduce the risk of falls in the elderly.21 Of all elderly surveyed subjects, 27.5% reported a fall. This number is close to that predicted by the Thailand Department of Disease Control report on the prevalence of falls during 2017-2021, in which falls among Thai elderly account for 27.0% (https://www.dop.go.th/th/know/side/1/1/1159). The area of the home with the most falls was the bathroom at 94.1 %, consistent with several studies on both Thais and in other countries.22–25 The bathrooms are areas where water is trapped with no separation between wet and dry areas. In addition, the present step in the room, no toilet or seat with hanging legs, and no shower seat/shower chair are causes of most falls in the bathroom.\n\nThe inter-rater reliability of the study subjects using the 44-question Thai-HFHAT was moderate (ICC = 0.74) and the test-retest reliability among the elderly was good (ICC = 0.80). Our results indicated that the 44-question Thai-HFHAT is as reliable as the 69-question Thai-HFHAT, whose inter-rater reliability was good (ICC = 0.87) and the test-retest reliability was good (ICC = 0.87). In our study, the 44-question Thai-HFHAT had lower ICC than the 69-question Thai-HFHAT. This is probably because the study was conducted with 30 elderly and caregiver participants and 1 VHV participant, resulting in the moderate level of inter-rater reliability.10 The smaller sample size of the 69-question Thai-HFHAT slightly affected the evaluation of reliability, causing minor errors. However, the inter-rater reliability of the 44-question version was similar to that of the 69-question version.\n\nThe inter-rater reliability of the 44-question version was higher than the Modified HOME FAST-SR (Thai version) (ICC = 0.64).12 This is probably because the Thai-HFHAT was designed to have questions listed in an organized manner with drawings to help illustrate each room in a house, allowing subjects to identify home hazards at ease. However, the text in the HOME FAST-SR may have been confusing. For instance, in the HOME FAST-SR question 8b asks “Does it take you several attempts to get up out from your sitting chair?”, and question 8c asks “When you lower yourself into the chair, can you do it without falling back on the chair?”. These two statements may have caused confusion that could lead to medical measurement errors.26\n\nWe found that the elderly subjects had a higher mean home hazard rating, followed by caregivers and VHV subjects. This is likely because most of our elderly subjects had a health issue and considered falling one of the health issues that cause the most damage,27 prompting the elderly to pay more attention to risk factors that contribute to falls than caregiver and VHV groups. Also, the difference in mean home hazard ratings between the elderly and VHV subjects was statistically significant (p = 0.012). Our results are consistent with the previous study by Morgan et al. (2005) who investigated the reliability of a self-report home hazard screening tool and found some questions, i.e. “Is lighting suitable for activities?”, could not be precisely answered by looking around the home environment. Such questions were viewed by the elderly subjects as increasing the risk of falls, whereas the VHV subjects may not.28 Thus, the self-report 44-question home hazard screening tool was preferred for the home hazards assessment among the elderly. In our study, the mean ratings of the 44-question Thai-HFHAT among the elderly, caregivers, and VHV groups were varied in the first and second assessments. We found a slight decrease in the mean rating of the elderly subjects on the second visit. This may be due to changes in the behavior of the elderly subjects and in the home environment between the first and the second visits. The study subjects may have removed obstacles like power cords from walkways before the second home visit. This phenomenon is called “reactivity” and can occur as a result of administering an instrument to the study subjects multiple times. Subjects become sensitized with the instrument and “learn” to respond when they perceive how they are expected to respond.29\n\nElderly participants with higher education levels had lower number of home hazards. These elderly participants might have greater awareness and more access information to assist with improving the safety of their home environment. Higher educational attainments are likely to be associated with better income and socioeconomic status, and therefore greater affordability for safer housing and home modification.30 Moreover, home hazards appeared to be associated with occupation. This study found that the group who were working in their own homes as housekeepers had a higher risk of falling, which may be caused by the clutter in the home.\n\nThe main limitation of our study was the small number of the sample size. To achieve the valid generalization that covers most types of Thai houses, this study should have been conducted with a larger sample size to ensure the applicability of the screening tool. Further studies are needed to investigate the changes in house environment after using the 44-question Thai-HFHAT to determine what particular changes could reduce fall risk. Finally, the 44-question Thai-HFHAT was developed in the Thai version. Therefore, cross-cultural translation of 44-question Thai-HFHAT is important for widespread use.\n\n\nConclusions\n\nOur study confirmed that the 44-question Thai-HFHAT is suitable for the home hazards assessment among the elderly in Thailand.\n\n\nAuthor contribution\n\nConceptualization, CL; Data curation, CL, YW; Investigation, CL, YW, JN, SL, LM; Methodology, CL, YW, JN, LM; Project administration, CL; Supervision, JN, SL, LM; Writing-original draft, CL, SL; Writing-review & editing, CL, RP, JN, SL, LM.", "appendix": "Data availability\n\nfigshare: Underlying data and extended data of Reliability on the 44-question Home Fall Hazard Assessment Tool and Personal Characteristics Associated with Home Hazards among thein Thai Elderly. https://doi.org/10.6084/m9.figshare.c.6239961.v1 31\n\n‐ General information of elderly. https://doi.org/10.6084/m9.figshare.21382278\n\n‐ General information of caregiver. https://doi.org/10.6084/m9.figshare.21343374\n\n‐ General information of village health volunteer. https://doi.org/10.6084/m9.figshare.21343380\n\n‐ 1st test done by elderly. https://doi.org/10.6084/m9.figshare.21343383\n\n‐ 1st test done by caregiver. https://doi.org/10.6084/m9.figshare.21343413\n\n‐ 1st test dons by VHV. https://doi.org/10.6084/m9.figshare.21343431\n\n‐ 2nd test done by elderly. https://doi.org/10.6084/m9.figshare.21343464\n\n‐ 2nd test done by caregiver. https://doi.org/10.6084/m9.figshare.21343470\n\n‐ 2nd test done by VHV. https://doi.org/10.6084/m9.figshare.21343476\n\n\n\n- Supplementary Table 1. https://doi.org/10.6084/m9.figshare.21304887\n\n- Inform consent. https://doi.org/10.6084/m9.figshare.21304920\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 thank all of the elderly who participated in the study.\n\n\nReferences\n\nKramarow E, Chen LH, Hedegaard H, et al.: Deaths from unintentional injury among adults aged 65 and over: United States, 2000-2013. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMorgan R, De Vito C, Stevens J, et al.: A self-assessment tool was reliable in identifying hazards in the homes of elders. J. Clin. Epidemiol. 2005; 58: 1252.e1–1252.e21. PubMed Abstract \| Publisher Full Text\n\nHendrickson AR, Massey PD, Cronan TP: On the test-retest reliability of perceived usefulness and perceived ease of use scales. MIS Q. 1993; 17: 227–230. Publisher Full Text\n\nRomli MH, Tan MP, Mackenzie L, et al.: Factors associated with home hazards: Findings from the Malaysian elders longitudinal research study. Geriatr. Gerontol. Int. 2018; 18(3): 387–395. PubMed Abstract \| Publisher Full Text\n\nLektip C:Underlying data and extended data of Reliability on the 44-question Home Fall Hazard Assessment Tool and Personal Characteristics Associated with Home Hazards among thein Thai Elderly. figshare. [Dataset]. Collection. 2022. Publisher Full Text" }	[ { "id": "161483", "date": "14 Feb 2023", "name": "Machiko R Tomita", "expertise": [ "Reviewer Expertise Fall prevention", "smart house", "e-health in gerontological population." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 purposes of the study are to establish reliability of 44-item home fall hazard assessment tool for Thai older adults and to find personal characteristics associated with the identified number of fall risks. The reliability section is done correctly but can be improved further.\n\nOne of the most comprehensive studies about reliability and validity of home hazard to prevent falls in older adults is missing1.\n\nThis study is a methodological study not cross-sectional.\n\nA study replication cannot be done easily. Explain how the sample size was determined. Fifty-one is enough for inter-rater and test-retest reliability but not enough for a regression analysis. Make inclusion criteria of ADL and MMSE clearer. What are the compositions of 107 participants? Fifty-one older adults, 47 caregivers, and 5 VHS make only 103.\n\nPersonal characteristics should include those related to a fall risk, in addition to demographic information. For example, falls in past one year, no falls or no vicarious falls so far, experiences in fall related injury and hospitalization, MMSE and ADL scores, readiness to make home safer, dizziness, balance problems etc. should be included. However, the sample size is too small for a multiple regression.\n\nIn Discussion, \"...the group who were working in their own homes as housekeepers...\" does not make sense. Revise this sentence.\n\nWhen we deal with human being for research, we use the word \"participants\" rather than \"subjects\". In Table 1, the statistical comparisons among these three groups are made; however, it is not the purpose of this study; therefore, they are not necessary. Descriptive statistics is sufficient.\n\nOverall impression of this study is that authors may be able to do more meaningful analyses using existing data for the personal characteristics part, although it has to be based on hypotheses derived from literature review.\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? Yes", "responses": [ { "c_id": "9357", "date": "21 Feb 2023", "name": "Charupa Lektip", "role": "Author Response", "response": "1. One of the most comprehensive studies about the reliability and validity of home hazards to prevent falls in older adults is missing. Answer: I will include that study in the discussion section of my research to discuss the similarities and differences of reliability and validity. 2. This study is a methodological study not cross-sectional Answer: This study is a prospective study 3. A study replication cannot be done easily. Explain how the sample size was determined. Fifty-one is enough for inter-rater and test-retest reliability but not enough for a regression analysis. Make inclusion criteria of ADL and MMSE clearer. What are the compositions of 107 participants? Fifty-one older adults, 47 caregivers, and 5 VHS make only 103. Answer: - 51 elderly people were adequate for examining inter-rater reliability and test-retest reliability following the reference in the article\" Rating the methodological quality in systematic reviews of studies on measurement properties: a scoring system for the COSMIN checklist\" that recommends 50-99 subjects are Good sample size. - I think a sample of 51 is sufficient for a regression analysis because correlation statistics will use 10-20 times the variable. And my main objective studies about the reliability and validity of home hazards to prevent falls in older adults. - I exclude those who were completely dependent or disabled (ADL scores: 0-4) and those who received no formal education had MMSE-Thai scores of ≤14, when the elderly who received only upper secondary education had scores of ≤17, and when the elderly who continued their education received a score of ≤22. - The compositions of 107 participants - Fifty-one older adults, 51 caregivers, and 5 VHV. 4. Personal characteristics should include those related to fall risk, in addition to demographic information. For example, falls in the past year, no falls or no vicarious falls so far, experiences in fall-related injury and hospitalization, MMSE and ADL scores, readiness to make home safer, dizziness, balance problems, etc. should be included. However, the sample size is too small for multiple regression. Answer: I think the variables you've suggested are very helpful in regression analysis. But with a small sample size, because the main objective of my work is to find reliability and validity, I only take personal characteristics variables that I show in the demographic table characteristics of study subjects. 5. In Discussion, \"...the group who were working in their own homes as housekeepers...\" does not make sense. Revise this sentence. Answer: I revise it to \" This research found that the group of people who acted as housekeepers in their own homes had a higher risk of falling, which may be related to the amount of clutter in the home. 6. When we deal with a human being for research, we use the word \"participants\" rather than \"subjects\". In Table 1, the statistical comparisons among these three groups are made; however, it is not the purpose of this study; therefore, they are not necessary. Descriptive statistics are sufficient. Answer: - I will use \"participants\" rather than \"subjects\". - I will only use descriptive statistics to descript the three groups. 7. Overall impression of this study is that authors may be able to do more meaningful analyses using existing data for the personal characteristics part, although it has to be based on hypotheses derived from the literature review. Answer: Thank you for your impression, I will add the literature review to support the personal characteristics associated with home hazards." } ] }, { "id": "158960", "date": "28 Feb 2023", "name": "Asmidawati Ashari", "expertise": [ "Reviewer Expertise Fall prevention and aged care research." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper by Lektip et al. analysed the reliability of the 44-question Thai Home Fall Hazard Assessment Tool (Thai-HFHAT) and determine the person characteristics associated with home hazards. This is an interesting study and the authors have collected a unique dataset using cutting edge methodology.\nOverall, the information presented represents valuable information regarding the feasibility of using (Thai-HFHAT). The main strength of this paper is that it addresses an interesting question and finds a novel solution based on a carefully selected set of rules and provides a clear answer in culturally context. The paper is generally well written and structured. The title and abstract are appropriate for the content of the text.\nHowever, in my opinion the paper has some shortcomings regarding some data analyses and discussion. The number of subjects for VHV group is too small (5) as compared to other groups. This number is too small which may affect the analysis. I also suggested to add further information on caregiver and VHF personal characteristic to explain any important aspects contributing to the variation in (Thai-HFHAT) score.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "9415", "date": "09 Mar 2023", "name": "Charupa Lektip", "role": "Author Response", "response": "Thanks for the compliment and advice on my research. Allow me to explain the number of 5 VHV, which seems too small for inter-rater and test-retest reliability. 1) The most important target group used by the 44-question Thai-HFHAT was the elderly, followed by caregivers, while VHV was the final target group in cases where the elderly were unable to use the assessment and lacked caregivers. 2) In Thailand, one VHV takes care of people in around 10-15 households. Similarly, this study used one VHV to assess 10 elderly homes. In this study, 51 elderly people were studied, so 5 VHVs were used to assess." } ] } ]	1	https://f1000research.com/articles/12-8
https://f1000research.com/articles/12-413/v1	18 Apr 23	{ "type": "Research Article", "title": "Validation of ageism scale for dental students in India: (Ageism Scale for Dental Students- India) – a cross sectional study.", "authors": [ "Ramya Shenoy", "Praveen S Jodalli", "Shushma Rao B", "Aishwarya Shodhan Shetty", "Manuel Thomas", "Kamal Shigli", "Leonardo Marchini", "Ramya Shenoy", "Shushma Rao B", "Aishwarya Shodhan Shetty", "Manuel Thomas", "Kamal Shigli", "Leonardo Marchini" ], "abstract": "Background: Ageism persists in many different societies as it is innate and subconscious in nature. Negative effects such as loneliness, mistreatment, and occupational discrimination are frequently present due to ageism. The dental students in our study were wary of the possible benefits of expensive dental care because ageism is rife in their field. There is no validated and reliable ageism scale to assess how dental students perceive ageism in India. The current study was carried out to validate the ageism scale for dental students in the Indian context. Methods: This was a cross sectional analytical study carried out among both males and females in Manipal College of Dental Sciences, Mangalore in which the instrument was 27-item Ageism scale for dental students. Content validity was done by six subject experts. The final version was administered to 213 students/Residents of dental school. The factorability of data was confirmed with KMO = 0.61 and Bartlett’s Test of Sphericity resulting in p < 0.001. Results: Final PCA model resulted in 15 items and six components that together accounted for 70.37% of overall variance. The six components had reliability ranging from marginal 0.51 (Component 6) to a high of 0.81 (Component 3). As per the gender differences by component females showed less ageism than men in “non-compliance” (-0.9(-1.66-0.14), p<0.05) and “practitioner perspective” (1.43 (0.84, 2.03), p<0.01). Statistical significance was seen in Barriers/concerns in dental treatment of elderly where residents showed reversed (1.4 (0.41, 2.38), p<0.01). Urban group showed more ageism for component ‘time restraint’ (-0.79 (-1.57, -0.02), p<0.05. Conclusion: Preliminary validation resulted in 15 item scale with six components with acceptable validity of the ageism scale and could be further tested in large samples. This scale will help recognize ageism in Indian context and provide necessary information to make changes in the curriculum as required.", "keywords": [ "agesim", "dental students", "geriatric dentistry", "oral health", "validation" ], "content": "Introduction\n\nButler coined the phrase “Age-Ism” in 1961 to describe age discrimination, or prejudice between different age groups.1 World Health Organization defines ageism as “the stereotyping, prejudice and discrimination toward people on the basis of age”.2 Ageism is found to be a persistent factor across various cultures primarily because it is inherent and subconscious in nature. The negative effect of ageism is found to be more pronounced in older individuals. The common detrimental consequences of institutional ageism include discrimination in the workplace, old job applicants receiving fewer positive ratings than the young applicants, mistreatment, loneliness and patronising speech.3,4 This can also be viewed as a consequence of negative portrayal of older people in media.5,6\n\nAging, now being a global phenomenon due to the prevalence of chronic disease and multimorbidity among elderly patients, requires essential attention and care. This reveals the importance of understanding “ageism” which is pervasive among health care providers and institutions. It is found that “elderspeak” is often employed while communicating to older patients which can be related to negative effects for the geriatric patients as it results in lowering their self-esteem and confidence.7 It also affects the treatment preferred, offered and provided.8 Ageist attitudes fundamentally alter how problems are portrayed and the kinds of solutions that are put forth, which limits the development of acceptable policies about ageing.5\n\nThere is also evidence that ageism is pervasive among the dental students.3 Research by Veenstra et al. and Rucker et al. reveals the feeling of empathy and respect towards older patients was observed among dental students.9,10 However, these students were apprehensive about the potential benefit of expensive dental treatment. Additionally, recent studies illustrate the students facing “patient compliance issues” and “preconceived notions about dental treatment” provided to older patients.11 Moreover, dental colleges where separate gerodontology departments are not required as per regulatory body and the absence of non-emphasis of geriatrics in dental schools can lead to negative consequences.6 To overcome such consequences, it is required to have culturally adaptive ageism scale for dental students to measure their perception. A valid and trustworthy ageism scale is not yet available to assess how dental students perceive ageism in India. In light of this, the current study was conducted to validate the ageism scale for dental students created in the United States (US)3 to an Indian context by subject experts, final year dental undergraduate students and residents. It also intended to gauge if there are any differences among the male and female participants as observed in literature.3,10 Differences in ageism in relation to other demographic data such as age, area of residence, year of study and history of living with elderly was also intended to be examined. The research objectives were to measure the construct validity, structural validity, and internal consistency of the ageism scale for dental students by final year undergraduate dental students and residents, as well as to quantify the content validity of the scale by subject experts.\n\n\nMethods\n\nThis was a cross-sectional analytical study carried out in Manipal College of Dental Sciences, Mangalore. The mode of conducting was through online platform conducted concurrently from March 2021 to June 2021.\n\nResidents and final-year undergraduate dentistry students were the eligible participants for this study. The sample size for the present study was based on at least five individuals responding for each item while subjecting to factor analysis.12 By implementing this method, the sample size would be 205. Following the universal sampling approach, the ageism scale for dental students was distributed to 250 final-year undergraduate dental students and residents after approval from the institution's head had been obtained in accordance with the inclusion criteria. The use of the universal sampling method eliminated the possibility of bias in the selection of participants. Finally, 213 students responded to the ageism scale. The method of self-reporting allowed for the identification of demographic information such as gender about the participants.\n\nPermission of Head of the Institution was taken. Institutional Ethics Committee clearance was obtained before commencement of the study (Protocol no. 21002, 9th April 2021). Informed consent was electronically collected along with the responses to the ageism scale questionnaire,13 and participation was completely voluntary. Confidentiality of the participants was maintained.\n\nDental students' ageism scale: The initial version of the survey had a total of 27 items to measure ageism attitudes among dental students. A team of professors with experience in teaching geriatric dentistry from the United States and Europe created the original version.3 A 27-item ageism scale specifically tailored for assessing ageism among dental students, which considers the specificities related to geriatric dentistry. The original version was tailored to developed countries health set –up. This is measured on six-point Likert scale (“Strongly disagree” = 1; “Disagree” = 2; “Slightly disagree” = 3; “Slightly agree” = 4; “Agree” = 5; “Strongly agree” = 6). The total score value is directly proportion to the understanding of the individual about ageism.\n\nWe asked six subject specialists with at least ten years of teaching experience and knowledge in working with senior citizens to take part in the study. None of these specialists were a part of the research team of this study. Through the online platform, the content was validated. The form's filling instructions was explained in detail through the information sheet.14 The specialists were asked to review each item critically and were asked to provide score for each item from 1 = “The item is not relevant to the measured domain”; 2 = “The item is somewhat relevant to the measured domain”; 3 = “The item is quite relevant to the measured domain”; 4 = “The item is highly relevant to the measured domain” and written comment to improve the relevance of items. Once they had fully provided the scores on all the items, the experts were requested to submit their comments to the researcher. We all agreed that “Old age home/Senior citizen house/Senior dwelling” should be used in place of “nursing home” for Question 8 and Question 24. Since none of the other items on the agism scale made reference to where the elderly resided, none of the phrases in those 25 remaining questions needed to be modified. This was then administered to the 213 final-year undergraduate dentistry students and residents who were open to taking part in an online platform. They received detailed directions14 on how to complete the electronic form.\n\nStatistical Package for Social Sciences (SPSS) version 26.0 (SPSS, Inc., Chicago, IL, USA) was used to calculate the results based on the data obtained.15 Values obtained from the participants were computed to obtain descriptive and inferential statistics. A test of discriminant validity was conducted to look for differences based on gender, life history with senior people, year of study, and living in an urban or rural region. Mean and standard deviation was calculated for “age” and frequency with percentage was calculated for other demographic data. The Independent t test was used wherever applicable for the quantitative data obtained and participant responses which had missing data were excluded from the analysis. To measure item-scale correlation and inter item correlation Pearson correlation coefficient was used.\n\nThe reliability of the scale was evaluated using item analysis, internal consistency, and split-half test.\n\nThe goal of principal component analysis is to increase the sum of the squared loadings for each factor that is separately extracted. The loadings obtained from any other method of factoring would not explain as much variance as the principal component factor so, Principal component method of factor extraction used to carry out factor analysis for construct validity, structural validity, and internal consistency. In order to achieve what is referred to as “simple structure” in data, the varimax rotation approach is used. This method maximises the variance of the loadings inside each factor. Large loadings on a small number of variables describe the factors produced by the varimax rotations’ solution and increases the accuracy of construct validity, structural validity, and internal consistency while using the principal component method.16 The Kaiser-Meyer-Olkin (KMO) test and Bartlett’s sphericity test was used to check the adequacy of the factorial analysis. A KMO greater than 0.60 and Bartlett’s significance p < 0.05 were considered acceptable.\n\nEigen values, also known as latent root in Principal Component method is the sum of squared values of factor loadings relating to a factor/component.16 All components with Eigen values > 1.0 were initially extracted, and the number to keep was chosen using a combination of Scree Plot analysis and the overall variance that each component contributed. Items that (a) loaded poorly on any component or (b) cross-loaded across several components were removed as the Principal Component Analysis (PCA) was run iteratively. PCA was continued until the strongest and most parsimonious final set of items was reached. Cronbach's Alpha was used to assess the internal consistency of the final components, with a minimum acceptable value of 0.60 and an ideal value of 0.80. To identify items that were either possibly redundant due to multicollinearity (r\|0.80\|) or not meaningfully associated to any other item (max r\|0.30\|), correlation matrix of all 27 items was evaluated. P < 0.05 was considered to be the level of significance. The content validity of the scale was analysed using Content Validity Index (CVI).17\n\nCalculating CVI17\n\nThere are two types of CVI: scale-based CVI and item-based CVI (S-CVI). There are two ways to calculate S-CVI: the proportion of items on the scale that receive a relevance value of 3 or 4 from all experts (S-CVI/UA), and the average of the I-CVI scores for all items on the scale (S-CVI/Ave).6 The following table summarises the formula and definition of the CVI indices.\n\nThe definition and formula of I-CVI, S-CVI/Ave and S-CVI/UA.\n\nThe above-mentioned calculation led to the conclusion that I-CVI, S-CVI/Ave, and S-CVI/UA meet satisfactory levels, indicating that the scale of questionnaire’s content validity has been attained to a satisfactory level. When writing the report, this study used the STROBE checklist.\n\n\nResults\n\nOf the 250 students a total of 213 undergraduate, including 30 male and 183 female, consented to take part in the study. Those participants who did not provide consent were not included in the study. Since this was a cross-sectional study, participation was limited to a single time point where questionnaires were sent electronically to all final year students and residents. Their age, gender and year of study were recorded along with history of living with elderly and urbanicity. The ‘semi urban’ was combined with ‘not urban’ as there was low sample size for that group (Table 1).\n\n1 Semi-urban was combined with “Not urban” due to low sample size.\n\nFirst, all items were coded so that a higher value indicated more Ageism, so ten items were reverse-coded where 1 = “Strongly Agree” and 6 = “Strongly Disagree”. We indicate in our results whenever one of these items are mentioned that it was reverse coded for clarity.\n\nThere were no items that posed a risk of biasing the PCA results due to a multicollinear or insignificant relationship with other items. The factorability of the data was confirmed with KMO = 0.61 and Bartlett’s Test of Sphericity resulting in p < 0.001. The final PCA model resulted in 15 items and six components that together accounted for 70.37% of overall variance (Table 2). The six components had reliability ranging from marginal 0.51 (Component 6) to a high of 0.81 (Component 3). While not ideal, the small number of items on each scale, which directly impacts Cronbach’s Alpha, may be the cause of these coefficients.18\n\nStatistically significant findings are highlighted in the tables for easy identification. Gender differences by component shows a statistically significant difference in scores on Component 4 where males (M = 6.93, SD = 2.08) scored 0.91 points lower than females (M = 7.84, SD = 1.94), p = 0.02 and Component 6 where Males (M = 5.93, SD = 1.66) scored 1.43 points higher on average, (95% CI = 0.84 – 2.03) than females (M = 4.5, SD = 1.5), p < 0.001 (Table 3). Overall, there was one missing data when testing the gender differences and also 3 missing data for component 1, 2 and 5.\n\nResults of independent t- test for history of living with elderly based on the components had no statistically significant results (Table 4). There was one missing data in this comparison and 3 missing data for component 1, 2 and 5. While comparing differences by component for year of study statistically there was significant difference in component one which was barriers/concerns in dental treatment of elderly. The residents (M = 11.56, SD = 3.89) and final year students (M = 10.16, SD = 3.26) had a mean difference of 1.4 (95% CI = 0.41 – 2.38) indicating residents had more barriers/concerns in treating the elderly (p = 0.06) and there were 3 missing data for component 1, 2 and 5.\n\nThe students residing in urban areas (M = 7.86, SD = 1.86) felt that it was more time consuming to treat the elderly than when compared to those residing in not urban areas (M = 7.07, SD = 2.32) where the mean difference was 0.79 (p= 0.04) (95% CI = -1.57 - -0.02). Components 3, 4, and 6 each had one missing data, while 1, 2, and 5 each had three. All of the missing data entries were excluded for component-based analysis. Regardless of statistical significance, it is very important to note that the actual differences between groups are quite small, so results must be interpreted with caution.\n\n\nDiscussion\n\nThe ageism dental scale, which was validated for the Indian context, produced a 15-item questionnaire distributed into the following six components; Barriers/Concerns in dental treatment of elderly, Patient Compliance, Opinions of elderly, Non-Compliance, Treatment success rate and Practitioner perspective. Due to the low loading of these questions over the components in principal component analysis, the remaining twelve questions—including questions 1, 4, 7, 10, 11, 15, 18, 20, 22, 23, 26 and 27—were omitted in accordance with the Indian context.\n\nAs per the gender differences by component females showed less agism as compared to men in the component of “Time consuming” and there was also statistically significant difference regarding “practitioner perspective”. A similar result was seen in validation study carried out in USA10 whereas in the Greek version men showed more sympathy towards the elderly than women.19 There was no difference in any of the components while comparing gender in the German20 and Brazilian21 versions whereas in the French version men scored significantly lesser than women in component three which dealt with education around older patients care.22 Additionally, gender distinctions in factors 1 and 4 were discovered. Since they displayed significantly fewer ageist attitudes than male students in factor one (Q16 and Q17), female students tended to have greater compassion and empathy for the elderly; however, they found it significantly more difficult to obtain medical histories from elderly patients (Factor 4, Q2 and Q3).23\n\nThere was no significant difference when it came to comparison between having history of living with elderly or not regarding all components. Similar results were seen with the USA,10 German,20 Brazil21 and French versions.22 But in the Serbian version students who had older family members displayed much more “ageist” attitudes than those who did not, for one particular question.23\n\nStatistical significance was seen in component 1 (Barriers/concerns in dental treatment of elderly) where residents showed more agism than final year undergraduate students. Similar result is seen in Greek version where ‘Cost’ is the Barrier.19 For components 1 (“negative opinion of older people”) and 3 (“oral health care education”), the students from the three years of study had significantly different results in the French version.22 Two items (Q18 and Q27) in factor one (“Negative view of older adults’ life and dental treatment”) showed differences based on the study semester in the Serbian version.23 These differences among the various versions of the agism scale can be attributed to different cultural backgrounds.\n\nWhen comparing urbanity differences, urban group showed more agism than the non-urban group for the component of ‘time consuming’. Statistical significance was seen in rural and non-rural regarding ‘Value/ethics about older people’ and ‘Elderly patient being more appreciative of care’ in the Greek version of the scale.19 No such difference was seen in the Romanian version9 and Serbian version.23\n\nThere were 4 items from the agism scale under component 1 which are 16, 17, 8 and 19 in descending order of factor loading. Item 16 was also seen in the dual institution validation study in USA version of agism scale under the component “Preconceived notions about dental treatment”,10 under “Values/ethics about older people” in the Greek version19 and under the same category as this study in the German version,20 in component 2 (“education around older patients care”) of the French version22 and factor 1 (“Negative view of older adults’ life and dental treatment”) of the Serbian version.23 The Q17 was “whether elderly patients make it long enough to make investment worthwhile” and was seen in the US version under “Preconceived notions about dental treatment”,10 under the component “negative view of older patients” in Brazil version,21 under “Values/ethics about older people” in the Greek version,19 component 2 (“education around older patients care”) of the French version22 and factor 1 (“Negative view of older adults’ life and dental treatment”) of the Serbian version.23\n\n‘If the elderly are better off in old age homes?’ was the eighth question in the agism scale and it was seen under the components “negative view of older patients” in Brazil version,21 under “Values/ethics about older people” in the Greek version19 and “Patient compliance” factor in German version.20 The last item in this component in this study was Q19 which was seen in complexity of providing care for older adults” in Brazilian version,21 under “Barriers to dental care” factor in Greek version,19 “Practitioner’s perspective” in German version20 and factor 1 (“Negative view of older adults’ life and dental treatment”) of the Serbian version.23\n\nThis component had 3 items; 5, 6 and 9 where all three were reverse-coded so that higher score indicated more agism. The Q5 which asked if they pay more attention to their elderly patients was also seen in the Brazilian version of agism scale under the component “Positive view of older adults”,21 under “Dentist–older patient interaction” in the Greek version,19 component “Perceptions of the older and their value in society” in the Romanian version9 and “Dental care in younger and older patients” in the Serbian version.23 The question 6 was seen in component “Positive view of older adults” in Brazilian version,21 under “Dentist–older patient interaction” in the Greek version,19 under “Opinions about elderly” in the German version,17 “Perceptions of the older and their value in society” in the Romanian version9 and “Dental care in younger and older patients” in the Serbian version.23 The item 9 which was regarding elderly patients being more appreciative of the care provided was seen in the component Dentist–older patient interaction” in the Greek version19 and “Patient compliance” factor in German version.21\n\nThe questions 13 and 14, were under this component. They were also seen in the component “Patient compliance” in USA version10 and Greek version,19 under “negative view of older patients” in the Brazil version,21 “general negative view” in the French version22 and “ethical values about older people and patient compliance” in the Serbian version.23\n\nThe Q2 which was regarding the opinion that taking medical history from elderly patients was time consuming and Q3 being that taking medical history was complex were present in this component of our study, in the Brazilian version of agism scale under “complexity of providing care for older adults”21 and “difficulties in medical history taking” in the Serbian version.23\n\nThe items 12 and 21 were grouped in the ‘Treatment success rate’ component. In the German version Q12 was seen under the component “Opinions about elderly” and Q21 was seen in “Barriers/concerns on dental treatment in elderly”20 and under “Exposure to geriatric dental training and experiences” in the Romanian version.9\n\nThe questions 24 and 25 in this component were reversed so that higher score indicated more agism. Q24 was not seen in any of the versions of the agism scale and Q25 was seen Under “Barriers to dental care” in the Greek version,19 in “education around older patients care” of the French version22 and under “barriers to dental treatment” in the Serbian version.23\n\nAs seen above, questions 13, 14, 16 and 17 are included in the dual institution validation of agism scale carried out in USA10 but under different components than seen in our study. In the Greek version questions 5, 6, 8, 13, 14, 16, 17, 19 and 25 were included in the scale where Q19 is under the same factor “Barriers/concerns”.19 The questions that were included in the German version were 6, 8, 9, 12, 16, 19 and 21 among which Q9 and Q16 were under same components of “Patient Compliance” and “Barriers/Concerns”.20 In the Brazilian versions the similar questions included were 2, 3, 5, 6, 8, 13, 14, 17 and 19 but none of the components were similar.21 Only three questions i.e., 5, 6 and 21 were similar in the Romanian version of agism scale.9 The following five questions were present in the French version: Q16, 17, 13, 14, and 25.22 Highest similarity was seen with the Serbian version as the questions 2,3,5,6,8,13,14,16,17 and 25 were included in their version of agism scale and Q8, 16 and 17 were under the component “Negative view of older adults’ life and dental treatment”.23 In this study it was included in “barriers/concerns in dental treatment of elderly” indicating that though named differently they point towards the negative aspect of treating an elderly patient. Although the results of this study are comparable to those of other studies on the ageism scale for a diverse nation like ours, generalizability is constrained.\n\nSince this study is done on a single institution the generalizability of its result is limited. In-spite of being statistically significant the differences are small and interpretation must be done cautiously. Similar studies of validation should be carried out in different geographical and cultural areas which can help in constructing a single scale for our country.\n\n\nConclusions\n\nPreliminary validation resulted in a 15-item scale with 6 components with acceptable validity of the agism scale and could be further tested in large samples. The female participants had more concern for the elderly patients but had an opinion that treating them would be time consuming. The residents expressed more barriers/concerns while treating the elderly and urban students felt it was more time consuming.\n\nThese results necessitate the need for educating the dental students regarding care towards the elderly patients. This scale will help recognise agism in Indian context and provide necessary information to make changes in the curriculum as required.", "appendix": "Data availability\n\nFigshare. Responses of dental students to ageism scale: India. https://doi.org/10.6084/m9.figshare.21931383.v2. 15\n\nThis project contains the following underlying data:\n\nAgeism scale for dental student. (This dataset contains consent of the participants. It contains demographic data such as gender, age, year of study, months of clinical experience, attending gerodontology course, presence of elderly member in the family and area of residence. It also depicts the responses of dental students to each of the 27 items in the ageism scale.).\n\nThis project contains the following extended data:\n\n- Ageism Scale consent form (This document contains information sheet both to the subject experts and the participants. It also contains the consent form.) https://doi.org/10.6084/m9.figshare.22001531.v1. 14\n\n- Agism Scale Questionnaire (This document contains survey instrument which is the ageism scale for dental students for both the subject experts and students. It also contains questions on demographic data.) https://doi.org/10.6084/m9.figshare.22001510.v1. 13\n\n- STROBE Checklist (This file contains data of STROBE checklist for this article. The corresponding page numbers for the questions in the checklist are mentioned accordingly.) https://doi.org/10.6084/m9.figshare.22121153.v1\n\nData are available under the terms of the Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.\n\n\nReferences\n\nButler RN: Age-ism: Another form of bigotry. Gerontologist. 1969; 9: 243–246. S2CID 42442342. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization: Ageing and Ageism. (Accessed on 11/02/2020). Reference Source\n\nRucker R, Barlow PB, Hartshorn J, et al.: Development and preliminary validation of an ageism scale for dental students. Spec Care Dent. 2018; 38(1): 31–35. PubMed Abstract \| Publisher Full Text\n\nAgeism and Age Discrimination. Accessed on December 3rd, 2022 at 11.50 am. Reference Source\n\nAyalon L, Dolberry P, Mikulioniene S, et al.: A systematic review of existing ageism scales. Ageing Res. Rev. 2019; 54: 100919. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShigli K, Nayak SS, Jirge V, et al.: Current status of gerodontology curriculum in India and other parts of the world: A narrative review. Gerodontology. 2020; 37(2): 110–131. Publisher Full Text\n\nO'Connor BP, St Pierre ES: Older persons' perceptions of the frequency and meaning of elderspeak from family, friends, and service workers. Int. J. Aging Hum. Dev. 2004; 58(3): 197–221. PubMed Abstract \| Publisher Full Text\n\nSchroyen S, Adam S, Marquet M, et al.: Communication of healthcare professionals: Is there ageism? Eur. J. Cancer Care (Engl). 2018; 27(1): 1–10. Publisher Full Text\n\nVeenstra L, Barlow P, Kossioni A, et al.: Translation and validation of the ageism scale for dental students in Romanian (ASDS-Rom). Eur. J. Dent. Educ. 2020; 25(June): 12–17. Publisher Full Text\n\nRucker R, Barlow PB, Hartshorn J, et al.: Dual institution validation of an ageism scale for dental students. Spec Care Dent. 2019; 39(1): 28–33. PubMed Abstract \| Publisher Full Text\n\nLamprecht R, Guse J, Schimmel M, et al.: Benefits of combined quantitative and qualitative evaluation of learning experience in a gerodontology course for dental students. BMC Med. Educ. 2020; 20(1): 1–12.\n\nCetin FC, Sezer A, Merih YD: The birth satisfaction scale: Turkish adaptation, validation and reliability study. North Clin. Istanbul. 2015; 2(2): 142–150. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShenoy R, Jodalli P, Rao S, et al.: Agism Scale Questionnaire. figshare. Conference contribution.2023. Publisher Full Text\n\nShenoy R, Jodalli P, Rao S, et al.: Ageism Scale consent form. figshare. Conference contribution.2023. Publisher Full Text\n\nShenoy R, Jodalli P, Rao S, et al.: Responses of dental students to ageism scale: India. Dataset. figshare. 2023. Publisher Full Text\n\nKothari CR: Research Methodology - Methods & Techniques. Multivariate analysis techniques. Revised 2nd ed.Daryaganj, New Delhi: New Age International (P) Limited, Publishers; 2004; pp. 315–343.\n\nYusoff MSB: ABC of content validation and content validity index calculation. Educ. Med. J. 2019; 11(2): 49–54. Publisher Full Text\n\nPett MA, Lackey NR, Sullivan JJ: Making Sense of Factor Analysis: Evaluating and refining the factors. Thousand Oaks: SAGE Publications; 2003.\n\nKossioni AE, Ioannidou K, Kalyva D, et al.: Translation and validation of the Greek version of an ageism scale for dental students (ASDS_Gr). Gerodontology. 2019; 36: 251–257. PubMed Abstract \| Publisher Full Text\n\nMichalopoulou E, Bornstein MM, Schimmel M, et al.: Translation and validation of an ageism scale for dental students in Switzerland. J. Oral Sci. 2022 Jan 19; 64(1): 74–79. PubMed Abstract \| Publisher Full Text\n\nRucker R, Barlow PB, Fernandes B, et al.: Translation and preliminary validation of an ageism scale for dental students in Brazil (ASDS-Braz). Gerodontology. 2020; 37: 87–92. PubMed Abstract \| Publisher Full Text\n\nPiaton S, Barlow P, Kossioni A, et al.: Translation and preliminary validation of a French version of an ageism scale for dental students. Gerodontology. 2022 Sep; 39(3): 291–296. PubMed Abstract \| Publisher Full Text\n\nPopovac A, Pficer JK, Stančić I, et al.: Translation and preliminary validation of the Serbian version of an ageism scale for dental students (ASDS-Serb). Spec. Care Dentist. 2022; 42: 160–169. PubMed Abstract \| Publisher Full Text" }	[ { "id": "170036", "date": "23 Jun 2023", "name": "Chandrashekar Byalakere Rudraiah (B. R)", "expertise": [ "Reviewer Expertise I am a specialist in Public Health Dentistry and I have worked in assessing the oral health status of populations in rural", "urban", "and tribal areas including the geriatric population." ], "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 focussing on validating an ageism scale for dental students in Indian context was very essential keeping in mind the lack of such scale for assessing the perception of dental students who will face the task of treating geriatric patients in their routine practice. The scale to assess perception of dental students in India becomes more important as we do not have a specialized subject of gerodontology in the existing curriculum prescribed by dental council of India.\nStrengths of the article: The introduction highlights the gap in Indian context while citing relevant literature on importance of having such customized scale for dental students. The methodology used is described in detail so that the study is replicable. The factor analysis (Principal component analysis) and other statistical methods for assessing the reliability and validity of the tool are explained and are relevant and appreciate. The results are rationally interpreted and discussed by citing existing relevant literature.\nNovelty: This is the first of its kind scale that is customized for assessing perceptions of graduating dental students in Indian context. The socio-cultural differences between different regions of the world makes it essential to validate any scale to the local context, which was attempted in this research.The scale helps in eliciting differences in perceptions in relation to socio-demographic characteristics.\nRecommendation for future studies: A mixed method research design using this questionnaire in quantitative research along with in-depth interviews/focus group discussions will increase validity evidence. Response process validity could be elicited using retrospective verbal probing technique on a sample of patients. Known group validity evidence can be assessed by comparing the scores in existing study with a group of senior dental professional who are trained in gerodontology.\nExpected outcome: The article highlights the importance of a customized scale for Indian dental graduates and perhaps may eventually lead to the mandatory establishment geriatric oral health units in all dental colleges in the country. The training on geriatric oral health by a multidisciplinary team of experts under one roof will be an eventual anticipated outcome if future studies are conducted using this scale which is validated to Indian context.\nOverall, it is a good tool to be used further in different settings to get additional validity evidence.\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": "179877", "date": "13 Jul 2023", "name": "Parvati Iyer", "expertise": [ "Reviewer Expertise Educational research", "curricular innovation", "cultural competency", "critical thinking skills" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 such an interesting topic and is very relevant for young dental graduates! Here are my thoughts:\nThe paper concludes that the preliminary validation of the ageism scale for dental students in India was successful. The scale can be further tested in larger samples to enhance its validity and reliability. The findings highlight the importance of addressing ageism in dental education and making necessary changes to the curriculum. By recognizing ageism, dental schools can promote a more inclusive and compassionate approach to geriatric dentistry.\nInsights and Suggestions for Improvement:\nThe paper provides valuable insights into the prevalence of ageism among dental students in India and the need for a validated ageism scale. The study contributes to understanding ageism and its implications for dental education and patient care. Here are some suggestions for improvement:\nClarify the research objectives: The paper could provide a clearer statement of the research objectives at the beginning to guide readers and enhance the overall coherence of the study.\n\nProvide more details on the participants: It would be helpful to provide more information about the participants, such as their age range, demographics, and any potential biases in the sample selection process.\n\nExpand the discussion on cultural influences: The paper briefly mentions cultural influences on ageism but could further explore how cultural factors specific to India might shape dental students' perceptions of ageism. This could enhance the understanding of ageism within a cultural context.\n\nConsider implications for dental education: While the paper briefly mentions the need for changes in the curriculum, it could expand on the specific areas where dental education can address ageism, such as communication skills, ethical considerations, and patient-centered care for older adults.\n\nProvide recommendations for future research: The paper could offer suggestions for future research, such as exploring the relationship between ageism and the quality of dental care provided to older adults or investigating interventions to reduce ageism among dental students.\nBy addressing these points, the paper can enhance its clarity, depth, and practical implications, thereby contributing further to the field of geriatric dentistry and combating ageism in dental education.\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": "9917", "date": "19 Jul 2023", "name": "PRAVEEN JODALLI", "role": "Author Response", "response": "Dear reviewer, thank you for the suggestions 1. “Clarify the research objectives: The paper could provide a clearer statement of the research objectives at the beginning to guide readers and enhance the overall coherence of the study.” The research objectives were to quantify the content validity of the ageism scale by subject experts and measure the construct validity, structural validity, and internal consistency of the ageism scale for dental students by final year undergraduate dental students and residents studying in one of the dental colleges of India. 2. “Age range, demographics, potential bias in sample selection” These parameters already explained in Table 1 and under study population 3. “Expand the discussion on cultural influences: The paper briefly mentions cultural influences on ageism but could further explore how cultural factors specific to India might shape dental students' perceptions of ageism. This could enhance the understanding of ageism within a cultural context.” Assessing the cultural influence on ageism was not the objective of the study and the same is also mentioned in the limitations. 4.“Provide recommendations for future research: The paper could offer suggestions for future research, such as exploring the relationship between ageism and the quality of dental care provided to older adults or investigating interventions to reduce ageism among dental students” The following is added “The paper could offer suggestions for future research, such as exploring the relationship between ageism and the quality of dental care provided to older adults to reduce ageism among dental students” along with the existing recommendation” Similar studies of validation should be carried out in different geographical and cultural areas which can help in constructing a single scale for our country.” 5. “Consider implications for dental education: While the paper briefly mentions the need for changes in the curriculum, it could expand on the specific areas where dental education can address ageism, such as communication skills, ethical considerations, and patient-centered care for older adults” This paper provides reasons for addition of geriatric dentistry in dental curriculum and to have a single window to treat older adults. This is to ensure that future oral health practitioners will have adequate knowledge, skill and empathy while treating older adults." } ] } ]	1	https://f1000research.com/articles/12-413
https://f1000research.com/articles/11-448/v1	21 Apr 22	{ "type": "Research Article", "title": "Malaria prevalence in Commune 5 in Tumaco (Nariño, Colombia)", "authors": [ "Pablo Enrique Chaparro Narváez", "Monica Marcela Jimenez-Serna", "Maria Luz Gunturiz Albarracin", "Gabriel Carrasquilla Gutierrez", "Monica Marcela Jimenez-Serna", "Maria Luz Gunturiz Albarracin", "Gabriel Carrasquilla Gutierrez" ], "abstract": "Background\nUrban malaria is a public health problem in Colombia and there is still lack of knowledge about its epidemiological characteristics, which are key to the implementation of control measures. The presence of urban malaria cases and disease diagnosis are some of the challenges faced by malaria elimination programs. The objective of this research was to estimate malaria prevalence, explore associated factors and detect pfhrp 2/3 genes, in the urban area of Tumaco between July and December 2019.\nMethods\nA prevalence study was conducted by using a stratified random probability sample. Structured surveys were administered and blood samples were taken and examined through optical microscopy, rapid diagnostic tests (RDT) and polymerase chain reaction (PCR). A logistic regression model was used to explore associated factors.\nResults\n1,504 people living in 526 households were surveyed. The overall prevalence was 2.97% (95% CI: 2.1 - 4.3%). It was higher in males, in the 10-19 age group and in asymptomatic cases. The prevalence of pfhrp2 amplification was 2.16% (95% CI: 1.6 - 2.9%). Households with three or more people had a higher risk of malaria infection (adjusted odds ratio (ORa) 4.05; 95% confidence interval (CI) 1.57-10.43). All cases were due to P. falciparum.\n\nConclusions\nThe prevalence of urban malaria was low. Strategies to eliminate malaria in urban areas should be adjusted considering access to early diagnosis, asymptomatic infection, and the RDTs used to detect the presence of the pfhrp2 gene.", "keywords": [ "prevalence", "diagnosis", "chromosome deletion", "urban malaria", "Colombia" ], "content": "Introduction\n\nMalaria elimination programs face several challenges, including urban malaria and disease diagnosis. Both in Colombia and worldwide, malaria transmission is mainly rural, but cases of malaria in urban and peri-urban areas have been continuously reported over the last decade, most of them in the Pacific region.1,2 These problems are compounded by the diagnosis of asymptomatic and submicroscopic malaria.\n\nDespite the fight against malaria, the World Health Organization (WHO) observed an increase in cases worldwide, increasing from 227 million in 2019 to 241 million in 2020 in the 85 countries where the disease is endemic. Similarly, in terms of mortality, 558,000 deaths were registered in 2019 and 627,000 in 2020. However, in the Americas region, the WHO reported a reduction in cases, from an estimated 893,000 in 2019 to 652,000 in 2020, 77% of them in Venezuela, Brazil and Colombia. Meanwhile, there was a reduction in deaths, from 509 in 2019 to 409 in 2020.3\n\nIt is worth mentioning that 91% of the Colombian territory has eco-epidemiological conditions that promote malaria transmission and it is estimated that 22% of the population lives in these areas. In 2020, 81,363 cases were registered (annual parasite index (API) 8.4 cases per 1,000 inhabitants) and 5 deaths were confirmed in the country. The predominant parasites were Plasmodium vivax (49.7%) and Plasmodium falciparum (49.5%).4 On the Pacific coast, in the department of Nariño, where Tumaco is located, 17,421 cases were reported (API 31.9 cases per 1,000 inhabitants).4 According to the Vector-Borne Disease Prevention and Control Program, cases of urban malaria have been identified mainly in the neighborhoods that are part of Commune 5 in Tumaco, where 1,024 cases were reported in 2015 (API 42.2 per 1,000 inhabitants) and 770 in 2016 (API 31.7 per 1,000 inhabitants).\n\nIn Colombia, the strategic action route for comprehensive care, health promotion, prevention, surveillance, control and elimination of malaria has been based on the “2019-2022 National Malaria Strategic Plan” which, among other aspects, includes disease diagnosis through the use of optical microscopy and rapid diagnostic tests (RDTs), and the elimination of urban and peri-urban malaria in 18 municipalities on the Pacific coast.5\n\nOptical microscopy can detect from 50 to 100 parasites/μL but it can lead to diagnostic errors when parasitemia is low.6 The purpose of RDTs is to detect one of three antigens in parasites: lactate dehydrogenase (LDH), aldolase, and histidine-rich protein 2 (hrp2), with significant differences from each other.7 The detection limit for RDTs is between 100-200 parasites/μL.8 It should be noted that hrp2 is specific for P. falciparum and that pfhrp2-based RDTs often detect the pfhrp3 antigen, rendering test interpretation difficult.9 Test performance may be affected by the antigenic variability of the target protein, the persistence of the antigen in blood after parasite elimination, and parasite density below the detection threshold. The presence of parasites with deletions or mutations of the pfhrp2 gene can lead to false-negative results, which has implications for RDT implementation, case diagnosis and treatment, and malaria control and elimination efforts.10\n\nTo overcome the limitations of optical microscopy and RDTs, molecular detection of malaria parasites through the polymerase chain reaction (PCR) was used, as it can detect parasitemia below 0.05 μL.7 On the other hand, PCR provides better information on the prevalence and distribution of parasitic species in endemic areas compared to that provided by optical microscopy and RDT.11\n\nRegarding urban malaria, there are challenges in terms of what is meant by “urban”, “peri-urban”, “rural” and “urban malaria”, because of the lack of established definitions to describe the socioeconomic and ecological contexts where the disease is transmitted.1,12 This situation is compounded by the failure to establish the origin of malaria cases, to identify mosquito breeding sites, and to confirm the vector's transmission capacity in these environments.1 Despite these difficulties, it has been established that urban and peri-urban malaria is caused by population traveling from rural to urban and peri-urban areas13 and trips from rural areas to urban areas and vice versa.14 In Latin America, peri-urban transmission has been reported in Brazil (Porto Velho)15 and Peru (Iquitos, Sullana, Piura y Lima).16–18 In Colombia, urban malaria has been identified in municipalities on the Pacific coast, where Tumaco is located. Peri-urban malaria is caused by the displacement of rural populations to peri-urban areas as a result of the armed conflict, presence of paramilitary groups, illicit crops, and illegal mining.1\n\nMost studies conducted in Colombia have addressed the prevalence of malaria in rural areas. Research focused on urban malaria has been scarce, reporting on total prevalence and the prevalence of asymptomatic and submicroscopic infections.1,12,19–25 Also, research aimed at detecting the pfhrp 2/3 gene deletion has been limited (Guapi 6%).26 Given the limited research on malaria prevalence carried out in the Colombian territory and the detection of pfhrp 2/3 genes in urban areas, this study was aimed at estimating malaria prevalence, detecting pfhrp 2/3 genes, and exploring associated factors in the urban area (Commune 5) in Tumaco during 2019.\n\n\nMethods\n\nThis study was approved by the ethics committees of the National Institute of Health (April 4, 2017 Minutes) and Fundación Santa Fe de Bogotá (April 22, 2019 Minutes). Participants’ written consent was obtained prior to data collection and blood sampling. The research with mosquitoes considered the Colombian scientific, technical, and administrative standards for biomedical research with animals. The mosquitoes were anesthetized with triethylamine before dying.\n\nBetween July and December 2019, a prevalence study was conducted in Commune 5 of Tumaco, a malaria-endemic urban area. This Colombian municipality is divided into communes and, in turn, each commune is made up of neighborhoods. A stratified (by neighborhoods) multistage random sample with proportional allocation was established. In the first stage, the primary sampling units were the Commune 5 neighborhoods. In the second stage, the secondary sampling units were groups of adjoining blocks. A grid was placed on the map of each selected neighborhood. Each cell included the residential units that make up a block. Sampling was carried out proportional to size, taking into account the number of inhabitants per block. Using the Teaching Sampling package of the statistical package R, the blocks in each of the selected neighborhoods were chosen. In the third stage, in the selected block, the house in the lower-left corner (southwest point) was located with the help of the Global Positioning System (GPS). In this dwelling began the collection of information. Then the selection of the next dwelling to the right or to the left depended on the outcome of a coin toss. Once the address was established, the collection of information continued until completing 12 contiguous houses. The units of analysis and observation were all individuals in the selected households.\n\nTo calculate sample size, a prevalence of 4.22% was considered, as reported by the “Vector-Borne Disease Prevention and Control Program in the Nariño Department” study in 2015. Accuracy was estimated to have a 15.0% expected relative standard error,27 95% confidence, and a 1.5 cluster design effect. Adjusting for a non-response rate of 10%, the final sample size was 1,424 individuals from households in Commune 5.\n\nOfficials from the departmental and municipal Vector-Borne Disease Prevention and Control Program, community leaders, and researchers informed the population of Commune 5 about the study. This ensured community participation in the study.\n\nThe inclusion criteria for the study were: (1) inhabitants of the selected dwelling who voluntarily wish to participate and who at the time of the visit were in the dwelling, (2) minors who have the authorization of the responsible adult or guardian, (3) people who have adequately filled out the informed consent. The exclusion criteria were: (1) people with mental problems unable to sign informed consent and (2) those for whom a blood sample was not possible to obtain.\n\nTumaco is located in southwestern Colombia (1° 48' 24” N; 78° 45' 53” W), on the Pacific coast, Nariño Department. It spreads over 3,778 km2 and the urban area is about 38 km2. This area is made up of three islands (El Morro, La Viciosa and Tumaco), which are divided into five communes and 82 neighborhoods.28 (Figure 1). The municipality is located 2 meters above sea level and has a warm humid weather. It has an average annual temperature of 26.1°C, a relative humidity of 84.8%, and annual precipitation ranging from 109 to 373 mm3. In 2021, its population was estimated at 257,042 inhabitants, out of which 33.7% lived in the urban area.29 Its economy is based on the production of African palm, cocoa and coconut and, to a lesser extent, tourism. In Tumaco, in the urban area, malaria is concentrated in Commune 5, where nearly 70% of the cases are found and there are breeding sites of Anopheles spp.\n\nSources: Google Maps: Maps Data: Google. © 2022 INEGI (retrieved on March 10. 2022). Google Earth: Maps Data: Google. © 2020 Maxar Technologies (retrieved on December 13. 2020)\n\nTwo structured questionnaires were designed. The first one included variables related to households characteristics, such as basic services and the presence and use of long-lasting insecticide-treated nets. The second one included sociodemographic variables (age, sex, ethnicity, marital status, occupation, educational level, socioeconomic stratum, belonging to the General Social Security Health System), symptoms, diagnosis and history of malaria. The questionnaires, created on mobile data capture devices (Android phones), were applied face-to-face by previously trained personnel. Interviews were conducted in Spanish. At the end of each study day, data collected were reviewed by the study coordinator, and any quality issues were flagged for immediate correction.\n\nOptical microscopy\n\nBlood samples were taken through finger puncture with a sterile lancet and each sample was then put on a clean film. Blood samples was taken at the household and thick smear was taken to the “Vector-Borne Disease” (VBD) control program and read by a bacteriologist according to national guidelines.30 Parasitemia was estimated based on a 200-leukocyte count (assuming a standard value of 8,000 leukocytes/μL of blood) and was expressed as parasites/μL (p/μL). The National Institute of Health performed quality control on 10% (153) of the samples. All participants with positive thick blood film received antimalarial treatment according to national guidelines.\n\nRapid diagnostic tests (RDTs)\n\nFor RDTs, a second drop of blood was obtained from the same finger puncture and it was then put in the RDT device, according to the manufacturer's instructions. The RDT used (SD BIOLINE Malaria Ag P.f/P.v) was the one distributed by the National VBD Prevention and Control Program to all municipalities in the country. The same bacteriologists who performed the optical microscopy diagnosis analyzed the RDTs at the household. The National Institute of Health performed quality control on 10% (153) of the RDT devices used.\n\nPolymerase chain reaction (PCR)\n\nFor the PCRs, the Invitrogen™ DNA polymerase Taq recombinant kit was used (Includes: Taq DNA Polymerase (5 U/μL); 10× PCR buffer (200 mM Tris-HCl pH 8.4, 500 mM KCl); Magnesium Chloride (50 mM). Bio-Rad C1000 Thermal Cycle was used for PCRs. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as housekeeping gene. The Table 1 shows the standardized amplification conditions for each gene, primers and expected fragment sizes.\n\nStandardization of protocols for genomic DNA extraction from whole blood and filter paper samples\n\nGenomic DNA (gDNA) extraction using filter paper\n\nThe saponin/chelex-100 method was used for DNA extraction. Briefly, a quarter of each dry droplet on filter paper was cut into small pieces and incubated at room temperature with a 0.5% saponin solution diluted in Phosphate buffered saline PBS. Then, the solution was mixed using a vortex and the supernatant was discarded. A wash was done with PBS, and 200 ul of a Chelex-100 solution diluted in water was added, then it was incubated at 56°C for 1 hour and at 100°C for 20 minutes. After incubation, the supernatant was transferred to sterile Eppendorf tubes and stored at -20°C until it was going to be used in the PCRs. gDNA was quantified by using a Nanodrop 2000, obtaining quality between 1.8 and 2.0. Once the gDNA had been extracted, diagnosis was performed through conventional PCR for the amplification of the gene fragments coding for the pfhrp2 and pfhrp3 proteins and the gene coding for the small subunit of Plasmodium vivax-PvSSU ribosomal RNA. DNA from reference strains was used as positive control. Negative controls without DNA and extraction controls obtained from filter paper without DNA were also included for each of the reactions. For the amplification of the different gene fragments mentioned before, specific primers were designed and PCR conditions were standardized for each of them. Guanine/cytosine (GC) content, dimer formation, loop formation, palindromes and melting temperature (MT) were taken into account for primer design. The sequences of the hrp2/hrp3 and PvSSU genes published in Genbank were used, an alignment was performed by using clustalW (Refseq), and primers were designed from conserved regions of the sequences obtained.\n\nPCR products were fractionated on 1.8% agarose gels stained with ethidium bromide, using a 100 bp molecular weight marker (Promega) as reference. The amplified products were visualized on a UV transilluminator and were purified on 1.8% agarose gels by using the GFX PCR DNA kit and Gel Band purification system (GE Healthcare). The purified products were sequenced by using the oligonucleotides used in the PCR, through the BigDye Terminator v3.1 cycle sequencing kit (Applied Biosystems) and the ABI PRISM 310 genetic analyzer. Sequence editing and analysis was performed through the DNA Sequencing Analysis software version 5.3.1.31,32 Sequence comparisons were made by using the blastn tool available at the National Center for Biotechnology Information (NCBI).\n\nThe entomological study did not use a probabilistic sample. The mosquito collection took place in homes that were included in the prevalence study and whose residents agreed to participate. Mosquitoes were collected through suction tubes and simultaneously with Centers for Disease Control and Prevention (CDC) and Shannon traps at rest (by the research group) and human bait (by the VBD staff) starting at 18:00 hours and ending at 6:00 hours in households in the Obrero neighborhood. Given the presence of illegal armed groups, collection in the Los Ángeles, Candamo, Unión Victoria and Ciudadela neighborhoods was authorized between 18:00 and 24:00 hours. From this time and until 6:00 hours, CDC traps were used. In the Once de Noviembre and Nuevo Milenio neighborhoods, permission was not obtained and mosquitoes were collected through traps that were installed between 18:00 and 6:00 hours. Mosquitoes were collected simultaneously inside and outside of selected households.\n\nThe collected mosquitoes were placed in containers labeled with date, neighborhood, house code, time of collection, number of mosquitoes and collector name. Specimens were killed with triethylamine and then individually packed in 1.5 ml vials with perforated caps. They were preserved in airtight bags with silica gel. Specimens of adult and immature mosquitoes were determined by using dichotomous keys for Anopheles in Colombia.33–36\n\nAlso, immature forms were searched in breeding sites within a radius of 1,000 meters around the selected households. Each breeding site was geo-referenced and its physical and environmental characteristics were registered. Sampling was carried out with a standard ladle, ten dips per square meter. Larvae were stored in 120 ml Whirl-Pak plastic bags with ethanol for preservation. Each larvae container was labeled with date, code, larva number, neighborhood and collector name.\n\nSymptomatic malaria. Individual with positive microscopy/RDT and symptoms of malaria, such as fever, chills, vomiting, convulsions, malaise, headache and/or loss of appetite.\n\nAsymptomatic malaria. Individual with positive microscopy/RDT or PCR, without symptoms.37,38\n\nSubmicroscopic malaria. Individual with positive PCR and negative microscopy/RDT. Submicroscopic infections are almost exclusively asymptomatic.38\n\nThe data were obtained through mobile devices. After quality control, they were exported and analyzed with the StataR version 12 statistical package. For statistical analysis, weights were generated according to strata, expansion factors and design effect, and the complex sample analysis module (svy command) was used. Categorical variables are presented as unweighted counts and weighted proportions with their corresponding 95% confidence intervals (95% CI), and continuous variables are expressed as means with 95% CI. The prevalence of malaria infection was estimated with the corresponding 95% CI. Malaria prevalence was calculated by age group, sex, symptoms and neighborhoods. The exploratory analysis of factors associated with urban malaria and households and urban malaria and individual was performed through logistic regression, first evaluating the relationship between each independent variable with the urban malaria variable. A p<0.05 value was considered statistically significant and those with p<0.05 were selected for the multivariate model.\n\n\nResults\n\nThe total number of respondents was 1,504 people (60.0% female) residing in 526 households in the selected neighborhoods of Commune 5 in Tumaco. The average age of the respondents was 29.75 years (95% CI, 28.75 to 31.22).\n\nHousehold characteristics are included in Table 2. More than half of the households' exterior walls were made of brick. More than two thirds had water service, while access to sewage service was scarce. Malaria was detected in 7.3% of households.\n\nTumaco, July to December 2019.\n\nRespondents' characteristics are shown in Table 3. There was higher participation of women and individuals between 20 and 49 years old. The majority were of African descent (95.2%). Nearly half of the individuals had lived in the households for over ten years (47%). Two-fifths of the respondents had high school education. One-third were workers and one-fourth were engaged in household activities. The family income for four-fifths of the participants was less than the minimum wage for one person. In the last year, 0.67% of the participants reported they had had malaria.\n\nTumaco, July to December 2019.\n\nThe total prevalence of malaria was 2.97% (95% CI: 2.1-4.3%). The prevalence obtained through microscopy/RDT was 0.81%, and through PCR it was 2.16%. All cases were due to P. falciparum. The highest prevalence of infection was found in the Candamo neighborhood. Most infections were asymptomatic and submicroscopic (Table 4).\n\nTumaco, July to December 2019.\n\nThe symptoms expressed by individuals who tested positive for malaria at the time of the survey were: fever (26.7%, 95% CI 9.9% - 54.7%), shivers (26.7%, 95% CI 9.9% - 54.7%), headache (24.0%, 95% CI 8.1% - 52.9%), diaphoresis (19.2%, 95% CI 5.0% - 51.8%), limb pain (24.3%, 95% CI 7.9% - 54.5%), and weakness (24.3%, 95% CI 7.9% - 54.5%). The mean parasite count of individuals who tested positive for malaria through optical microscopy was 653.5 parasites/μL (95% CI 101.5 to 1,205.5).\n\nQuality control performed by the National Institute of Health on the samples analyzed through optical microscopy and RDT indicated a 100% positivity rate concordance and 100% negativity rate concordance.\n\nOut of the 1,504 blood samples collected, 1,492 were examined through PCR because some samples had very small amounts of blood. The prevalence of amplification of the pfhrp2 gene was 2.16% (95% CI: 1.58% - 2.94%), and for the pfhrp3 gene and the PvSSU gene it was 0. In the fragment sequences of the gene coding for pfhrp2, no polymorphisms were found when compared to the sequences reported in GenBank. We do not have many photographs of uncut gels available. The positive samples were obtained in different assays; there is not a gel with the amplification of all the positive samples.\n\nThe entomological study was conducted in 25 households in the Obrero, Los Ángeles, Candamo, Unión Victoria, Ciudadela, Nuevo Milenio and Once de Noviembre neighborhoods. The presence of immature and adult Anopheles mosquitoes was registered.\n\n37 Anopheles mosquitoes belonging to the albimanus species were collected. The highest number of mosquitoes was identified in the Los Ángeles and Candamo neighborhoods. No malaria vector mosquitoes were identified in the Nuevo Milenio and Once de Noviembre neighborhoods. Between 18:00 and 19:00 hours, the highest activity occurred in the peri-domestic area, with a 0.018 human-biting rate (HBR) per hour and indoor between 21:00 and 22:00 hours, with a 0.007 HBR (Figure 2). The average human biting rate (HBR) at night was 0.74 and the HBR was 0.06 for all studied areas.\n\nCommune 5 neighborhoods, Tumaco (Nariño, Colombia). October 2019.\n\n83 breeding sites were found. Out of those, two had Anopheles mosquito larvae, one in the Unión Victoria neighborhood and the other one in the Obrero neighborhood. One breeding site was a pond and the other one was a well. 32 larvae were collected in both breeding sites. 27 of them were in late stages (3rd and 4th) and were identified as belonging to An. albimanus.\n\nThe exploration of associated factors in households where malaria infections occurred is shown in Table 5. The presence of three or more people living in the households (OR 4.98; 95% CI 1.99-12.45) and having three and more sleeping rooms (OR 2.38; 95% CI 1.10-15.13) were suggested as risk factors, and the use of a protective net for sleeping (OR 0.18; 95% CI 0.03-0.97) was suggested as a protective factor. However, the multivariate analysis indicated that households with three or more people had a higher risk of malaria infection (ORa 4.05; 95% CI 1.57-10.43).\n\nTumaco, July to December 2019.\n\nThe exploration of risk factors for individuals with malaria infection is presented in Table 6. None of the evaluated factors was statistically associated with a higher probability of having malaria.\n\n\nDiscussion\n\nThis study conducted in Commune 5, urban area of Tumaco, estimated malaria prevalence, pfhrp2 gene amplification, and explored factors associated with infection. The prevalence of malaria was 2.97%. It was higher (4.42%) in the 10 to 19 age group, decreased with age, and was higher in cases of asymptomatic and submicroscopic infection. The pfhrp2 gene was found and the disease was positively associated with households inhabited by three or more people.\n\nThe study found malaria in Commune 5, an area believed to have high transmission according to reports from the Vector-Borne Disease Prevention and Control Program in the Nariño Department (API 2014 84.0 cases per 1,000 inhabitants; API 2015 220.5 and API 2016 165.8). In South America, the prevalence of symptomatic and asymptomatic infections have ranged from 0.1% to 33% in urban areas of Porto Velho,15 Manaos,39 and Mâncio Lima40 in Brazil. In Colombia, prevalence has ranged from 0% to 5.8%. In Quibdó, the estimated asymptomatic prevalence in a group of schoolchildren was 0% (95% CI: 0-1.4).41 Two cases of submicroscopic infection were reported in Yesquita, Silencio and Roma neighborhoods of Quibdó.42 In the Santa Mónica de Guapi neighborhood (Cauca Department, on the Colombian Pacific), four successive measurements reported asymptomatic prevalence of 2.7%, 1.2%, 0.6% and 0.3%, respectively.26 In Buenaventura, the prevalence was 4.4%20 and in the California neighborhood in Tumaco it was 5.8%.25 These figures are not comparable with those reported in this study due to differences in terms of study design, type of sampling used, selection of individuals, diagnostic techniques, time of year in which the study was conducted, and the area where it was carried out. Concerning this last aspect, although there is no consensus on the definition of urban and peri-urban, the presence of symptomatic and asymptomatic malaria in Commune 5 of Tumaco was demonstrated, turning it into a potential human reservoir and a challenge for disease elimination strategies.\n\nThe persistence of urban malaria may be caused by people moving back and forth between urban and rural areas. People travel from urban to rural areas, where the endemic is higher, either for work or leisure. People also travel from endemic rural areas to urban areas to access health services or to engage in commercial activities, causing them to stay for a long period of time there.14 Rural areas are the main source of malaria infection in urban areas.43\n\nIn urban areas, malaria infection is not expected to be prevalent due to better-designed households with better basic utilities, better access to health services, and the absence of mosquito breeding sites.33 However, in the study area, most households were found to belong to a low socioeconomic stratum, lack sewage, have few mosquitoes and breeding sites, and have low biting rates, which could in part contribute to disease transmission.\n\nIn this study, households with higher occupancy showed higher malaria risk. Studies in Rwanda and Tanzania found that mosquitoes are more attracted to houses with many people44,45 because there is a higher production of cues that attract them and increase the risk of transmission, compared to households with lower occupancy.46\n\nSomething that stands out is the high percentage of households in which people slept with nets (98%). Although no distinction was made between untreated nets, those treated at some point in time, and those treated with insecticide, the bivariate analysis allows us to see their protective effect when households with and without malaria cases were compared. If nets are a major part of malaria elimination strategies, implementation, monitoring and evaluation of their use and efficacy should be routinely carried out in Commune 5 of Tumaco.47\n\nIn terms of case detection, as in other studies, PCR had the highest diagnostic performance,38 followed by microscopy. When comparing microscopy/RDT results with PCR results, lack of concordance was observed. Those with a positive diagnosis through microscopy/RDT were not detected through PCR and those with a positive diagnosis through PCR were not detected through microscopy/RDT. It is possible that people who were positive according to microscopy/RDT did not have the parasite's DNA so it could not be detected through PCR, as described by Mudare et al.,48 or the sample may have had a low amount of parasitic DNA or it may have degraded. Another possibility is that there were changes in the primer ringing site, which would prevent amplification of the gene fragment under study.\n\nThe species detected through the various diagnostic tests was P. falciparum, a finding that also corresponds to the most frequently reported species for malaria on the Colombian Pacific coast.4\n\nIn this study, differences were found in terms of the prevalence of malaria among men and women. As reported in other studies, malaria was more prevalent in men. This could be due to the fact that they spend more time doing outdoor activities, arrive to their households late in the evening, and have an indifferent attitude towards malaria prevention.49\n\nIn terms of age groups, the highest prevalence of malaria was observed in the 10 to 19 age group and as age increased, prevalence decreased. This result is similar to that reported in other studies. Older people are likely to have a lower risk of becoming ill because they may develop some immunity if they have been previously exposed to the infection.19,20 Recent studies in areas with high and low malaria transmission rates have revealed that asymptomatic infections contribute to malaria transmission.50 Furthermore, asymptomatic malaria may precede symptomatic disease, and may confer partial immunity against infection.51\n\nThis study found the presence of the pfhrp2 gene in samples from the urban area of Commune 5 in Tumaco. The findings suggest that a low proportion of malaria infections are not detected through the RDTs used in Colombia. In South America, gene deletions have been reported in Peru (prevalence between 20.7% and 41.0%) and Brazil (one case).52 In Colombia, these deletions have been reported in the Amazonas Department, where they reached a prevalence of 67%53; in Guapi (Cauca Department), where 6% of the parasite simples analyzed showed pfhpr2/3 gene deletion.26 The factors promoting the appearance of these parasites in some regions still remain unknown.54 The estimates obtained in this study do not exceed the minimum WHO criteria (>5%); however, it is important to monitor the hrp2-based RDTs used in the country. On the other hand, continuous monitoring related to submicroscopic infections and negative pfhrp2 results should be performed when using RDT. It is suggested that submicroscopic infections with parasites with pfhrp2/3 gene deletion could have infectious potential for mosquitoes and thus favor malaria transmission.53\n\nOn the other hand, in the Commune 5 neighborhoods of Tumaco, An. albimanus was found in artificial ponds and wells, as described in the Buenaventura urban area.19 Breeding sites were found in all the neighborhoods that were part of the study, except in Nuevo Milenio and Once de Noviembre. The differences between neighborhoods are caused by the urbanization level. Stilt houses predominate in some neighborhoods, while there is no sewage system in others, which leads to the construction of ditches where water stagnates and mosquitos breed. Although there is ongoing entomological surveillance, mosquito control interventions need to be strengthened and the community should be involved. An. albimanus had greater hematophagic activity in peri-domestic areas between 18:00 and 19:00 hours, a time when people engage in social activities outdoors and when they can possibly contract the disease,20 and indoors, between 21:00 and 22:00. However, given the low densities of An. albimanus and the limited observation, it was not possible to determine whether the mosquito was highly active at other times at night.\n\nThis study results should be studied with caution, given the limitations. First, the samples to be analyzed through PCR and pfhrp2/3 gene detection were taken on filter paper and were extracted after prolonged storage (due to the prioritization of PCR for Covid-19), which may have limited the amount of DNA to be used or may have promoted its degradation. Second, some samples collected on filter paper had little blood so the amount of gDNA was also variable. Third, the vast majority of individuals detected who were found to have malaria had no symptoms, which may not have allowed the researchers to detect the prevalence of pfhrp2/3 genes in symptomatic individuals. Fourth, the presence of illegal armed groups did not allow for an adequate entomological study because only partial observation was allowed in some neighborhoods, while in others the research group was not allowed. Fifth, due to study design, the participants were only questioned at sampling and there was no follow-up, so it is not possible to know if those who were asymptomatic later became symptomatic. Sixth, during survey application a memory bias may have been present, which could have altered the respondents' way of answering the questions.\n\nA strength of this research was the participation of the “Vector-Borne Disease Prevention and Control Program in the Nariño Department” officials and the municipality of Tumaco. Their intervention will promote the use of these results for decision making in activities related to the pre-elimination of urban malaria in Tumaco.\n\nIn summary, the prevalence of malaria was estimated at 2.97% and the prevalence of asymptomatic infection was 2.16% in the urban area of Commune 5 of Tumaco. Parasites positive for the pfhrp2 gene were found. An. albimanus larvae were found in breeding sites and adult forms were found indoors and in peri-domestic areas. All of the cases were caused by P. falciparum. The disease was positively associated with households inhabited by three and more people. Based on these results, pre-elimination of urban malaria should include early diagnosis strategies and continuous active surveillance of asymptomatic infection, which requires the inclusion of molecular diagnostic tests. In addition, the RDTs used to diagnose should be monitored for potential pfhrp2 gene deletion, which will be focused on considering alternatives. Additionally, work should be coordinated with other sectors to establish activities aimed at improving basic sanitation and conduct continuous educational activities aimed at preventing the disease.\n\n\nData availability\n\nZenodo: Malaria Prevalence in Commune 5 in Tumaco (Nariño, Colombia). https://doi.org/10.5281/zenodo.639534055\n\nThis project contains the following underlying data:\n\n- Malaria Prevalence in Commune 5 in Tumaco – house – readme.xlsx\n\n- Malaria Prevalence in Commune 5 in Tumaco – house.xlsx\n\n- Malaria Prevalence in Commune 5 in Tumaco – persons – readme.xlsx\n\n- Malaria Prevalence in Commune 5 in Tumaco – persons.xlsx\n\n- Breeding sites.xlsx\n\n- Determination Anopheles.xlsx\n\n- Malaria gel images.pdf\n\nZenodo: Malaria Prevalence in Commune 5 in Tumaco (Nariño, Colombia). https://doi.org/10.5281/zenodo.639534055\n\nThis project contains the following extended data:\n\n- Housing survey.docx\n\n- Housing survey English.docx\n\n- People survey.docx\n\n- People survey English.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nCompeting interests\n\nNo competing interests were disclosed.\n\n\nGrant information\n\nThis study was funded by Minciencias “Malaria Elimination: A Challenge for Colombia” Project. 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Publisher Full Text" }	[ { "id": "135485", "date": "16 May 2022", "name": "Martha Cecilia Suárez-Mutis", "expertise": [ "Reviewer Expertise Malaria epidemiology and molecular epidemiology of Plasmodium infections", "malaria diagnosis", "Pfhrp2/3 deletion detection", "asymptomatic Plasmodium infections." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMalaria prevalence in Commune 5 in Tumaco (Nariño, Colombia)\nThis is a very interesting study about the prevalence of malaria in an urban area of the Pacific Coast of Colombia. The data is relevant, but there are some areas that need further clarification before indexing.\nIntroduction\nPage 3:\nThe authors said, “To overcome the limitations of optical microscopy and RDTs, molecular detection of malaria parasites through the polymerase chain reaction (PCR) was used”. It is true that optical microscopy and RDT have imitations, but it is important that the authors describe the context in which molecular assays are important.\nThe authors said, “Regarding urban malaria, there are challenges in terms of what is meant by “urban”, “peri-urban”, “rural” and “urban malaria”. “Urban malaria” is repeated in this sentence.\nThe authors said, “Despite these difficulties, it has been established that urban and peri-urban malaria is caused by population traveling from rural to urban and peri-urban areas13 and trips from rural areas to urban areas and vice versa”. This information is not exact. It depends on the context. Several African and Amazonian cities have larval habitats that determine autochthones malaria cases. On the other hand, what is the difference between “traveling from rural to urban and peri-urban” and “trips from rural areas to urban areas and vice versa”?\nThe authors said, “Given the limited research on malaria prevalence carried out in the Colombian territory and the detection of pfhrp 2/3 genes in urban areas, this study was aimed at estimating malaria prevalence, detecting pfhrp2/3 genes, and exploring associated factors in the urban area (Commune 5) in Tumaco during 2019”. From Public Health programs, it is important to detect the percentage of deletions of the Pfhrp2/3 genes in a population.\nPage 4:\nAbout the inclusion criteria, the authors said that “minors who have the authorization of the responsible adult or guardian” were included. Was there not a minimum age for inclusion of children? The authors said that “a prevalence study was conducted in Commune 5 of Tumaco, a malaria-endemic urban area”. The authors should inform the criteria for selection of Commune 5 in Tumaco municipality. Is this the only Commune that has malaria? A better description of Commune 5 is necessary. How many inhabitants live there? Where is Commune 5 located? In the middle or in the periphery of the city? In the figure it seems that there is a river? What is the name of the river? The authors said that “In Tumaco, in the urban area, malaria is concentrated in Commune 5, where nearly 70% of the cases are found and there are breeding sites of Anopheles spp.”. 70% of urban cases are originated of the Commune 5? The idea is not clear. It is much better to say: In the urban area of Tumaco, 70% of malaria cases are found in the Commune 5 where there are breeding sites (our larval habitats) for Anophelines spp. too. What kind of larval habitats are in this Commune 5?\nPage 6:\nThe authors collected blood for thick smear, RDTs and whole blood and filter paper samples, but in the methods, there is no information about the methods and the quantity of total blood was collected for PCR and filter paper samples. Please add this information.\nOn the other hand, for better understanding, we suggest that data about DNA extraction will be added before PCR experiments. The authors only add information about DNA extraction from filter paper but not for the whole blood extraction. Was it made? If whole blood extraction was done, DNA was extracted from what quantity of blood?\nPage 7:\nPlease add the reference of the protocol that was used for amplified Pfhrp2/3 genes.\nFor entomological collections, how many capture points were sampled? How many days, or how many times were the adult captures done?\nThe authors defined “Asymptomatic malaria as Individual with positive microscopy/RDT or PCR, without symptoms”. It is important to remember that with this definition, individuals could be in a prepatogenic period or be an asymptomatic individual. The same reasoning goes for “Submicroscopic malaria”. The individual can be in the prepathogenic period or she/he can be in recovering period. Questions about malaria in the last month or to use malaria drugs in the last month were done?\nResults:\nTable 3 included some categories that should not be included. For example, the variables “Educational level” and “civil status” for children under 5 years old.\n\nPage 11:\nAuthors said that “and through PCR it was 2.16%”. Exclude “it” in this sentence. Notably, only one individual with symptoms was PCR (+) and 6 with thick smear/RDT were symptomatic. Were these individuals negative in the PCR or was the PCR not done in these patients?\nAuthors said that, “The prevalence of amplification of the pfhrp2 gene was 2.16% (95% CI: 1.58% - 2.94%), and for the pfhrp3 gene and the PvSSU gene it was 0”. The literature for Pfhrp2/3 usually shows the percentage of gene deletion not the percentage of detection of these genes. It is expected that P. falciparum samples carry the gene. It is extremally important that authors confirm if they effectively detected the gene or if they are showing the deletion of the gene. What does the percentage actually mean?\n\nPage 14:\nDiscussion:\nThe authors said that “The prevalence of malaria was 2.97%. It was higher (4.42%) in the 10 to 19 age group”, but in the table 4, the 0-9 age group the prevalence was 4.06. Was there any statistical difference found in malaria cases in children between 0 and 9 years old and 10 and 19 years old?\nThe authors said that “The study found malaria in Commune 5, an area believed to have high transmission according to reports from the Vector-Borne Disease Prevention and Control Program in the Nariño Department (API 2014 84.0 cases per 1,000 inhabitants; API 2015 220.5 and API 2016 165.8)”. Please add a reference. A better discussion using previous knowledge of malaria in this area must be added. If this area was classified as high malaria risk in the past, why did the results show this low prevalence? How do we interpret these results? What´s causing the different prevalence between age groups? How do we understand this epidemiology?\nIn order to better interpret the results it is necessary to add more information. For example, when was the study done? (Year and month)? In this locality, is malaria seasonal? Was the study carried out during the high malaria season?\nThe authors said that “In urban areas, malaria infection is not expected to be prevalent due to better-designed households with better basic utilities, better access to health services, and the absence of mosquito breeding sites”. They use a reference about taxonomy and not specifically urban malaria. Studies about urban malaria around the world show that there are specific determinants for malaria transmission in these areas. Larval habitats usually are very near to these urban areas. This does not seem to be the case in this area where the prevalence was very low.\nThe authors found a lack of concordance between microscopy/RDT and PCR tests. As they did not separate microscopy and RDT is difficult to interpret this result. A technical problem can occur when a positive microscopy is comparing with PCR. One question is, did the authors do quality control for thick smears? As primers are very specific, it is difficult to explain a positive thick smear with a negative PCR.\nOn the other hand, a positive microscopy with a negative RDT is probably because the limit of detection of RDT. The same rational is true for negative RDT with positive PCR. Cases of negative thick smear with positive RDT could be explained because Pfhrp2 antigen could be detected in the blood until 30 days after a good malaria treatment.\nAnyway, it is necessary that authors add this information in the discussion and include it in the results a separate data for microscopy, RDT and PCR results (including in symptomatic and asymptomatic individuals).\nPage 15:\nThe authors said that “In terms of age groups, the highest prevalence of malaria was observed in the 10 to 19 age group and as age increased, prevalence decreased. This result is similar to that reported in other studies. Older people are likely to have a lower risk of becoming ill because they may develop some immunity if they have been previously exposed to the infection”. Was there any question about malaria antecedents in the questionnaire? How many malaria episodes did the participants have before the study? Or, how many participants had at least one previous malaria episode before the study? These are important questions that the authors did not address.\nThe authors said that “Furthermore, asymptomatic malaria may precede symptomatic disease, and may confer partial immunity against infection”. Asymptomatic Plasmodium infection is an important field of study and until now many questions continue open for discussion. It seems clear that asymptomatic infections occur in individuals with several past malaria episodes and this status is product of clinical immunity develop along time. This “status of Plasmodium asymptomatic infection” is different of those individuals whose blood were collected during the pre-pathogenic period before the beginning of malaria paroxysm. They could be in the “incubation period” and the number of parasites circulating in blood do not still reach the parasitic threshold for clinical symptoms. A better discussion about authors results and their interpretation must be added.\n\nAbout discussion of Pfhrp2, we added above this sentence: “Authors said that “The prevalence of amplification of the pfhrp2 gene was 2.16% (95% CI: 1.58% - 2.94%), and for the pfhrp3 gene and the PvSSU gene it was 0”. The literature for Pfhrp2/3 usually show the percentage of gene deletion not the percentage of detection of these genes. It is expected that P falciparum samples carry the gene. It is extremally important that authors confirm if they effectively detected the gene or if they are showing the deletion of the gene. What does the percentage actually mean?”. For the discussion, it is very important to know what was really detected by the authors - the deletion of gene or the gene?\nThe authors said that “On the other hand, in the Commune 5 neighborhoods of Tumaco, An. albimanus was found in artificial ponds and wells”. This data was not added in the results section.\nRegarding anopheline transmission in this study, it would be interesting if the authors added a discussion about ecological conditions for malaria transmission of An. albimanus. Furthermore, a critical analysis of the constraints of entomological studies must be incorporated.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "8701", "date": "08 Sep 2022", "name": "Pablo Enrique Chaparro Narváez", "role": "Author Response", "response": "Thank you for your constructive review. These are our answers for your review: Introduction Page 3: The authors said, “To overcome the limitations of optical microscopy and RDTs, molecular detection of malaria parasites through the polymerase chain reaction (PCR) was used”. It is true that optical microscopy and RDT have imitations, but it is important that the authors describe the context in which molecular assays are important. The following paragraph was included: “PCR is a more sensitive diagnostic method to detect asymptomatic infections with very low parasite density. It may be useful in studies of submicroscopic infections, although its utility depends on the epidemiological importance of low-density infections, which have not yet been characterized” (Framework for malaria elimination) The authors said, “Regarding urban malaria, there are challenges in terms of what is meant by “urban”, “peri-urban”, “rural” and “urban malaria”. “Urban malaria” is repeated in this sentence. We corrected The authors said, “Despite these difficulties, it has been established that urban and peri-urban malaria is caused by population traveling from rural to urban and peri-urban areas13 and trips from rural areas to urban areas and vice versa”. This information is not exact. It depends on the context. Several African and Amazonian cities have larval habitats that determine autochthones malaria cases. On the other hand, what is the difference between “traveling from rural to urban and peri-urban” and “trips from rural areas to urban areas and vice versa”? We adjusted: “Despite these difficulties, it has been established that urban and peri-urban malaria may be transmitted by population traveling from rural to urban and peri-urban areas (14,15) Local transmission has also been suggested in urban areas where the presence of Anopheles, as a competent vector, and infected people converge (13)” The authors said, “Given the limited research on malaria prevalence carried out in the Colombian territory and the detection of pfhrp 2/3 genes in urban areas, this study was aimed at estimating malaria prevalence, detecting pfhrp2/3 genes, and exploring associated factors in the urban area (Commune 5) in Tumaco during 2019”. From Public Health programs, it is important to detect the percentage of deletions of the Pfhrp2/3 genes in a population. One of the objectives of the study was to detect gene fragments of Pfhrp2/3. The deletion of these genes was not evaluated. However, to improve malaria elimination programs, it is necessary to determine these deletions since, at least in Colombia, the RDTs used for diagnosis are based on these genes, and of course, deletions would generate false negatives. Methods Page 4: About the inclusion criteria, the authors said that “minors who have the authorization of the responsible adult or guardian” were included. Was there not a minimum age for inclusion of children? There is no minimum age for the inclusion of children. The authors said that “a prevalence study was conducted in Commune 5 of Tumaco, a malaria-endemic urban area”. The authors should inform the criteria for selection of Commune 5 in Tumaco municipality. Is this the only Commune that has malaria? We corrected: In the urban area of Tumaco, all five communes are endemic to malaria. In this city, 70% of malaria cases are reported from commune 5 in the last ten years A better description of Commune 5 is necessary. How many inhabitants live there? Where is Commune 5 located? In the middle or in the periphery of the city? In the figure it seems that there is a river? What is the name of the river? We corrected: Commune 5, with 26,000 inhabitants, is in the continental area of Tumaco on the low-tide land and nearby estuaries. The presence of Anophelines sppn breeding sites (ponds, puddles, and lakes for shrimp farming) and the high density of the population make this commune of high risk of malaria transmission. In the figure, the image corresponds to an estuary. It's not a river. The authors said that “In Tumaco, in the urban area, malaria is concentrated in Commune 5, where nearly 70% of the cases are found and there are breeding sites of Anopheles spp.”. 70% of urban cases are originated of the Commune 5? The idea is not clear. It is much better to say: In the urban area of Tumaco, 70% of malaria cases are found in the Commune 5 where there are breeding sites (our larval habitats) for Anophelines spp. too. What kind of larval habitats are in this Commune 5? We included the suggested phrase and larval habitats. Page 6: The authors collected blood for thick smear, RDTs and whole blood and filter paper samples, but in the methods, there is no information about the methods and the quantity of total blood was collected for PCR and filter paper samples. Please add this information. We have included: For PCR, two drops of blood were obtained from the same finger puncture and were then put on the filter paper On the other hand, for better understanding, we suggest that data about DNA extraction will be added before PCR experiments. We have made the suggested change. The authors only add information about DNA extraction from filter paper but not for the whole blood extraction. Was it made? If whole blood extraction was done, DNA was extracted from what quantity of blood? We have included: 10 mm² of Whatman #3 filter paper impregnated with blood were taken and genomic DNA extraction was performed according to the protocol described in the article. This procedure was performed in duplicate. Page 7: Please add the reference of the protocol that was used for amplified Pfhrp2/3 genes. We have included: For the amplification of the different fragments of the genes mentioned, we designed the specific primers and the PCR conditions for each of them were standardized. For the design of the primers, the GC content, dimer formation, loop formation, palindromes and Tm were taken into account. The sequences of the HRP2/HRP3 and PvSSU genes published in the Genbank were used, an alignment was performed using clustalW (Refseq) and the primers were designed from conserved regions of the sequences obtained. For entomological collections, how many capture points were sampled? How many days, or how many times were the adult captures done? We have included: Between October 1 and 23, 2019, 81 capture points were sampled in 25 homes and 83 breeding places. The authors defined “Asymptomatic malaria as Individual with positive microscopy/RDT or PCR, without symptoms”. It is important to remember that with this definition, individuals could be in a prepatogenic period or be an asymptomatic individual. The same reasoning goes for “Submicroscopic malaria”. The individual can be in the prepathogenic period or she/he can be in recovering period. Questions about malaria in the last month or to use malaria drugs in the last month were done? In the applied questionnaire were included the questions: Have you had malaria in the last year, apart from the current episode? When was the last time you had malaria? Have you taken antimalarial drugs in the last 15 days? Results: Table 3 included some categories that should not be included. For example, the variables “Educational level” and “civil status” for children under 5 years old. We corrected: Table 3. Characteristics of the Surveyed Population. Tumaco, July to December 2019 Characteristics Total Unweighted count Weighted count n % 95% Confidence Interval Age groups 0-9 272 18,32 16,0 20,9 10-19 318 21,47 19,1 24,1 20-49 626 40,88 38,64 43,15 ≥50 288 19,33 16,94 21,98 Sex Male 531 35,56 33,5 37,7 Female 973 64,44 62,3 66,5 Ethnic group Black, African descent 1.439 95,23 91,4 97,4 Others 65 4,77 2,6 8,6 Years living in the house 0 to 4 373 25,60 22,5 28,9 5 to 9 397 25,97 22,4 29,9 10 or more 714 47,03 42,6 51,5 No information 20 1,40 0,8 2,3 Educational level* Preschool, primary 555 40,75 37,05 44,55 High school 628 45,79 42,88 48,73 University 113 8,54 6,43 11,24 None 72 4,93 3,57 6,77 Civil status** Has a partner 585 52.78 49.08 56.45 No partner 526 47.22 43.55 50.92 Occupation Worker 450 30,04 26,4 34,0 Housework 399 26,26 24,0 28,7 Early childhood 158 10,46 8,8 12,4 Childhood 178 12,26 10,7 14,0 Adolescence 218 14,49 12,7 16,5 Unemployed 36 2,29 1,6 3,2 Pensioner 14 0,86 0,5 1,4 Other 51 3,34 2,4 4,6 Family income <1 MLW (Monthly Legal Wage) 1.219 79,37 72,8 84,7 1 or more MLW 281 20,33 15,1 26,8 Does not know 4 0,30 0,1 1,7 Malaria in the last year 10 0,67 0,32 1,40 * In the “Educational level” variable, 136 children under 5 years of age were excluded. ** In the “Civil status” variable, 393 children under 14 years of age were excluded. Page 11: Authors said that “and through PCR it was 2.16%”. Exclude “it” in this sentence. We exclude “it” in this sentence. Notably, only one individual with symptoms was PCR (+) and 6 with thick smear/RDT were symptomatic. Were these individuals negative in the PCR or was the PCR not done in these patients? Yes, these individuals were negative in the PCR. All these persons were examined by PCR. Authors said that, “The prevalence of amplification of the pfhrp2 gene was 2.16% (95% CI: 1.58% - 2.94%), and for the pfhrp3 gene and the PvSSU gene it was 0”. The literature for Pfhrp2/3 usually shows the percentage of gene deletion not the percentage of detection of these genes. It is expected that P. falciparum samples carry the gene. It is extremally important that authors confirm if they effectively detected the gene or if they are showing the deletion of the gene. What does the percentage actually mean? Fragments of the Pfhrp2/3 genes were detected by PCR amplification. No assays were performed to assess the deletion of these genes. The percentage shown corresponds to the percentage of amplification of the Pfhrp2/3 genes. Discussion: Page 14: The authors said that “The prevalence of malaria was 2.97%. It was higher (4.42%) in the 10 to 19 age group”, but in the table 4, the 0-9 age group the prevalence was 4.06. Was there any statistical difference found in malaria cases in children between 0 and 9 years old and 10 and 19 years old? There were no statistically significant differences (p: 0.83). We adjust: It was higher in the 10 to 19 (4.42%) and 0 to 9 (4.06%) age groups The authors said that “The study found malaria in Commune 5, an area believed to have high transmission according to reports from the Vector-Borne Disease Prevention and Control Program in the Nariño Department (API 2014 84.0 cases per 1,000 inhabitants; API 2015 220.5 and API 2016 165.8)”. Please add a reference. We add: Pilar Perez, Vector-Borne Disease Prevention and Control Program in the Nariño Department, personal communication A better discussion using previous knowledge of malaria in this area must be added. If this area was classified as high malaria risk in the past, why did the results show this low prevalence? How do we interpret these results? What´s causing the different prevalence between age groups? How do we understand this epidemiology? We add: The decrease in the prevalence of malaria over time is possibly due to the intensification of actions to search for and eliminate breeding sites, massive use of mosquito nets, and social participation as measures implemented for Commune 5. Diagnosis and treatment actions also have contributed, despite the difficulties that exist in accessing services. In this way, it has reduced human contact (infected) —a vector that has contributed to the decline in the burden of this disease. The higher prevalence of malaria in people under 20 years of age suggests that the infection may have been acquired locally. Unlike Africa, which has a high transmission and where the population, most affected in terms of morbidity and mortality is under 5 years of age, in areas of low transmission such as Colombia, malaria occurs in older age groups. Among the aspects that are considered to think that the transmission occurs in the urban area are confirming the infection in the residents of these areas; evidence of the presence of adult Anopheles that are biting the inhabitants of urban dwellings and identifying breeding sites near them (40). In order to better interpret the results it is necessary to add more information. For example, when was the study done? (Year and month)? In this locality, is malaria seasonal? Was the study carried out during the high malaria season? The blood samples were taken during the dry season, between July and September 2019. Malaria in the urban area of Tumaco has not shown a clear seasonal behavior. The authors said that “In urban areas, malaria infection is not expected to be prevalent due to better-designed households with better basic utilities, better access to health services, and the absence of mosquito breeding sites”. They use a reference about taxonomy and not specifically urban malaria. Studies about urban malaria around the world show that there are specific determinants for malaria transmission in these areas. Larval habitats usually are very near to these urban areas. This does not seem to be the case in this area where the prevalence was very low. We change the reference: Larson P, Eisenberg J, Berrocal V, Mathanga D, Wilson M. An urban-to-rural continuum of malaria risk: new analytic approaches characterize patterns in Malawi. Malaria Journal 20, 418 (2021) (ref 46) The authors found a lack of concordance between microscopy/RDT and PCR tests. As they did not separate microscopy and RDT is difficult to interpret this result. A technical problem can occur when a positive microscopy is comparing with PCR. One question is, did the authors do quality control for thick smears? As primers are very specific, it is difficult to explain a positive thick smear with a negative PCR. The National Institute of Health performed quality control on 10% (153) of the samples analyzed by optical microscopy in accordance with national recommendations. On the other hand, a positive microscopy with a negative RDT is probably because the limit of detection of RDT. The same rational is true for negative RDT with positive PCR. Cases of negative thick smear with positive RDT could be explained because Pfhrp2 antigen could be detected in the blood until 30 days after a good malaria treatment. Anyway, it is necessary that authors add this information in the discussion and include it in the results a separate data for microscopy, RDT and PCR results (including in symptomatic and asymptomatic individuals). We add: “On the other hand, positive microscopy with a negative RDT is probably because of the limit of detection of RDT. The same rationale is true for negative RDT with positive PCR. Cases of negative thick smear with positive RDT could be explained because Pfhrp2 antigen could be detected in the blood until 30 days after a good malaria treatment.” We include in the results: Table 5. Test results according to symptoms. Unweighted count Commune 5 neighborhoods, Tumaco (Nariño, Colombia). October 2019 Test Symptoms Total Yes No Optical microscopy (RDT) 6 (5) 5 (3) 11 (8) PCR 1 27 28 Total 7 33 39 In parentheses, the cases diagnosed with RDT Page 15: The authors said that “In terms of age groups, the highest prevalence of malaria was observed in the 10 to 19 age group and as age increased, prevalence decreased. This result is similar to that reported in other studies. Older people are likely to have a lower risk of becoming ill because they may develop some immunity if they have been previously exposed to the infection”. Was there any question about malaria antecedents in the questionnaire? How many malaria episodes did the participants have before the study? Or, how many participants had at least one previous malaria episode before the study? These are important questions that the authors did not address. We included in the study the questions Have you had malaria in the last year, apart from the current episode? When was the last time you had malaria? Have you taken antimalarial drugs in the last 15 days? The results are presented in the corresponding section as follows: Ten individuals had malaria in the last year. Of them, none had malaria in the last month. They also did not have positive test results for malaria in the last 15 days, and they had not consumed antimalarial drugs. Less than 1% of participants had malaria in the last year and none in the last month. It is possible that in areas of low endemicity, such as Colombia, the lowest prevalence in older age groups is due to the fact that the population that may have less exposure was interviewed. For example, women who remain at home dedicated to household chores and individuals of school age who go to school. The authors said that “Furthermore, asymptomatic malaria may precede symptomatic disease, and may confer partial immunity against infection”. Asymptomatic Plasmodium infection is an important field of study and until now many questions continue open for discussion. It seems clear that asymptomatic infections occur in individuals with several past malaria episodes and this status is product of clinical immunity develop along time. This “status of Plasmodium asymptomatic infection” is different of those individuals whose blood were collected during the pre-pathogenic period before the beginning of malaria paroxysm. They could be in the “incubation period” and the number of parasites circulating in blood do not still reach the parasitic threshold for clinical symptoms. A better discussion about authors results and their interpretation must be added. In this study, participants were sampled at a single point in time. Those who were classified as asymptomatic had no history of illness in the last month and had not used antimalarial drugs in the last 15 days. For them, it is difficult to establish if they were in the incubation period of the disease or if they were carriers of a low number of parasites. Resolving a situation like this requires follow-up. In this regard, a study of 268 people followed for 29 months in western Kenya, in a high-transmission area, discovered that asymptomatic infections were highly likely to be followed by symptomatic disease (ref 55). However, this does not seem to be the case in Commune 5 of Tumaco, which has a low transmission and where complicated malaria and malaria mortality do not occur. About discussion of Pfhrp2, we added above this sentence: “Authors said that “The prevalence of amplification of the pfhrp2 gene was 2.16% (95% CI: 1.58% - 2.94%), and for the pfhrp3 gene and the PvSSU gene it was 0”. The literature for Pfhrp2/3 usually show the percentage of gene deletion not the percentage of detection of these genes. It is expected that P falciparum samples carry the gene. It is extremally important that authors confirm if they effectively detected the gene or if they are showing the deletion of the gene. What does the percentage actually mean?”. For the discussion, it is very important to know what was really detected by the authors - the deletion of gene or the gene? We included: In the context of our study due to insufficient resources, we did not evaluate the deletion of these genes, we only amplified a fragment of these genes by means of PCR. However, in order to improve the management of clinical cases and design strategies for diagnosis, the detection of deletions in the HRP2/3 genes is relevant, since, as has been described, these can affect the accuracy of PDR in malaria endemic regions and of course in malaria control programs. The authors said that “On the other hand, in the Commune 5 neighborhoods of Tumaco, An. albimanus was found in artificial ponds and wells”. This data was not added in the results section. These data is in the results section: “83 breeding sites were found. Out of those, two had Anopheles mosquito larvae, one in the Unión Victoria neighborhood and the other one in the Obrero neighborhood. One breeding site was a pond and the other one was a well. 32 larvae were collected in both breeding sites. 27 of them were in late stages (3rd and 4th) and were identified as An. albimanus.” Regarding anopheline transmission in this study, it would be interesting if the authors added a discussion about ecological conditions for malaria transmission of An. albimanus. An albimanus is considered a primary malaria vector in Colombia and particularly in Tumaco (ref 59). The presence of An. albimanus in different neighborhoods of Commune 5 provides partial evidence of the possible local transmission of malaria. This mosquito has been considered an opportunistic species due to its ability to adapt to different breeding sites (ref 60). Despite the small number of adults collected, there is a risk of transmission, taking into account that the maximum biting activity occurs in the peridomicile between 18:00 and 19:00 hours. Furthermore, a critical analysis of the constraints of entomological studies must be incorporated. Particular attention requires the limitation related to entomological aspects. The results presented are only an approximation to the subject. The difficulties presented did not allow them an adequate study of the ecology of the vector and to characterize the aspects related to the vector's biting density, feeding patterns, biting activity, parity rates, and resting behavior, among other issues that represent important factors for malaria transmission within the Commune 5." } ] }, { "id": "135483", "date": "23 May 2022", "name": "Meor Termizi Farah Haziqah", "expertise": [ "Reviewer Expertise Parasitology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper discusses malaria prevalence based on several methods (microscopy examination, RDT, and PCR), detection of pfhrp 2/3 genes as well as explores the associated factors for malaria infection in the urban area (Commune 5) in Tumaco, Colombia in 2019. The main contribution of the paper is mainly on the information on malaria infection in Tumaco, Colombia with the most recent status of malaria infection was found to be very low with only 2.97% prevalence out of 1,504 individuals being examined. Other than that, it was found that all the positive cases were caused by Plasmodium falciparum and this study also manages to detect the main vector species for this parasite which is the Anopheles albimanus. The larvae were detected in a pond and a well whereas the adults were detected indoors and in peri-domestic areas.\nHowever, there are a few suggestions that need to be considered such as follows:\nFigure 1: it is advisable to have a better mapping as the map provided is not clearly demonstrating the study areas. For example, putting the legends on the map indicating Commune 5 and the map becomes more legible.\n\nThe total number of samples for each of the laboratory procedures (i.e. techniques used to detect malaria) need to be stated clearly.\n\nIt would be better and more understandable to include a schematic diagram of the study sampling technique.\n\nAs for DEFINITION in methods, reword the sentence and provide it in the form of a paragraph which explains in detail the definition used in this paper.\nTherefore, I recommend that this paper be Approved after minor revision.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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": "8702", "date": "08 Sep 2022", "name": "Pablo Enrique Chaparro Narváez", "role": "Author Response", "response": "Thank you for your review. These are our answers for your review: Figure 1: it is advisable to have a better mapping as the map provided is not clearly demonstrating the study areas. For example, putting the legends on the map indicating Commune 5 and the map becomes more legible. A: We have shown the study area on the map and have included the legends The total number of samples for each of the laboratory procedures (i.e. techniques used to detect malaria) need to be stated clearly. A: The prevalence was established from 1,504 microscopic examinations, 1,504 rapid diagnostic tests, and 1,504 PCR. It would be better and more understandable to include a schematic diagram of the study sampling technique. A: We have included the schematic diagram of the study's sampling technique As for DEFINITION in methods, reword the sentence and provide it in the form of a paragraph which explains in detail the definition used in this paper. A: This study assumed the definitions of symptomatic malaria, asymptomatic malaria, and submicroscopic malaria. Symptomatic malaria corresponded to an individual with positive microscopy/RDT and symptoms of malaria, such as fever, chills, vomiting, convulsions, malaise, headache and/or loss of appetite. Asymptomatic malaria corresponded to an individual with positive microscopy/RDT or PCR, without symptoms. 38,39. Submicroscopic malaria corresponded to an individual with positive PCR and negative microscopy/RDT. Submicroscopic infections are almost exclusively asymptomatic. 39" } ] } ]	1	https://f1000research.com/articles/11-448
https://f1000research.com/articles/11-136/v1	02 Feb 22	{ "type": "Systematic Review", "title": "The effectiveness of different aerobic exercises to improve pain intensity and disability in chronic low back pain patients: a systematic review", "authors": [ "Shabbir Ahmed Sany", "Maria Mitsi", "Taukir Tanjim", "Minhazur Rahman", "Maria Mitsi", "Taukir Tanjim", "Minhazur Rahman" ], "abstract": "Background: Physical activity, including aerobic exercise, is highly recommended for chronic low back pain (CLBP) patients to improve pain intensity and functional disability. Objectives: To assess the effectiveness of different aerobic exercises to reduce pain intensity and functional disability in patients with CLBP. Methods: A computer-aided search was performed to find Randomised controlled Trials (RCTs) that evaluated the effectiveness of different aerobic exercises in CLBP. Articles published between January 2007 to December 2020 were included in the review. Quality assessment using the PEDro scale, extraction of relevant information, and evaluation of outcomes were done by two reviewers independently. Results: A total of 17 studies were included that involved 1146 participants. Outcomes suggested that aerobic exercise combined with other interventions was more effective than aerobic exercise alone. Aerobic exercise with higher frequency (≥ 5 days/week) and longer duration (≥ 12 weeks) were effective to gain clinically significant (≥ 30%) improvements. Environment and using pedometer did not seem to influence the outcomes. Conclusions: Pain intensity and functional disability in CLBP patients can be minimized by prescribing aerobic exercise. However, to get better improvements, aerobic exercise should be done in combination with other interventions and at optimum frequency and duration. Further studies should emphasize examining the optimal doses and period of different aerobic exercises.", "keywords": [ "Aerobic exercise", "chronic low back pain", "cycling", "running", "walking." ], "content": "Introduction\n\nLow back pain (LBP) is one of the leading causes of disability-related musculoskeletal conditions globally.1,2 It is reported that 70-80% of the population suffer from LBP at some point in their lifetime.2,3 80-90% of those patients recover spontaneously from the acute phase of LBP within six weeks without taking any specific treatment.4–6 However, the remaining 10-20% of patients develop chronic low back pain (CLBP), which is very difficult to treat and may lead to significant disability.5–7 The National Health Service (NHS) spends more than £9 billion to provide CLBP patients treatment.8 CLBP is now regarded as a significant public health problem globally, and the prevalence of CLBP has risen noticeably in the past decades.9\n\nChronic low back pain (CLBP) is defined as pain, muscle tension, or stiffness located between the lower rib margins and above the lower gluteal folds that persists for more than 12 weeks (three months) with or without symptoms in the lower limbs.10 Decreased physical activity is regarded as one of the main contributing factors to chronic musculoskeletal pain conditions, including CLBP.11 Hence, the patients suffering from CLBP are encouraged to do regular exercise, and research showed that exercise was effective in preventing LBP by 35-45%.12 Different clinical practice guidelines also recommended exercise as the first-choice treatment of CLBP.13–16 Short-term and long-term improvements in pain and disability in CLBP patients can be achieved by doing exercises including aerobic exercise, flexibility training, stretching exercise, and resistance training.17–20 However, there is still insufficient evidence regarding the best approach, intensity, and form of exercise program or physical activity that produces optimal outcomes for people with CLBP.19,21\n\nAerobic exercise (AE) is one of the most recommended and widely used CLBP patients' interventions.22,23 According to The American College of Sports Medicine (ACSM), AE is any structured physical activity that is rhythmic, uses large muscle groups of the body, and can be maintained continuously.24,25 Walking, swimming, cycling, jogging, running, and hiking are typical AE examples.25,26 Patients with CLBP can benefit from doing AE, as it increases the blood flow and nutrients supply to the soft tissue in the back, which facilitates the healing process.27 Moreover, AE can significantly reduce pain intensity in CLBP patients by decreasing pain perception and muscle stiffness at the back.18,28,29\n\nRecently, some systematic reviews and meta-analyses, including by Vanti et al.,30 Sitthipornvorakul et al.,31 and Lawford et al.,32 showed that walking exercise was as effective as other exercise and non-pharmacological interventions. Nevertheless, they evaluated only walking exercise; therefore, other forms of aerobic exercise were missed. To our knowledge, only two reviews have been conducted so far that assessed the effectiveness of different AE in CLBP patients.23,33 However, neither of these reviews included a study published after 2013. Therefore, we carried out this systematic review to evaluate the recently published articles and provide up-to-date information. This review aimed to evaluate different AE's effectiveness in improving pain intensity and disability in CLBP patients.\n\n\nMethods\n\nThis review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.34\n\nDifferent databases were searched, including PubMed, CINAHL, PEDro, MEDLINE, and SPORTDiscus, to identify the relevant studies. We searched articles published between January 2007 to December 2020 as we focused on evaluating the recently published articles. The following keywords were used independently and in combination: low back pain, backache, aerobic exercise, walking, treadmill walking, cycling. The first and second authors examined titles, abstracts, and complete articles of potentially relevant papers independently to determine eligibility. Any disagreements on eligibility were scrutinized by the third and fourth authors and were resolved through discussion.\n\nRandomized controlled trials (RCTs) that evaluated the effectiveness of AE with or without other intervention that recruited subjects ≥ 18 years with CLBP were included in this review. Non-randomized controlled trials that recruited subjects with acute, subacute, and chronic LBP together were excluded. Papers published before 2007 and other than the English language were also excluded.\n\nDetails of inclusion and exclusion criteria are shown in Table 1.\n\n\n\n• Used a randomized controlled trial design.\n\n• Examined aerobic exercise with or without other intervention in at least one group.\n\n• Papers published between January 2007 to December 2020.\n\n\n\n• The study that investigated patients with chronic low back pain and acute and/or subacute LBP together.\n\n• Papers published other than the English language.\n\n\n\n• Aged ≥ 18 years\n\n• Patients with low back pain for a minimum of 3 months (≥12 weeks).\n\n\n\n• Patients with acute or subacute low back pain.\n\n• Patients with cauda equine syndrome.\n\n• Patients with inflammatory or tumoral back conditions.\n\n• Patients with osteoporosis of spine and pregnancy.\n\n• Patients with a history of surgery in the lumbosacral region, spinal fracture, and dislocation.\n\n\n\n• Studies that evaluated at least pain intensity or functional disability as the outcome with or without other measurements.\n\nThe Physiotherapy Evidence Database (PEDro) scale was employed to assess the methodological quality and risk of bias of included studies. PEDro scale is regarded as a valid and reliable risk of bias tool.35,36 PEDro scale has 11 components or items including eligibility criteria, random allocation, concealed allocation, baseline similarity, blind subjects, blind therapists, blind assessors, sufficient follow up (85% follow up for at least one key outcome), intention-to-treat analysis, between-group statistic comparison (for at least one key outcome), and point estimates and variability (for at least one key outcome).37 Eight items (item 2-9) are used to evaluate the risk of bias and last two items (10 and 11) are related to statistical reporting.36 The first item which is eligibility criteria is not counted in the total score as it is related to external validity. Hence, PEDro score ranges between 0 and 10 points, where the article with higher score regarded as better article in terms of risk of bias and statistical reporting. Any study with a score between 6 and 10, score with 4 or 5, and score ≤ 3 is considered good quality, fair quality, and poor quality study, respectively.38,39 However, it is impossible to blind therapists and all subjects in clinical trials because of ethical standards. Hence any study with a score of 8/10 is regarded as low risk of bias.39 PEDro scoring was done using the PEDro scale by the first two authors independently, and the other two authors resolved any discrepancy through discussion.\n\nRequired data were extracted from studies by using a data extraction form. The first two reviewers extracted relevant information on sample size and subject characteristics; type, frequency, intensity, and duration of interventions; instruments used to assess the outcomes; and outcomes of pain intensity and functional disability. The third and fourth authors further evaluated the extracted data, and any disagreements were resolved through discussion. The outcomes were continuous variables, and treatment effects were reported as mean differences and mean percentage changes. Mean percentage changes ≥ 30% were regarded as minimal clinically significant differences (MCID) described by the previous studies.40–42\n\n\nResults\n\nAfter searching databases, a total of 1,145 studies were identified. After removing duplicates, 1135 articles were screened by title and content of the abstract. After that screening, 1055 articles were excluded, and the remaining 80 articles were evaluated for eligibility. Finally, a total of 17 studies met all inclusion criteria and were included for this review. A PRISMA flow diagram of the study selection process is shown in Figure 1.\n\nAll included studies were RCTs, involved a total of 1146 patients. The number of participants ranging from 1443 to 246,44 and patients were >18 years. The duration of included studies' intervention was between 4 weeks45 and 12 months.46 Among these, eleven studies followed up for short term (<3 months or 12 weeks),45,47–56 eleven studies followed up for intermediate-term (3 months to <12 months)43,44,46–48,52,53,56–59 and two studies followed up for long term (≥12 months).46,55 Studies examined the effectiveness of different types of AE. Eleven studies evaluated the effectiveness of different forms of AE alone43–47,49,54,56–58 while seven studies examined AE in conjunction with other intervention including stabilization exercise,47 back school program,50 rehabilitation program,51 group exercise class,52 traditional physiotherapy55 and home exercise.48\n\nAs an intervention, ten studies used walking exercise45–49,51,53,54,58; three studies used stationary cycling exercise45,50,52; one study used treadmill running exercise57; one study used both walking and running exercise43; one study used combined treadmill walking, stair climbing and stationary cycling exercise59; one study used walking and jogging exercise with elliptical trainer56; one study used individually designed and supervised aerobic exercise.55\n\nIn this review, we focused on the improvement in pain intensity and functional disability. To measure pain intensity, nine studies used the Visual Analogic Scale (VAS),43,47–49,51,52,55,56,59 six studies used Numerical Pain Rating Scale (NRS),44–46,50,53,58 one study used McGill Pain Questionnaire (MPQ)57 and one study did not measure pain intensity.54 Functional disability was evaluated by using Oswestry Low Back Pain Disability Index (ODI, 0-100) in eleven studies,43–45,47,49,52–54,56,58,59 Oswestry Low Back Pain Disability Index (ODI,10-60) in one study,51 Roland and Morris Disability Questionnaire (RMDQ) in four studies46,48,50,57 and Aberdeen Low Back Pain Disability Scale (ALBPS) in one study.55\n\nQuality assessment of included studies using the PEDro scale is shown in Table 2, which demonstrated that the range of the scores was between 4/10 and 8/10 (mean 6.35 ± 1.46). Two studies scored the minimum (4/10),45,51 while five studies reached the best possible score (8/10).49,52–54,58 Eleven studies obtained the threshold score (6/10) to be considered a good quality study.43,44,46,47,49,52–55,58,59 Studies that scored the lowest had a lack of concealed allocation, blind assessors, adequate follow-up, and intention-to-treat analysis.45,51\n\nWalking alone exercise\n\nBello et al.50 compared walking exercise alone to lumbar stabilization exercise by involving a total of 50 patients who were divided into walking exercise group (WG) and lumbar stabilization exercise group (LSG). WG received walking exercise on the treadmill at an intensity of 65-80% HRR, while LSG received 30 mins of lumbar stabilization exercises following the McGill protocol for eight weeks (three times/week).50 After intervention, both groups showed improvement in pain (WG vs LSG = 32.8% vs 59.4%) and disability (WG vs LSG = 14.4% vs 48.9%), while LSG demonstrated better outcomes.50\n\nIn another study, Shnayderman and Katz-Leurer54 evaluated the effectiveness of walking exercise (WG) against specific low back strengthening exercises (SG) by recruiting 52 patients. WG received 40 minutes of walking exercise on the treadmill at 50% heart rate reserve.54 Both groups received exercises two days a week for six weeks.54 Outcomes revealed that both groups showed significant improvements in disability without significant differences between groups where ODI scores were reduced by 34.3% in WG and 30.6% in SG.54\n\nBoth studies' significant limitations included lack of a control group, no long-term follow-up, and a short intervention period. Conversely, Hurley et al.44 evaluated walking exercise's effectiveness with a larger sample size and long-term follow-up. 246 patients aged 18-65 were equally divided into three groups. The first group (WG) received supervised walking exercise for a minimum of 10-minutes to 30 minutes walk/day at 40-60% HRR, at least four times/week for seven weeks.44 The second group (ECG) trained with group exercise class (Back to fitness program, a one-hour long class per week for eight weeks) and exercise including warm-up and stretching. The third group (UG) received usual physiotherapy.44 Results showed that pain and disability improved in all three groups.44 Authors reported that 48% in WG, 45% in ECG, and 31% in UG participants achieved minimal clinically significant difference (MCID) in the ODI score.44 Whereas 44%, 29%, and 37% of WG, ECG, and UG participants reached MCID in the NRS score.44 Authors also reported that the walking program had the greatest adherence and the lowest costs.44 A significant limitation of this study was that a total of 40 therapists were involved in this study to train the patients; hence therapist effects could influence the outcomes.\n\nWalking exercise in conjunction with other intervention\n\nCho et al.51 studied whether treadmill walking exercise combined with a low back pain rehabilitation program helped reduce pain and disability in CLBP patients. Twenty men were equally divided into an experimental group (EG) and a control group (CG).51 EG received treadmill walking exercise without a slope at 3-3.5 km/h, for 30 minutess and low back pain rehabilitation program; whereas, CG received only a low back pain rehabilitation program.51 Both groups received 30 minutes long low back pain rehabilitation program, three days/week, and the duration of intervention was eight weeks.51 After the intervention, both groups showed improvement in pain (VAS) and disability (ODI) scores without any significant difference between groups.51 In EG, VAS and ODI scores were reduced by 46.1% (vs 43.5% in CG) and 21.5% (vs 12.7% in CG) respectively. Overall, additional treadmill exercise did not provide additional improvements.51 The small sample size was a major drawback of this study.\n\nKoldas et al.48 experimented with a larger sample of sixty patients to examine combined walking exercise and home exercise effectiveness. Twenty patients (AHE) received 40-50 minutes of exercise on a treadmill at 65-70% HRR, three times/week with home exercise.48 At the same time, the remaining 40 patients were assigned to receive either physical therapy (PT) or home exercise only (HE).48 Home exercises included basic flexion, extension, mobilization, and stretching, and the patients were asked to perform the exercise once a day with 15-20 repetitions.48 All groups received their specific exercises for six weeks.48 Results showed that pain reduced significantly in all three groups after the treatment (AHE vs. PT vs. HE: 39.6% vs. 36.5% vs. 28.6%) and at one-month follow-up (AHE vs. PT vs. HE: 38.8% vs. 53% vs. 40%).48 Disability was improved significantly in AHE and PT at both post-intervention (25.2% vs. 25.2%) and follow-up (22.7% vs. 30.3%), while in HE, it was negligible.48\n\nIn another study, Suh et al.47 utilized 48 patients aged > 20 years to compare walking exercise alone (WE) to three different interventions, including combined walking and stabilization exercise (SWE), flexibility exercise (FE), and only stabilization exercise (SE). The WE group received 30 mins of fast walking exercise on flat ground with abdominal bracing, whereas the SWE group trained with 30 minutes of walking exercise and 30 minutes of stabilization exercise.47 Outcomes were measured at baseline, within two weeks after intervention and six weeks after the intervention.47 Results indicated that pain intensity decreased in all four groups both during activity (FE vs WE vs SE vs SWE: 45.26% vs 38.7% vs 48.19% vs 44.06%) and at rest (FE vs WE vs SE vs SWE: 33.61% vs 18.25% vs 35.33% vs 38.9%) after the intervention.47 Further assessment at six weeks after intervention showed that all groups retained enhancement in pain scores.47 Disability evaluation demonstrated that after the intervention, the ODI score was decreased by 19.93% in WE; while in FE, SE and SWE, it was 16.05%, 19.43%, and 18.09%, respectively.47 The frequency of exercise in SE and WE increased significantly after the intervention. However, the SWE group showed the opposite trend, which demonstrated poor adherence to exercise, and it was difficult for the participants of the SWE group to perform 60 minutes of exercise.47\n\nPedometer-driven walking exercise\n\nEadie et al.58 experimented on 60 patients aged 18-70 years by distributing them into three groups (WG, SG, PG). WG received walking exercise for 30 minutes at moderate intensity, five days/week, and they were asked to wear a pedometer during walking to record the progress.58 SG Received a supervised exercise class (back to fitness program) once per week, whereas PG received usual physiotherapy.58 The total intervention duration was eight weeks, and outcomes were measured at three months and six months.58 Pain score evaluation showed that both WG (12.1%) and SG (12.9%) gained similar improvements, whereas PG (32%) obtained more significant improvements.58 However, unlike the other two groups, WG (-1.79%) failed to retain the improvements at six months.58 Moreover, the smallest improvement in disability also was in WG (9.4%) compared to SG (22%) and PG (27.3%).58 The authors reported small sample size and a high drop-out rate during the follow-up period could impact the outcomes.58\n\nBesides, McDonough et al.53 examined 57 patients aged between 43 and 53 years. The experimental group (EG) received combined pedometer-driven walking exercise and education, whereas the control group (CG) received only education or advice. Participants were familiarized with wearing a pedometer, and they were asked to record their daily steps in a walking diary.53 The intervention duration was nine weeks, and measurements were done after intervention and six months after randomization.53 Results indicated pain intensity improved in both groups; however, EG showed greater improvement (16.7% vs. 15.2% at nine weeks and 29.6% vs. 10.9% at six months).53 EG showed a better outcome in disability (17.2% vs 3.3% at nine weeks and 25.7% vs 5.5% at six months).53 However, the sample size was relatively small, which was a weakness of this study.\n\nIn contrast, Krein et al.46 experimented with a larger sample size and long-term follow-up to examine whether additional support affected patients' improvement. They examined 229 patients by separating them into two groups: experimental group (EG) and usual care group or control group (CG).46 EG received an uploading pedometer and additional support, access to a website that provided information about walking goal progress, and patients received feedback, motivational and informational messages.46 In contrast, CG received an uploading pedometer but did not receive any walking goal and did not access the website.46 This study's duration was 12 months, and outcome measurements were done at baseline, six months, and 12 months.46 Results demonstrated pain intensity improved in both groups at six months (EG vs CG = 21.7% vs 14.8%) and 12 months (EG vs CG = 10% vs 8.2%), where improvements were greater at six months.46 Disability improvement was also greater in EG at six months (20.9% vs. 6.1%).46 Patients were recruited from one medical center, which was indicated as a limitation of this study.46\n\nStationary cycling exercise\n\nBarni et al.50 evaluated the effectiveness of a combined back school program and stationary cycling exercise by recruiting 22 patients. Patients were assigned to either the experimental group (EG) who received exercise on the stationary bike at 65% HRR and back school program; or the control group (CG) who received only the back school program.50 The interventions' total duration was five weeks (90 minutes session, two sessions/week).50 Post-intervention measurements showed a greater reduction in NRS and RMDQ index in the experimental group than in the control group (NRS = 27% vs 13.14% and RMDQ = 25.58% vs 10.3%).50 This study's major limitations were lack of long-term follow-up, short duration of intervention, and a small number of participants.\n\nMarshall et al.52 experimented with a relatively larger sample size (64 patients) and a longer duration to observe whether stationary cycling exercise combined with exercise class (CEG) was more effective than specific trunk exercise conjunction with exercise class (SEG). Both groups received their specific exercise for 35-40 minutes and 50-60 minutes of exercise classes (three sessions/week) for eight weeks.52 Outcomes were recorded at baseline, post-intervention, and six months from the start of the intervention.52 Results showed that pain decreased in both groups (SEG vs CEG = after intervention: 52.8% vs 17.8%, at six months: 44.4% vs 26.7%), where SEG showed better improvements.52 56% of SEG and 50% of CEG participants showed clinically relevant changes (≥ 30%) after intervention.52 Disability was significantly lower in SEG compared to CEG after the intervention (40.9% vs. 16.3%), and 66% of SEG and 44% of CEG participants demonstrated clinically significant change (≥30%) in ODI score.52 The authors concluded that both exercises effectively improved pain and disability without significant differences between groups.52 Although trunk exercise showed better improvements than stationary cycling immediately after the intervention, long-term follow-up outcomes were similar.52\n\nChulliyil et al.45 examined whether stationary cycling exercise is superior to treadmill walking to improve CLBP. A total of 30 patients aged 18-30 years were divided into two groups.45 One group (TG) received AE by treadmill walking, while another group (SCG) received AE by stationary cycling.45 Both groups received AE at moderate intensity (13-14 RPE) for 10-20 minutes for four weeks (five days/week).45 Post-intervention measurements demonstrated that both groups showed significant improvements in all measurements without any significant differences between groups (TG vs SCG = NRS at rest: 80.1% vs 69.3%, NRS on activity: 55.4% vs 45.3%, ODI: 53.8% vs 49.8%).45 However, the very short duration of the study and the absence of long-term follow-up were the major drawbacks of this study.\n\nTreadmill running exercise\n\nChatzitheodorou et al.57 recruited 20 patients to examine the effectiveness of running exercise to improve CLBP. Ten patients in the experimental group (EG) received high-intensity AE by running on the treadmill at 60%-85% of HRR, 30-50 minutes session, three sessions/week.57 Whereas the remaining ten patients in the control group (CG) received passive modalities (45 minute session) without any physical activity.57 After intervention (12 weeks) EG showed significantly better improvement in pain (40.1% vs. 0.6%) and disability (30.4% vs. 0.7%) compared to CG.57\n\nCombination of different aerobic exercises\n\nMurtezani et al.59 examined 101 patients with CLBP by assigning them either to the experimental group (EG) or the Control group (CG). EG received high-intensity AE, including treadmill walking, stair climbing, and stationary bicycling at 50%-85% HRR, 30-50 mins sessions, three sessions/week for 12 weeks.59 In contrast, CG received passive modalities (45 min session, three times/week).59 Results showed significant improvements in all parameters in EG (pain 66.7% and disability 49%), while the improvements in CG were non-significant (pain 1.6%, disability 0.3%).59\n\nIndividually designed and supervised aerobic exercise\n\nChan et al.55 utilized 46 patients who were included either in the experimental group (EG) or control group (CG). EG received conventional physiotherapy and 20 minutes of aerobic training at 40%-60% HRR, gradually progressed up to 85% at a 5% increment each weak for eight weeks (three sessions per week).55 Subjects in EG were also asked to perform a minimum of one additional training per week at home.55 Participants selected the type of that training according to their preference, including treadmill walking or running, stepping, and cycling.55 Subjects in the control group received only conventional physiotherapy for eight weeks.55 Post-intervention measurements indicated significant improvements in pain and disability in both groups without any significant differences between groups.55 EG attained clinically significant improvements (≥ 30%) in VAS and ALBPS scores at all time points.55 The short duration of intervention and relatively small sample size are major limitations of this study.55 In addition, the authors reported poor baseline fitness level of patients, which could be a factor to influence the outcomes.55\n\nInfluence of the environment\n\nKanitz et al.43 experimented on 14 patients to see the impact of the environment on AE outcomes. Participants were randomly allocated into two groups and received 35 minutes of walking/running exercise at moderate intensity (85-95% HRvt2) for 12 weeks (two times/week) either on land (LG) or in water (AG).43 Outcomes showed improvements in pain and disability score in both groups without any difference between groups (LG vs. AG = pain: 66.67% vs. 47.27% and disability: 40.59% vs. 48%).43 However, small sample size and absence of long-term follow-up were reported as weaknesses of this study.43\n\nPeriodized progressive overload training\n\nKell and Asmundson56 carried out an experiment to observe periodized progressive overload training effectiveness. A total of 27 patients with CLBP were equally divided into three groups (AT, RT, and CG).56 AT received periodized progressive overload aerobic training (elliptical trainer and treadmill walking and jogging. 20-35 min session, three sessions/week), while RT received periodized resistance training.56 Patients in the control group (CG) maintained regular activity.56 The intervention's total duration was 14 weeks, consisting of two phases (seven weeks per phase).56 Outcomes were measured after completing each phase (at eight weeks and 16 weeks).56 Results showed significant improvement in pain (27.8% at eight weeks and 38.9% at 16 weeks) and disability (30.2% at 8 weeks and 40.1% at 16 weeks) in RT. In contrast, AT demonstrated improvement only in cardiorespiratory performance (VO2max), body fat, and body mass.56 However, an experiment with a larger sample size is needed to conclude the efficacy of periodized progressive overload aerobic training on CLBP patients.\n\nThe summary of interventions, measurements, outcomes, and main limitations of the included studies are shown in Table 3 and Table 4.\n\n\n\n• Group 1 (LG): Received aerobic exercise on land.\n\n• Group 2 (AG): Received aerobic exercise in deep water.\n\n• Aerobic exercise included walking/running at moderate intensity (85-95% HRvt2) for 35 mins.\n\n• Duration: 12 weeks (Two times a week).\n\n\n\n• Pain (VAS)\n\n• Disability (ODI)\n\n• Measurements were done at baseline and after the intervention\n\n\n\n✓ Improvements in pain and disability score were observed in both groups without any difference between groups.\n\n\n\n▪ Small sample size.\n\n▪ Low frequency of training.\n\n▪ No long-term follow-up.\n\n\n\n• Group 1 (LSG): Received lumbar stabilization exercises following the McGill protocol (30 minutes session).\n\n• Group 2 (WG): Received treadmill walking exercise (at 65%-80% HRR).\n\n• Duration: 8 weeks (three times a week).\n\n\n\n• Pain intensity (VAS).\n\n• Functional disability (ODI).\n\n• Measurements were done at baseline and after the intervention.\n\n\n\n✓ Significant improvements in pain intensity and disability in both groups were observed.\n\n✓ LSG showed significantly greater improvements in all parameters than WG.\n\n\n\n▪ EMG activity of muscles could not be measured by using needle insertion.\n\n▪ No long-term follow-up.\n\n▪ Short duration of intervention.\n\n\n\n• Group 1 (TG): Received aerobic exercise by treadmill walking.\n\n• Group 2 (SCG): Received aerobic exercise by stationary cycling.\n\n• Aerobic exercise was at moderate intensity (13-14 RPE) for 10-20 mins.\n\n• Duration: 4 weeks (5 days/week).\n\n\n\n• Pain intensity at rest and on activity (NRS)\n\n• Disability (modified ODI)\n\n• Measurements were done at baseline and after the intervention.\n\n\n\n✓ Both groups showed significant improvements in all measurements without any significant differences between groups.\n\n\n\n▪ Very short duration of intervention.\n\n▪ Man and woman participants were not the same in number.\n\n▪ No follow-up was done.\n\n\n\n• Group 1 (WG): Received supervised walking exercise (minimum 10 min to 30 min walk/day at 40-60% HRR, for at least 4 days per week for 7 weeks.\n\n• Group 2 (ECG): Received group exercise class (Back to fitness program, a one-hour long class per week for 8 weeks.) and exercise including warm-up and stretching.\n\n• Group 3 (UG): Usual physiotherapy (education, exercise therapy, and manipulative therapy).\n\n• Duration: 8 weeks\n\n\n\n• Pain (NRS 0-10)\n\n• Functional disability (ODI)\n\n• Measurements were done at baseline and at 3, 6, and 12 months after randomization.\n\n\n\n✓ Significant improvements were observed in all three groups, with no significant differences between groups at all time points.\n\n✓ No difference in the efficacy of all three programs.\n\n✓ WG had the greatest adherence\n\n✓ WG had the lowest costs.\n\n\n\n▪ Lack of blinding of therapists and patients.\n\n▪ Treating therapists were high in number.\n\n\n\n• Group 1 (WG): Received walking exercise (30 mins at moderate intensity, 5 days per week). (Pedometer was used to record the progress)\n\n• Group 2 (SG): Received supervised exercise class (back to fitness program, once per week).\n\n• Group 3 (PG): Received usual physiotherapy (advice, manual therapy, and exercise)\n\n• Duration: 8 weeks.\n\n\n\n• Pain (NRS)\n\n• Disability (ODI)\n\n• Measurements were done baseline, 3 months, and 6 months.\n\n\n\n✓ Greater pain intensity and disability improvements were observed in PG than WG and SG in all time points.\n\n\n\n▪ Small sample size.\n\n▪ High drop-out rate during the follow-up period.\n\n\n\n• Group 1 (WG): Received walking exercise on a treadmill (at 50% heart rate reserve, 40 min session, 2 sessions per week).\n\n• Group 2 (SG): specific low back strengthening exercises (2 times per week).\n\n• Duration: 6 weeks.\n\n\n\n• Disability (ODI)\n\n• Measurements were done at baseline and after the intervention.\n\n\n\n✓ Both groups showed significant improvements in all outcomes.\n\n✓ No significant differences between groups.\n\n\n\n▪ The participants were not classified and divided into groups according to sign and symptoms.\n\n▪ Short study duration.\n\n\n\n• EG: Received high-intensity aerobic exercise including treadmill walking, stair climbing, and stationary bicycling (at 50%-85% HRR, 30-50 mins sessions, three sessions per week).\n\n• CG: Passive modalities including interferential current, TENS, ultrasound, heat. (45 min session, three times per week)\n\n• Duration: 12 weeks.\n\n\n\n• Pain intensity (VAS)\n\n• Disability (ODI)\n\n• Measurements were done at baseline and after the intervention.\n\n\n\n✓ The experimental group showed significant improvements in all parameters.\n\n✓ Improvements in the control group were not significant\n\n\n\n▪ No long-term follow-up was done.\n\n▪ Not single or double-blinded.\n\n\n\n• RT group: Received periodized resistance training.\n\n• AT group: Received periodized progressive overload aerobic training (elliptical trainer and treadmill walking and jogging. 20-35 min session, 3 sessions per week).\n\n• CG: Maintained normal activity.\n\n• Duration: Total 14 weeks of exercise. (2 phases, 7 weeks per phase)\n\n\n\n• Pain (VAS)\n\n• Disability (ODI)\n\n• Measurements were recorded at baseline, at 8 weeks, and at 16 weeks.\n\n\n\n✓ RT groups – Significant improvement in pain, disability.\n\n✓ AT group - More significant improvement in ODI compared to the control group but lesser than RT.\n\n\n\n▪ Small sample size.\n\n\n\n• EG: High-intensity aerobic exercise (running on a treadmill at 60%-85% of HRR 30-50 mins session, 3 sessions per week).\n\n• CG: Received passive modalities including short-wave diathermy, ultrasound, laser, and electrotherapy without any PA. (45 min session).\n\n• Duration: 12 weeks.\n\n\n\n• Pain intensity (MPQ)\n\n• Disability (RMDQ)\n\n• Measurements were done at baseline and after the intervention.\n\n\n\n✓ Significant improvements in pain and disability were observed in the experimental group.\n\n\n\n▪ Small sample size.\n\n▪ No long-term follow-up.\n\n\n\n• FE group – Received flexibility exercise (stretching exercise for 30 mins).\n\n• WE group – Received Walking exercise. (fast walking on flat ground with abdominal bracing for 30 mins)\n\n• SE group – Received stabilization exercise (5 min warm-up and 25 mins of stabilization exercise according to patients exercise capacity).\n\n• SWE – stabilization and walking exercise (30 mins SE and 30 mins WE).\n\n• Duration: 6 weeks (30 to 60 minutes session, 5 sessions per week), and patients were advised to continue the exercise till the second follow-up at 12 weeks.\n\n\n\n• Pain intensity during rest and physical activity (VAS).\n\n• Disability (ODI)\n\n• Measurements were done at baseline, within 2 weeks after the intervention, and at 6 weeks after the intervention.\n\n\n\n✓ Pain intensity during physical activity was significantly decreased in all 4 groups.\n\n✓ Exercise frequency was significantly increased in the SE and WE group.\n\n✓ The endurance of supine, side-lying, and prone posture were significantly improved in the WE and SWE groups.\n\n\n\n▪ Short study period\n\n▪ No control groups.\n\n\n\n• EG: Received 15 minutes of aerobic exercise (on the stationary bike at 65% HRR) and back school program.\n\n• CG: Received only back school program.\n\n• Duration: 5 weeks (2 sessions per week, per session, consisted of 90 minutes).\n\n\n\n• Pain intensity (NRS)\n\n• Disability (RMDQ).\n\n• Measurements were recorded before and after the intervention.\n\n\n\n✓ More significant reduction in NRS and RMDQ index in the experimental group than in the control group.\n\n\n\n▪ No long-term follow-up.\n\n▪ Small sample size.\n\n▪ Short duration of intervention.\n\n▪ Functional test was not performed.\n\n\n\n• Group 1 (WG): Received walking exercise (30 mins at moderate intensity, 5 days per week). (Pedometer was used to record the progress)\n\n• Group 2 (SG): Received supervised exercise class (back to fitness program, once per week).\n\n• Group 3 (PG): Received usual physiotherapy (advice, manual therapy, and exercise)\n\n• Duration: 8 weeks.\n\n\n\n• Pain (NRS)\n\n• Disability (ODI)\n\n• Measurements were done baseline, 3 months, and 6 months.\n\n\n\n✓ Greater pain intensity and disability improvements were observed in PG than WG and SG in all time points.\n\n\n\n▪ Small sample size.\n\n▪ High drop-out rate during the follow-up period.\n\n\n\n• EG: Received an uploading pedometer and had access to a website that provided automated walking goals, feedback, motivational messages, and social support through an e-community.\n\n• CG: Received an uploading pedometer but did not receive any walking goal and did not have access to the website (usual care group).\n\n• Duration: 12 months.\n\n\n\n• Pain intensity (NRS)\n\n• Pain-related disability (RMDQ)\n\n• Measurements were done at baseline, 6 months, and 12 months.\n\n\n\n✓ Greater improvement in RMDQ was observed in the experimental group at 6 months.\n\n✓ Pain intensity improved in both groups at 6 months and 12 months; however, at 6 months, improvements were more significant.\n\n\n\n▪ Patients were recruited from one medical center.\n\n\n\n• Group 1 (SEG): Received specific trunk exercise (35-40 min session, 3 sessions per week).\n\n• Group 2 (CEG): Received stationary cycling exercise (35-40 min session, 3 sessions per week).\n\n• Both groups attended exercise classes (50-60 min session, 3 times per week).\n\n• Duration: 8 weeks.\n\n\n\n• Pain (VAS)\n\n• Disability (ODI)\n\n• Measurements were done at baseline, after the intervention, and at 6 months from the start of the intervention.\n\n\n\n✓ Disability significantly lower in the SEG compared to CEG after the intervention.\n\n✓ Pain decreased in both groups after the intervention, while SEG showed better improvement.\n\n✓ Overall results suggested no long-term differences in outcomes between groups.\n\n\n\n▪ Severely impaired patients were not recruited.\n\n▪ No blind exercise supervision.\n\n\n\n• EG: Pedometer-driven walking program + education.\n\n• CG: Received only education or advice.\n\n• Duration: 8 weeks.\n\n\n\n• Pain intensity (NRS 0-10)\n\n• Functional disability (ODI 0-100)\n\n• Measurements were recorded at baseline, at week 9 (immediately after intervention), and at 6 months.\n\n\n\n✓ Pain intensity improved in both groups; however, EG showed greater improvement.\n\n✓ EG showed a better outcome in disability.\n\n\n\n▪ Relatively small sample size.\n\n\n\n• EG: Received aerobic exercise including treadmill walking or running, stepping, cycling exercises; selected by patient's preference (20 min session, 3 times a week at 40%-60% HRR, gradually progressed up to 85% at a 5% increment each weak) + conventional physiotherapy\n\n• Control group: Only conventional physiotherapy\n\n• Duration: 8 weeks.\n\n\n\n• Pain intensity (VAS)\n\n• Functional disability (ALBPS)\n\n• Measurements were done at baseline, 8 weeks, and 12 months from the start of the intervention.\n\n\n\n✓ Significant improvement in pain and disability in both groups at 8 weeks.\n\n✓ Improvement in disability sustained in both groups at 12 months.\n\n✓ No significant differences were observed between groups.\n\n✓ No significant difference in LBP relapse at 12 months between two groups.\n\n\n\n▪ The poor baseline fitness level of patients.\n\n▪ Short duration of intervention.\n\n▪ Relatively small sample size.\n\n\n\n• Group 1 (AHE): Aerobic exercise (40-50 min of exercise on a treadmill at 65-70% HRR, 3 times a week for 6 weeks) + home exercise.\n\n• Group 2 (PT): Physical therapy (hot pack, ultrasound, and TENS).\n\n• Group 3 (HE): Home exercise only (basic flexion, extension, mobilization, and stretching with 15-20 repetitions, once a day for 6 weeks).\n\n• Duration: 6 weeks.\n\n\n\n• Pain intensity (VAS)\n\n• Disability (RMDQ)\n\n• Measurements were done at baseline and at the end of the intervention. Follow-up was done at 1 month after the intervention.\n\n\n\n✓ Pain reduced significantly in all three groups after the treatment and at 1-month follow-up.\n\n✓ Disability improved significantly in PT at follow-up.\n\n✓ No significant differences in pain intensity, disability were observed between three groups after the treatment and at follow-up.\n\n\n\n▪ No control groups.\n\n▪ Relatively small sample size.\n\n▪ Short duration of intervention.\n\n\nDiscussion\n\nWalking is a highly cost-effective AE that is regularly advised to patients with CLBP.44,60,61 This exercise is easy to perform and does not require any particular skill or facilities.60,62 It is regarded as one of the safest exercises because of its low injury rate.60,62 Also, walking enhances cardio-respiratory capacity, maximum oxygen uptake, and prevents LBP by increasing the isometric endurance of muscles.63,64\n\nIn this review, three good-quality studies (PEDro score ≥ 7) compared walking alone exercise to other interventions.44,49,54 Studies showed that walking alone exercise effectively reduced pain and disability in CLBP patients.44,49,54 However, there was no evidence that walking alone exercise was superior to other interventions. Similar outcomes were reported in three different reviews, and they concluded that walking exercise was as effective as other interventions.30–32 Moreover, in this review, walking alone exercise was not effective in attaining clinically significant improvements (≥ 30%) in pain intensity and disability on most occasions.44,49,54 In previous studies, exercise alone therapy was not effective to make clinically significant changes (≥ 30%) in CLBP patients; therefore, it was suggested to apply combined treatment in clinical trials.22,65 Lawford et al.32 also asserted in their review that combined walking exercise was more effective than walking exercise alone.\n\nIn this review, three studies (fair to good quality) examined the effectiveness of walking exercise combined with other interventions.47,48,51 Results indicated that walking exercise combined with other interventions effectively reduced pain intensity in CLBP patients, and the improvements were clinically meaningful (≥30%).47,48,51 Besides, disability improvements were statistically significant in all three studies.47,48,51 However, these enhancements (<30%) were not remarkable enough to be clinically significant. It was claimed that to get better improvements in any intervention, patients should be trained for a sufficiently longer period.51 The duration of these studies was ≤ 8 weeks; hence, the duration could be too small to make any clinically significant improvement in disability. Moreover, exercise effectiveness can be improved by adjusting the intensity and duration of exercise according to patients' capacity.66 Research showed that atrophic changes in lumbar paraspinal muscles are common in CLBP patients, which could decrease patients' ability to do prolonged exercise.67,68 One of the included studies also showed that it was difficult for the patients to continue 60 minutes of exercise.47 Hence the authors advised selecting an exercise program with a duration of about 30 minutes.47\n\nRecently, internet-based programs are used to promote healthy behaviors.69–71 Some studies were carried out to see if pedometer-driven walking exercise could benefit CLBP patients' conditions.46,53,58 In this review, the findings of three included RCTs (PEDro score = 8) indicated that walking exercise in conjunction with advice, education, or support effectively improved CLBP patients' conditions.46,53,58 However, there was no clear evidence that using a pedometer had any extra benefits. A pedometer can guide a patient to track their progress, but further research is needed to recommend pedometer as rehabilitation tools for CLBP patients.\n\nStationary cycling exercise is another form of AE which is regarded as one of the most effective exercises to improve muscular coordination.50,72 Three fair to good quality RCTs were included in this review that examined the effectiveness of stationary cycling exercise, and outcomes demonstrated that stationary cycling exercise was as effective as walking exercise, and stationary cycling exercise was not inferior to other interventions.45,50,52 In addition, Chatzitheodorou et al.56 showed that high-intensity AE, including running, was adequate to improve pain and disability in CLBP patients significantly. In another study, Murtezani et al.59 demonstrated that a combination of different AE effectively improved conditions of CLBP patients. These included studies also showed the possible influence of exercise frequency and duration of intervention on outcomes. The study with the higher frequency of exercise (five days/week)50 and longer duration (12 weeks) of intervention57,59 showed clinically significant (≥ 30%) changes in both pain and disability scores.50 The American College of Sports Medicine recommended that physical activity should be performed for 30 minutes at moderate intensity with a frequency of five days/week.73–75 Therefore, the exercise frequency and duration of intervention could be the keys to obtain clinically significant improvements in pain intensity and disability in CLBP patients. However, future studies with a larger sample size and long-term follow-up are required to justify it.\n\nIndividually tailored and supervised exercise programs were suggested by Hayden et al.76 in their meta-analysis. In this review, one good quality study (PEDro = 7) showed that individually designed and supervised aerobic exercise effectively made clinically significant improvements in patients with CLBP.55 In addition, one good quality study (PEDro = 7) was included in this review that examined the impact of the environment on the effectiveness of aerobic exercise.43 Patients were randomly allocated and received the same exercise either on land or in water, and results indicated that the environment did not influence the outcomes.43 However, more studies with a large sample size and long-term follow-up are required for further evidence.\n\nOnly one included study in this review did an experiment to observe the effectiveness of periodized progressive overload training.56 Results showed that periodized progressive overload aerobic training failed to improve pain intensity and disability in CLBP patients.56 However, the study was regarded as fair quality (PEDro score 5); therefore, a good quality study with a larger sample size is warranted to conclude the effectiveness of periodized progressive overload aerobic training on CLBP patients.\n\n\nStrengths and limitations of the review\n\nThere are several strengths of this review. A highly sensitive search of different databases was performed to find the relevant studies. A total of 17 RCTs were included in this review that involved an adequate sample size of 1146 participants after applying strict inclusion and exclusion criteria. Moreover, PEDro scoring was done to assess quality and risk of bias, and all included studies scored ≥ 4 to be considered fair to good quality.\n\nIn contrast, in this review, only improvements in pain intensity and disability were evaluated, which was considered a major limitation. Other outcomes, including fear-avoidance beliefs, mental and physical health, quality of life, and cost-effectiveness of interventions, were missed. In addition, studies published other than the English language were excluded in this review. Therefore, it is highly recommended for further review to include studies in different languages and from lesser-known databases.\n\n\nConclusion\n\nOverall, this review showed that AE effectively reduced pain intensity and functional disability in CLBP patients. It also demonstrates the appositeness of using AE as an intervention in future studies. Findings of most of the included studies demonstrated that patients gained statistically significant pain intensity and disability improvements. Results indicated that exercise should be done under supervision at a minimum frequency of 5 days/week, for at least 12 weeks, and in combination with other interventions including education, physiotherapy, home exercise, or other forms of exercise to get clinically significant outcomes. Future studies should emphasize training patients at the optimum frequency, intensity, and duration so that the participants can achieve clinically meaningful improvements.\n\n\nData availability\n\n\n\n\nUnderlying data\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReporting guidelines\n\nMendeley Data: PRISMA checklist for ‘The effectiveness of different aerobic exercises to improve pain intensity and disability in chronic low back pain patients: A systemic review.’\n\nhttps://doi.org/10.17632/79vnhtfh85.277\n\nThis project contains the following data:\n\n• PRISMA checklist.doc\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nVos T, Allen C, Arora M, et al.: Global, regional, and national incidence, prevalence, and years lived with disability for 310 diseases and injuries, 1990–2015: a systematic analysis for the Global Burden of Disease Study 2015. 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Publisher Full Text\n\nSuh JH, Kim H, Jung GP, et al.: The effect of lumbar stabilization and walking exercises on chronic low back pain: A randomized controlled trial. Medicine (Baltimore). 2019 June 1; 98: e16173. Publisher Full Text\n\nKoldaş Doǧan Ş, Sonel Tur B, Kurtaiş Y, et al.: Comparison of three different approaches in the treatment of chronic low back pain. Clinical Rheumatology. 2008; 27: 873–881. PubMed Abstract \| Publisher Full Text\n\nBello B, Adeniyi AF: Effects of lumbar stabilisation and treadmill exercise on function in patients with chronic mechanical low back pain. International Journal of Therapy and Rehabilitation. 2018; 25: 493–499. Publisher Full Text\n\nBarni L, Calabretta L, Lepori L, et al.: Does an aerobic exercise improve outcomes in older sedentary nonspecific low back pain subjects? A randomized controlled study. Topics in Geriatric Rehabilitation. 2018; 34: 88–94. Publisher Full Text\n\nCho YK, Kim DY, Jung SY, et al.: Synergistic effect of a rehabilitation program and treadmill exercise on pain and dysfunction in patients with chronic low back pain. Journal of Physical Therapy Science. 2015; 27: 1187–1190. PubMed Abstract \| Publisher Full Text\n\nMarshall PWM, Kennedy S, Brooks C, et al.: Pilates exercise or stationary cycling for chronic nonspecific low back pain: Does it matter? A randomized controlled trial with 6-month follow-up. Spine (Phila Pa 1976). 2013; 38: E952–E959. Publisher Full Text\n\nMcDonough SM, Tully MA, Boyd A, et al.: Pedometer-driven walking for chronic low back pain: A feasibility randomized controlled trial. The Clinical Journal of Pain. 2013; 29: 972–981. PubMed Abstract \| Publisher Full Text\n\nShnayderman I, Katz-Leurer M: An aerobic walking programme versus muscle strengthening programme for chronic low back pain: A randomized controlled trial. Clinical Rehabilitation. 2013; 27: 207–214. PubMed Abstract \| Publisher Full Text\n\nChan CW, Mok NW, Yeung EW: Aerobic exercise training in addition to conventional physiotherapy for chronic low back pain: A randomized controlled trial. Archives of Physical Medicine and Rehabilitation. 2011 October; 92: 1681–1685. Publisher Full Text\n\nKell RT, Asmundson GJG: Comparison of two forms of periodized exercise rehabilitation programs in the management of chronic nonspecific low-back pain. Journal of Strength and Conditioning Research. 2009 March; 23: 513–523. Publisher Full Text\n\nChatzitheodorou D, Kabitsis C, Malliou P, et al.: A pilot study of the effects of high-intensity aerobic exercise versus passive interventions on pain, disability, psychological strain, and serum cortisol concentrations in people with chronic low back pain. Physical Therapy. 2007 March 1; 87: 304–312. Publisher Full Text\n\nEadie J, Van De Water AT, Lonsdale C, et al.: Physiotherapy for sleep disturbance in people with chronic low back pain: Results of a feasibility randomized controlled trial. Archives of Physical Medicine and Rehabilitation. 2013; 94: 2083–2092. PubMed Abstract \| Publisher Full Text\n\nMurtezani A, Hundozi H, Orovčanec N, et al.: A comparison of high intensity aerobic exercise and passive modalities for the treatment of workers with chronic low back pain: a randomized, controlled trial. undefined. 2011.\n\nHurley DA, O’Donoghue G, Tully MA, et al.: A walking programme and a supervised exercise class versus usual physiotherapy for chronic low back pain: A single-blinded randomised controlled trial. (The Supervised Walking in comparison to Fitness Training for Back Pain (SWIFT) Trial). BMC Musculoskeletal Disorders. 2009; 10. PubMed Abstract \| Publisher Full Text\n\nMiranda H, Viikari-Juntura E, Martikainen R, et al.: Individual factors, occupational loading, and physical exercise as predictors of sciatic pain. Spine (Phila Pa 1976). 2002 May 15; 27: 1102–1108. Publisher Full Text\n\nSiegel PZ, Brackbill RM, Heath GW: The epidemiology of walking for exercise: Implications for promoting activity among sedentary groups. American Journal of Public Health. 1995; 85: 706–710. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCallaghan JP, Patla AE, McGill SM: Low back three-dimensional joint forces, kinematics, and kinetics during walking. Clinical Biomechanics. 1999 March; 14: 203–216. Publisher Full Text\n\nHootman JM, Macera CA, Ainsworth BE, et al.: Association among physical activity level, cardiorespiratory fitness, and risk of musculoskeletal injury. American Journal of Epidemiology. 2001 August 1; 154: 251–258. Publisher Full Text\n\nJull G, Moore A: Systematic reviews assessing multimodal treatments. Manual Therapy. 2010 August 1; 15: 303–304. Publisher Full Text\n\nKim CR, Park DK, Lee ST, et al.: Electromyographic Changes in Trunk Muscles During Graded Lumbar Stabilization Exercises. PM&R. 2016 October 1; 8: 979–989. Publisher Full Text\n\nArokoski JP, Valta T, Airaksinen O, et al.: Back and abdominal muscle function during stabilization exercises. Archives of Physical Medicine and Rehabilitation. 2001; 82: 1089–1098. Publisher Full Text\n\nIl Lee H , Lee ST, Kim M, et al.: Sex differences in predicting chronicity of low-back pain after acute trauma using lumbar muscle area. American Journal of Physical Medicine & Rehabilitation. 2015 February 21; 94: 123–130. Publisher Full Text\n\nLorig KR, Ritter PL, Laurent DD, et al.: Internet-based chronic disease self-management: A randomized trial. Medical Care. 2006 November; 44: 964–971. Publisher Full Text\n\nNeve M, Morgan PJ, Jones PR, et al.: Effectiveness of web-based interventions in achieving weight loss and weight loss maintenance in overweight and obese adults: A systematic review with meta-analysis. Obesity Reviews. 2010 April; 11: 306–321. Publisher Full Text\n\nVan Den Berg MH, Schoones JW, Vlieland TPMV: Internet-based physical activity interventions: A systematic review of the literature. Journal of Medical Internet Research. 2007; 9: 9. Publisher Full Text\n\nDamiano DL, Norman T, Stanley CJ, et al.: Comparison of elliptical training, stationary cycling, treadmill walking and overground walking. Gait & Posture. 2011 June; 34: 260–264. Publisher Full Text\n\nBennett GG, Wolin KY, Puleo EM, et al.: Awareness of national physical activity recommendations for health promotion among US adults. Medicine and Science in Sports and Exercise. 2009 October; 41: 1849–1855. Publisher Full Text\n\nGarber CE, Blissmer B, Deschenes MR, et al.: Quantity and quality of exercise for developing and maintaining cardiorespiratory, musculoskeletal, and neuromotor fitness in apparently healthy adults: Guidance for prescribing exercise. Medicine and Science in Sports and Exercise. 2011 July; 43: 1334–1359. Publisher Full Text\n\nNelson ME, Rejeski WJ, Blair SN, et al.: Physical activity and public health in older adults: Recommendation from the American College of Sports Medicine and the American Heart Association. Circulation. 2007 August; 116: 1094–1105.\n\nHayden JA, Van Tulder MW, Malmivaara AV, et al.: Meta-analysis: Exercise therapy for nonspecific low back pain. Annals of Internal Medicine. 2005 May 3; 142: 765–775. Publisher Full Text\n\nSany SA, Tanjim T: The effectiveness of different aerobic exercises to improve pain intensity and disability in chronic low back pain patients: A systemic review.2021; 2." }	[ { "id": "121997", "date": "04 Feb 2022", "name": "Navid Moghadam", "expertise": [ "Reviewer Expertise Low back pain" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThanks for the opportunity to review.\nIt is an update to previous systematic reviews but I have some concerns before approval:\n\n1. The search query is not disclosed; it should at least be contained as a supplement.\n2. The reason for not doing a meta-analysis is not described, is this due to issues of heterogeneity?\n3. The main outcome measure is not described in terms of the questionnaire.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly", "responses": [ { "c_id": "9883", "date": "29 Nov 2023", "name": "Shabbir Ahmed Sany", "role": "Author Response", "response": "Thank you for allowing us to submit a revised version of our manuscript. We appreciate your time and effort in providing informative feedback on the manuscript. We appreciate your constructive feedback on our paper. We have carefully considered your comments and made the suggested changes which are described below: The search query is not disclosed; it should at least be contained as a supplement. Response: Thank you for pointing this out. We have included a brief description of the search query in Appendix 1 as a table. The reason for not doing a meta-analysis is not described, is this due to issues of heterogeneity? Response: We did not perform the meta-analysis due to the heterogenicity of participants, intervention, and outcome measures. We mentioned it in the method section under the subheading \"Data synthesis and measurement of treatment effect\". The main outcome measure is not described in terms of the questionnaire. Response: Thank you for your comment. We have included and described the main outcome measures under a different sub-heading “Types of outcome measures” in the method section. Outcome measures are also demonstrated in table 3 and 4." } ] }, { "id": "126016", "date": "11 Mar 2022", "name": "Moshiur Rahman Khasru", "expertise": [ "Reviewer Expertise Rheumatic disease", "Stem cells", "and pain" ], "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\nThanks for providing an opportunity to review this systematic review.\nI have a few comments:\nInformation regarding inclusion or exclusion of Inflammatory back pain should be stated clearly in this review.\n\nWas this review registered to any registration authority?\n\nIt would be great if meta-analysis could be addressed - factors directing authors not to go for meta-analysis could be stated in the methods.\nHowever, this manuscript can be accepted for publication.\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": "9884", "date": "29 Nov 2023", "name": "Shabbir Ahmed Sany", "role": "Author Response", "response": "Thank you for your time and reviewing the manuscript and providing valuable suggestions to improve the quality of the manuscript. Here is a point-by-point response to the reviewers' comments and concerns. Information regarding inclusion or exclusion of Inflammatory back pain should be stated clearly in this review. Response: Thank you for your comment. We have mentioned the exclusion and inclusion criteria in Table 1. We also stated that studies involving patients with inflammatory or tumoral back conditions were not included in this review. Was this review registered to any registration authority? Response: This review was not registered to any registration authority. It would be great if meta-analysis could be addressed - factors directing authors not to go for meta-analysis could be stated in the methods. Response: We did not perform the meta-analysis due to the heterogenicity of participants, intervention, and outcome measures. We mentioned it in the method section under the subheading \"Data synthesis and measurement of treatment effect,\" as suggested." } ] } ]	1	https://f1000research.com/articles/11-136
https://f1000research.com/articles/12-457/v1	02 May 23	{ "type": "Review", "title": "The Taxonomy of Blockchain-based Technology in the Financial Industry", "authors": [ "Andry Alamsyah", "Syahputra Syahrir", "Syahputra Syahrir" ], "abstract": "The decentralized approach of blockchain technology has resulted in innovations across various industries, including finance which is facing challenges due to the rise of decentralized finance (DeFi) in the market. Decentralization improves business processes and spurs product innovation through increased transparency and removing intermediaries. A taxonomy, created through literature review and expert interviews, outlines the four dimensions of these advancements: key drivers, products, benefits, and emerging threats. Proposed solutions are also included to tackle the threats.", "keywords": [ "Blockchain", "Financial Innovation", "Decentralization", "FinTech", "Decentralized Finance", "Review" ], "content": "1. Introduction\n\nThe financial sector is one of the largest in the world, and as of Q1 2022, the market cap of the top 100 banks globally was 6.1 trillion USD.1 Technological advancements have had a major impact on the financial industry, leading to the rise of Financial Technology (FinTech) companies. FinTech refers to financial companies that utilize technology, mainly internet-related as the media, to launch products/services and to innovate.2 This technology can also bring new products to market with improved security, efficiency, flexibility, and opportunities. An example is using technology to make credit card payments with smartphones and tablets,3 increasing payment efficiency by allowing access to the user’s device without carrying the card or cash.\n\nFinTech has a long history in the financial industry development. The evolution of FinTech consists of three digitalization phases, shown in Table 12 and explained in the subsequent paragraph.\n\nThe first digitalization phase, called “internal,” concentrates on enhancing financial institutions’ internal operations by automating financial products and services. An example of this phase is the ATM, which allows customers to access banking services without visiting the bank. The second phase of digitalization is called provider oriented. It focuses on the provider’s integration by standardizing the processes and applications across different functions in the company. The goal is to establish a synchronized business process, resulting in a lower in-house production degree. The last phase is known as customer-oriented digitalization. As the name suggests, it emphasizes the services around the customer needs, which would establish a new financial ecosystem. Users are able to conduct peer-to-peer transactions without the third party’s involvement.\n\nBlockchain is a technology capable of disrupting business processes and triggering innovations. But first, we need to know what blockchain is. It refers to a ledger secured by a chain of blocks guarded by cryptograpic techniques to secure its integrity.4 Blockchain implementation covers two sectors, the financial and the non-financial industry.5 The revolution brought by blockchain to the organizational structure is through Decentralized Autonomous organization (DAO). DAO offers a decentralized system rather than a pyramid hierarchy, which is often used in conventional institutions. The decentralization also drives the innovation of numerous new products, eliminating intermediaries’ functions. For instance, blockchain is the technology behind the worldly-renowned Bitcoin, which Satoshi Nakamoto proposed back in 2008.6 Blockchain is a staggering technology with a decentralized mechanism that enables peer-to-peer payment. In other words, it could unlock payment without the interference of a third-party. The blockchain utilizes two key drivers: The Smart Contract and a Distributed Ledger Technology (DLT). Smart Contracts have unalterable terms, so both parties must carefully review them before signing. DLT records transactions more securely than centralized systems by sharing records among multiple nodes and using a consensus algorithm to validate data. The DLT ensures all nodes have the latest updated information.\n\nThe decentralization idea of blockchain drives new product innovation, allowing stakeholders to interact directly without the interference of a central authority. In finance, we can imagine if financial activities, such as saving, lending, and lending, are made between individuals. The decentralization idea drives the establishment of Decentralized Finance (DeFi). DeFi enables its users to manage their virtual assets, unlike the conventional financial institution that manages the user’s assets. Another blockchain product in the financial sector is Centralized Finance (CeFi). However, it doesn’t inherit the essence of blockchain’s decentralized trait since CeFi is an institution that manages its users’ assets. Therefore, we will focus on the discussion of DeFi and its byproducts. Our study aims to provide a classification of blockchain’s integration in finance. The first section covers the introduction, which discusses the financial industry and blockchain background. The second section concerns the literature review that formed the methodology of this review article. The third section presents the taxonomy based on the dimensions of key drivers, benefits, products, and threats. The fourth section addresses potential solutions to threats. The two final sections discuss and conclude the paper. Finally, we hope the taxonomy enlightens academicians and financial industry practitioners about the blockchain technology ecosystem.\n\n\n2. Literature review\n\nThis paper employs an extensive literature review as its research methodology. The literature review thoroughly examines numerous scholarly works on blockchain technology and its practical applications. For instance, the investigation conducted by Zhang and Chan7 inspection energy consumption in blockchain consensus algorithms, while Tarr’s research8 delves into blockchain applications within the insurance sector. Blockchain technology is applicable across a multitude of industries. However, despite its vast potential for implementation, a limited number of enterprises have adopted it, primarily due to its nascent state. The literature review examines 73 academic articles from various reputable sources, including Elsevier, Emerald, MDPI, IEEE, ACM, and Taylor & Francis. The pertinent keywords encompassed blockchain technology, application, implementation, and terms related to blockchain products in the financial industry. Additionally, we have collected information from various crypto projects, exchanges, crypto industries, wallet services, crypto platforms information, and regulators/central bank through their website, whitepapers, and source code.\n\nBased on the member’s participation, the blockchain is divided into permissioned and permissionless blockchains.9 The permissioned blockchain only allows a particular authorized party to access information and participate in the system. In contrast, everyone can enter and oversee the information contained in the permissionless blockchain system. Financial institutions can choose whether to use one or both blockchain types based on their needs. For instance, to secure privacy, an insurance company implements the permissioned blockchain to prevent data exposure to the public. Blockchain has two key drivers: Smart Contracts and DLT. The Smart Contract refers to a legal contract capable of being implemented and expressed in the software.10 In other words, a directly coded self-executing terms of agreements between buyer and seller.11 The Smart Contract works by inserting code into the blockchain; as we know, the code embedded in the blockchain is unaltered (immutable) once deployed to the network and can only operate once the terms are met. The second key driver of blockchain is DLT. DLT contains multiple copies of transactions distributed among numerous participants and updated by the parties’ consensus.12 This technology synchronizes information across multiple nodes, ensuring each node has the most recent ledger update.\n\nBlockchain technology’s decentralization distinguishes it from conventional systems. Centralized systems store records on a single server with backups on additional devices, while decentralized systems employ consensus algorithms to synchronize records across multiple devices. Notable consensus algorithms include Proof of Work (PoW) and Proof of Stake (PoS). PoW rewards miners based on their capacity to solve network-generated mathematical problems, with greater computational power increases the likelihood of reward. Bitcoin, the preeminent cryptocurrency, utilizes PoW, which aims to prevent any miner from possessing over 50% of total computational power to maintain network integrity. Conversely, PoS rewards miners according to the quantity and duration of coins held within the network,13 making it difficult for malicious actors to gain control, as doing so requires significant investment. PoS is considered more secure and energy-efficient than PoW, as it selects network leaders based on the stake and time commitment, reducing energy consumption compared to PoW’s reliance on substantial computational power.14\n\nBlockchain technology’s attributes can revolutionize FinTech firms’ operations, encompassing security and governance. “Security” pertains to properties such as immutability, transparency, traceability, data record, and tokenization. For example, FinTech firms can facilitate enhanced procurement agreements via Smart Contracts. The second attribute involves modifying companies’ governance systems and decentralizing organizational structures to optimize business processes. Voluntariness, equality, and mutual benefit characterize relationships between nodes in the blockchain’s governance system.\n\nBlockchain tokenization allows users to manage digital assets more decentralized than traditional methods. Tokenization entails digitalizing assets to facilitate fractional investment and ownership.15 These tokens can be traded or transferred like conventional securities.11 Tokenization-driven economies replace intermediaries with technical protocols,16 streamlining asset tracking for origin, authenticity, and rights.17 Tokenized assets extend beyond physical items to intangible assets such as Non-Fungible Tokens (NFTs). For example, someone owning 30% of a digitalized yellow dog NFT, has the right to sell his NFT, limited to his 30% ownership stake.\n\nDeFi embodies the core principles of blockchain in the FinTech sector. This paper focuses on DeFi’s discussion since it portrays the essence of blockchain: decentralization. However, Centralized Finance (CeFi) is also classified as a blockchain-based FinTech byproduct. DeFi lets users take care of their financial assets. Meanwhile, CeFi refers to a financial institution that controls its users’ financial assets.18 DeFi combines one or more elements: decentralization, DLT and blockchain, smart contracts, disintermediation, and open banking.19 On the other hand, examples of CeFi are companies like Binance, Coinbase, and Uphold.\n\nDespite the various advantages blockchain technology offers, it is not flawless. Blockchain could cause new threats that come from both internal and external factors. Those threats might eventually be harmful to financial institutions if not appropriately handled. However, researchers have made efforts to address these risks, which we will outline in section 4. We have identified five specific threats to the implementation of blockchain in the financial industry, which include: scalability and speed, security, cost, regulation, environment, and energy.\n\nScalability and speed present significant challenges for blockchain implementation. In contrast to Visa’s capacity for around 2000 transactions per second, Bitcoin’s blockchain processes a mere seven transactions per second.20 The generation of only 1 MB of data every 10 minutes21 limits transaction volume. Storage and network capacity further hinder scalability and speed, as data generated by multiple devices must be processed and stored on the network, leading to block propagation delays and high resource consumption. Despite FinTech benefits, blockchain remains susceptible to security threats. The PoW algorithm enables the 51% attack, where malicious parties control over 50% of the total computational power, potentially dominating the blockchain and implementing rules to their advantage.22 Phishing poses another security threat,23 as fake wallets on popular apps allow scammers to seize victims’ funds by controlling private keys.\n\nEven though blockchain can reduce the intermediaries cost through decentralization, it causes a new problem. The limited size of a blockchain system causes the miner to put in a higher mining fee. Moreover, the larger the transaction being sent, the higher the fees. The miners of blockchain, especially Ethereum, are being paid in the form of gas instead of fiat currency. The Gas price refers to the fees required to perform the computational effort.24 The calculation of the total transaction fee in Ethereum is the gas limit multiplied by the gas price.25 The gas limit refers to the maximum quantity of gas the creator is eager to spend, while the gas price determines the amount of Gwei the creator is willing to pay.26 For the record, Wei is the smallest part of Ether, where 1 Ether equals 10.18 Wei, whereas 1 GWei equals 1,000,000,000 Wei.25 Over time and with the surging popularity and high demand for blockchain, the gas cost keeps increasing to the point where Ethereum has to manage millions of transactions daily.\n\nWeak regulations could increase the risk of criminality. For instance, criminals use blockchain-based assets such as cryptocurrency to launder money and cease the money’s origin. There are two reasons blockchain-based digital assets are prone to the money laundering act.27 The first is the governance of global anti-laundering agencies only worried about illegal financial flows and transactions and whether they meet standard theoretical money. Fiat money and blockchain-based digital assets are treated the same in tackling the money laundering act. The second reason is the novel manner digital asset offers, such as verification, undertaking, and transaction publication, are done almost in real-time.\n\nBlockchain could consume more energy than traditional technology. For the record, the estimation to mine 1 Bitcoin requires the same energy to generate electricity for one US household for two years.28 It indicates the enormous energy consumption of blockchain, consequently leaving more carbon footprints on the earth. A consensus algorithm such as PoW requires lots of power since the reward for the miner will be given when they find a new block in the network.29 The increased work rate will consume energy which will eventually damage the environment. The blockchain’s energy consumption is often criticized due to its impact on the surroundings. As the title suggests, our paper’s discussion focuses on the impact of blockchain on the financial industry. We do not highlight blockchain’s implementation in other industries. However, we highlight how blockchain technology works in general. It is done to give an overview to the readers regarding the broad understanding of how blockchain works before pursed it to its implementation in the financial industry.\n\n\n3. The taxonomy\n\nBased on the discussion in the literature review section, our finding divides the taxonomy into four dimensions: key drivers, benefits, products/services, and threats (Figure 1) represents the taxonomy:\n\nWe thoroughly discuss each of those four dimensions, from key drivers to threats. In addition, we analyze the dimension’s relationship to understand how one could affect another. The bold line represents the branching of its original dimensions. For instance, the Smart Contract consists of three branches: Decentralized Autonomous Organizations (DAO), Decentralized Applications (DApp), and Automated Market Makers (AMM). The dotted line represents the traits of the originator. For example, DLT traits are transparency, immutability, data consistency, and traceability.\n\nTwo important drivers are identified as the core of blockchain technology capabilities in supporting many complex interactions in the financial industry. They are Smart Contracts and DLT. Smart Contracts act as an unbiased and precise alternative to human decision-making, while DLT provides consistent records, transparency, and a robust database. Here is the discussion of each driver.\n\n3.1.1 Smart Contract\n\nA Smart Contract refers to a self-executing program that automatically executes and enforces the contract’s terms. Since it is written on the blockchain, it inherits its characteristics, such as being immutable or cannot be modified, tamper-proof, and transparent. Once a Smart Contract is created, it can be executed on the blockchain network and applied to any actor in the network. The Smart Contract can be substitute intermediaries in the financial industry, enabling decentralized transactions.31 This means that users can carry out transactions with each other directly, rather than relying on a financial institution to set the terms of the trade. The peer-to-peer interaction characteristic in the financial industry is commonly known as DeFi. Furthermore, Smart Contracts create a financial ecosystem in which users have the power to manage their assets. While financial companies still exist in the DeFi space, they only serve as platform providers to facilitate asset trading among users and do not actually hold any assets themselves.\n\nThe Smart Contract enables unaltered and globally enforced agreements between parties since it has a synchronized record. The Smart Contract’s code is self-executing once it meets the agreed conditions. For instance, a company uses a Smart Contact to schedule the employee’s payroll. The only requirement is when it reaches the 25th day of each month. Thus, the performance and other factors are not embedded in the contract. As a result, the employees will automatically receive their salary on the 25th day of the month, despite their bad performance and other negative factors. A Smart Contract is the base principle for several technologies. These include DAO, DApp, and AMM, which we explain in the following subsection.\n\n3.1.1.1 Decentralized Autonomous Organization\n\nA decentralized Autonomous Organization, also known as DAO, is a blockchain-based system that allows entities in the organization to govern and coordinate themselves by a set of registered rules.30 DAO can transform the organization’s hierarchical structure into a decentralized one. Conventional corporate governance contains two fundamental problems.31 Everyone in the organization may not always be obedient to the rules, and others may not always agree with the rules. Fortunately, DAO possesses the ability to overcome those problems with the following characteristics32:\n\n1. The absence of hierarchical structure and central authority. It means the connections between nodes are not controlled by managerial association but rather by the value of voluntariness, equality, and mutual benefit.\n\n2. The distributed organizations. Stakeholders arrange all the rules and collaboration patterns in DAO. Therefore, the DAO implementation would increase trust and reduce communication and transaction costs.\n\n3. The reliance on the Smart Contract. The Smart Contract enhances DAO’s transparency and openness regarding participants’ responsibility, authority, operational rules, penalties, and rewards.\n\nDAO allows the organization to work in synchronized continuously with the help of computer code or Smart Contract. DAO has become a fundamental concept of how governance does not necessarily need a central authority to function correctly, thus, it promotes transparency, democratic decision-making, and organizational efficiency. When large crowds participate in community or project initiatives, it can be more effective and engaging if decisions or actions are automatically arranged while maintaining order.\n\n3.1.1.2 Decentralized Application\n\nDApps represent practical implementations of DAOs. DApps distribute authority and control among users rather than a single institution. There are three primary application types: centralized, distributed, and decentralized. Centralized applications have a single controlling authority, distributed applications spread information across multiple nodes, and decentralized applications lack a single control point. DApps exhibit four main features33:\n\n1. A DApp is an open-source application, allowing for transparency within the network. However, it is vulnerable to plagiarism as the content is accessible to anyone in the network.\n\n2. DApp developers engage in economic activities by creating a coin that they can control the distribution and supply of, and its value is determined by public perception.\n\n3. To validate transactions within DApps, the implementation of blockchain and a consensus algorithm is essential. Transactions are recorded immutably in the blockchain, ensuring their history and preventing them from being altered by malicious parties.\n\n4. DApps are designed to avoid the effect of server shutdown by ensuring that another node takes over the application’s functions if one node fails.\n\n3.1.1.3 Automated Market Maker\n\nAMM is an innovative approach to the traditional market that employs a third party to operate the order book. AMM is an algorithm or Smart Contract that enables importation and participation in an electronic market.34 The main benefit of AMM utilization is liquidity, which refers to the ability to convert assets into cash without significantly impacting the market price. AMM works as a single-function algorithm that matches trading orders and determines execution prices.35 Thanks to a liquidity pool, it provides superior liquidity than a conventional order book. A liquidity pool works as a vault, or a “pool”, where the liquidity provider (investor) puts one or many tokens for the trader so they can use it in many ways, such as lending, borrowing, derivatives, insurance, and swapping.36 By conducting a transaction in the liquidity pool, the trader must pay the service fee, which is then transferred to the liquidity provider as the reward for providing the liquidity. The AMM covers numerous blockchain-based FinTech companies such as Uniswap, Balancer, PancakeSwap, Osmosis, and 1inch.\n\n3.1.2 Distributed Ledger Technology\n\nThe DLT records, stores, and shares information across the network of computers, thus making it more resilient compared to the centralized ledger.37 The DLT’s characteristic brings nodes synchronized with the latest information update across the network. Therefore, if one node fails to receive updated information, another node will inform it. For example, a centralized system backs the data every hour and records it an hour later. The system records the transaction at 07.00 AM and backups data at 08.00 AM. However, a system malfunction occurred at 7.30 AM, forever changing every data from 07.00-07.30 AM. In contrast, the decentralized system synchronizes the transaction record simultaneously to every node in the system. DLT consists of three main layers.38\n\n1. Foundation. It refers to the entire DLT system’s foundation. It describes the rules on how the system governs the whole network in distributing the information.\n\n2. Network. It’s a network where interconnected nodes or actors share, store, and process data.\n\n3. Data. As the name suggests, the layer refers to the data stored in the DLT system as records.\n\nInnovative technology, like blockchain, is crucial for businesses to stay competitive in today’s ever-evolving market. Blockchain has the potential to revolutionize operations, streamline processes, increase efficiency, reduce costs, and improve overall performance. Its implementation in FinTech companies provides crucial benefits such as enhanced security and governance, making it a valuable addition to the taxonomy.\n\n3.2.1 Security\n\nThe improved security in a financial system would result in a condition where the institutions and their users can conduct activities without worrying about their assets being stolen or information being compromised. The blockchain’s features, namely the Smart Contract and DLT, are crucial in improving FinTech’s security sector. The Smart Contract establishes the agreement between two or more parties and only becomes effective once the conditions agreements are met. DLT, on the other hand, synchronizes the record to each authorized node simultaneously. Generally, what makes blockchain brings a high degree of appeal when it comes to security while still maintaining privacy is the ability to support several properties such as immutability, transparency, traceability, data consistency, tokenization, and governance. In the financial industry scenario, A FinTech company could easily release fully digital products/services which can be guaranteed to perform similarly to the conventional product but with the flexibility of digital nature.\n\nAnother security aspect incorporated in blockchain features is Public Key Infrastructure (PKI). PKI basically uses public key cryptography to secure transactions and provide privacy and authentication. Each user has a public key and a private key. The public key is used to receive transactions, while the private key is used to sign transactions. When a user initiates a transaction, they sign it with their private key, and the transaction is broadcast to the network. Other nodes on the network can then verify the transaction by using the sender’s public key. A digital signature is used to provide authenticity and transaction integrity. The digital signature is generated by using the sender’s private key to encrypt the transaction data. The signature can then be verified by using the sender’s public key.\n\nIn summary, there are three layers of mechanisms to enhance security in the blockchain:\n\n1. Hashing and encryption. The purpose of hashing is to connect every node to attain a synchronized record. The node is encrypted using a private or public key.\n\n2. Consensus algorithm. It selects the blockchain’s participants, so the transaction validators are only the selected ones. The types of consensus algorithms may vary among different blockchain\n\n3. Network consensus. It refers to the community’s decision to decide the latest consensus state. Therefore, any suspicious transaction would be ignored.\n\n3.2.1.1 Immutability\n\nImmutability refers to a condition where the transactions are unaltered once they are verified and recorded in the system.39 The distributed nature of the record across the network poses significant challenges for any potential attacker looking to manipulate it, as they would need to replace each record with their own version of events. Thus, blockchain guarantees the single source of truth of a network. As the network expands in size, the possibility of an attacker replacing the records on every node becomes increasingly infeasible. As such, immutability provides a guarantee of information security, and is a fundamental characteristic that underpins the trustworthiness of the Smart Contract. Consequently, parties engaging with the Smart Contract must diligently read the contract terms before agreeing to them, as once launched to the system, no party can alter them. The Smart Contract’s immutability feature enhances the trust between parties, obviating the need for constant monitoring to ensure compliance with the agreed-upon terms.\n\n3.2.1.2 Transparency\n\nTransparent data would result in improved traceability, consistency, and immutability. Blockchain enables parties to share replicated ledgers, which act as a trusted record system and the sole source of truth of activities or transactions.40 The blockchain’s DLT allows anyone or a particular party(es) to oversee the transaction activity. The network may determine who has the right to observe the data by choosing whether to use the permissioned or permissionless blockchain. Data transparency has become an essential key in establishing trust between stakeholders. In DeFi, where peer-to-peer transactions are encouraged, transparency is fundamental in establishing trust and stakeholder reputations. As no central authority can verify the stakeholder’s legitimacy, it is impossible to endorse an untrustworthy stakeholder in DeFi.\n\n3.2.1.3 Traceability\n\nTraceability refers to a system’s ability to trace and track the history of transactions, interactions, or movements. The demand for traceability information has recently increased among companies, consumers, and governments, as it is linked to the quality and safety of products and services. Therefore, utilizing blockchain technology provides a feasible solution to address these concerns. The blockchain’s DLT is the crucial reason the system’s information is easily trackable since the block contains information from the previous block. The recorded history plays a vital role for any stakeholder to have a full picture of any item, such as digital assets representing financial products/services. Therefore, traceability unmasks the flow of information.41 It comes from the fact that DLT is a decentralized system where the information contained in the system is visible to all participants.42 Every node in the DLT includes a complete record of the transactions, thus increasing the traceability of the asset’s movement.\n\n3.2.1.4 Data consistency\n\nData consistency refers to the ability of blockchain technology to ensure that all copies of information on each stakeholder are identical and up-to-date. This requires record synchronization throughout the operation. It implies that all nodes in the network share the same information, ensuring the information’s consistency and accuracy throughout the network. The improved data consistency originated from DLT implementation, where the transactions are recorded and distributed simultaneously to every node. Hence every node has the latest transaction update. Moreover, participants in the system can notice the double-spending issue,43 a flaw where money or assets are spent more than once.\n\n3.2.1.5 Tokenization\n\nTokenization converts physical assets into digital tokens using blockchain technology, ensuring security, robustness, and privacy protection. As financial instruments and products are essentially abstractions, it makes sense to represent them as digital assets. Tokenized asset ownership is embedded within the system, allowing owners to view transaction records and identify buyers and sellers. Tokenized assets can be derived from tangible or intangible assets, such as artwork, precious stones, airplanes, intellectual property, or company equity. There are three primary benefits of tokenizing an asset44:\n\n1. Fractional ownership: Facilitates participation from retail and small investors.\n\n2. Efficiency enhancement: Streamlines transactions, contracts, interest, and dividend execution, while minimizing intermediary involvement.\n\n3. Improved transparency: Offers greater visibility into the asset’s history and transactions.\n\n3.2.2 Governance\n\nGovernance refers to the rules, processes, and decision-making mechanisms that govern the operation and management of organizations, communities, and crowds. Blockchain technology advocates the decentralized mechanism throughout their operation. As the opposite of centralized and hierarchical operations, each stakeholder has their share proportions of the organization’s decision based on the agreed-upon preliminary rules or protocol. Therefore, societies and interactions are governed by various actors’ networks.43 Blockchain-based governance aims to balance accountability and decentralization to ensure the organization’s long-term sustainability. Blockchain governance consists of on-chain and off-chain governance.45 The on-chain governance explicitly defines the governance arrangement in the protocol, allowing stakeholders to vote or make changes to the proposal. Off-chain governance refers to the external governance structure protocol. DAO represents the implementation of decentralized corporate governance, which utilizes tokenized tradable shares to give network participants the weight of voice in governing the organization. It could function to provide dividends to shareholders.30\n\nRecent technological advancements have led to the development of innovative products offering various features and benefits. In the financial industry, the core idea of enabling peer-to-peer transactions has led to the creation of decentralized finance, decentralized exchange, P2P lending, equity crowdfunding, stablecoins, and more. These products have been developed due to key drivers, features, and benefits offered by technology.\n\n3.3.1 Decentralized finance\n\nDeFi, a blockchain product in the financial industry valued at over fifty billion US dollars, challenges the fundamentals of traditional finance by removing intermediaries.19 Smart Contracts replace these intermediaries, acting as transaction supervisors. Though financial institutions exist in the DeFi ecosystem, they primarily serve as platforms for user activities. Traditional financial institutions’ drawbacks, such as complex service policies, high costs, and limited transparency, are mitigated through DeFi, enabling peer-to-peer transactions, reduced bureaucracy, lower costs, and a transparent ecosystem.\n\nThe recent surge in DeFi projects and ideas has prompted regulators, financial institutions, and banks to reassess their practices. The COVID-19 pandemic accelerated the digital economy, increasing online interactions and transactions. Digital natives or younger generations often seek opportunities for value creation among peers. Regulators, such as central banks, are adapting to the digital economy and peer-to-peer financial activities like DeFi by introducing Central Bank Digital Currencies (CBDCs). CBDCs enable effective monetary policy implementation, protect the public from malicious financial activities, and support innovation.46 As mentioned above, it is hoped that CBDC could increase financial inclusions, enable faster and cheaper transactions, improve transparency, and reduce fraud. Notably, the most important regulator could have control over their monetary policy from the threat of the shadow economy. The CBDC workflow can be illustrated in Figure 2.47\n\nFigure 2 demonstrates how a commercial bank can facilitate the usage of CBDCs by verifying customer identities through a KYC mechanism.48 Verified customers can then utilize a digital wallet as an interface to engage with DLT/Blockchain technology in the bank’s central or commercial back office. This wallet also enables customers to interact, transact, collaborate, create content, and play with their peers in a fully digital world, like the Metaverse. Additionally, the digital wallet provides secure and private digital identity protection against malicious internet activities and serves as a storage for crypto/digital assets, including NFTs, cryptocurrencies, and other assets.\n\nWe discuss several important DeFi products in the subsequent subsection. While DeFi characteristics are shown in Figure 3:\n\n1. Decentralization: Refers to the capacity for conducting peer-to-peer transactions in DeFi, thus eliminating intermediaries’ roles.\n\n2. Trustlessness: Smart Contracts remove the need for middlemen, enabling the automatic execution of agreement terms between users without manual verification of fulfillment.\n\n3. Transparency: DeFi’s DLT system permits authorized users to monitor transaction activities, promoting data traceability, consistency, and immutability.\n\n4. Censorship Resistance: Users can create unaltered transactions without interference from intermediaries.\n\n5. Programmability: Pertains to the adaptability of Smart Contract users in setting agreement terms, limiting intermediaries to platform provider roles without the authority to dictate terms.\n\n6. Permissionlessness: DeFi enables all users to conduct financial activities within the platform, without restrictions on participation.\n\n7. Modularity: Refers to the ability of a contract to integrate with other contracts, such as combining savings and insurance, offering users flexibility in merging contracts based on preferences and needs.\n\n3.3.1.1 Decentralized exchanges\n\nA decentralized exchange (DEX) provides users with a platform to exchange assets without the involvement of third-party intermediaries,49 unlike centralized exchanges (CEX), in which financial institutions mainly operate. One of the primary benefits of DEX is liquidity,50 which refers to the ability to convert assets without a significant impact on the market price. The Automated Market Maker (AMM) mechanism determines DEX liquidity. DEX provides a way of transparency, symmetry information between parties, affordable to acquire financing, and proper risk management. Cryptocurrencies are currently the most commonly traded assets on DEX, but it is possible to trade fiat currencies, stocks, and other commodities in the future. For example, Uniswap, one of the most popular DEX platforms, allows users to swap between Bitcoin and Ethereum based on the Bitcoin to Ethereum ratio stored in the Smart Contract.51 Users have complete control over their private keys in DEX, while financial institutions hold the keys in CEX. However, DEX can be challenging to comprehend since it is an emerging solution that lacks intermediaries. This makes it challenging to explain to new users.\n\n3.3.1.2 P2P lending\n\nP2P (Peer-to-peer) lending is a business model that facilitates borrowing and lending money between individuals through profit-driven online platforms, bypassing traditional financial institutions as intermediaries. P2P lending implementations cater to two user types: general platforms for any individual or small business and professional platforms for specific application domains. Blockchain technology can transform P2P lending in the following ways:\n\n1. A transaction request is broadcasted to P2P nodes.\n\n2. Nodes verify transactions and the user’s status.\n\n3. Verified transactions are combined into a new data block for the ledger.\n\n4. The new block is added to the existing blockchain.\n\nSeveral prominent decentralized P2P lending platforms have emerged, such as:\n\n1. Aave: A decentralized platform enabling lending and borrowing of various cryptocurrencies without intermediaries, utilizing smart contracts for P2P lending.\n\n2. Compound: A decentralized platform for lending and borrowing various cryptocurrencies, leveraging smart contracts to execute loans in a trustless and secure manner.\n\n3. MakerDAO: A decentralized platform allowing users to borrow a stablecoin called DAI using other cryptocurrencies as collateral, employing an intricate smart contract system to maintain DAI token stability.\n\n4. BlockFi: Initially a centralized lending platform, BlockFi has expanded into decentralized lending with its BlockFi Interest Account (BIA), enabling users to earn interest on their cryptocurrencies by lending them to others.\n\n3.3.1.3 Equity crowdfunding\n\nEquity crowdfunding is a business model specifically designed to secure external funding for new ventures.52 Unlike other forms of crowdfunding, equity crowdfunding primarily aims to connect entrepreneurs with investors who have an interest in investing in a particular firm(s).53 Blockchain technology offers two significant advantages to equity crowdfunding54:\n\n1. Secure transaction of company ownership: Blockchain’s consensus algorithm and public key cryptography ensure that the transfer of company ownership is secure and tamper-proof. This adds an additional layer of trust and security for both entrepreneurs and investors.\n\n2. Task automation: Blockchain technology allows for the automation of various tasks, such as interest payments and dividend distribution, through smart contracts. This automation eliminates the need for intermediaries, streamlining the process and reducing potential inefficiencies or transaction delays. This benefits both entrepreneurs and investors by simplifying the overall investment process and reducing associated costs.\n\nRepublic, StartEngine, and Wefunder are decentralized equity crowdfunding platforms enabling startups and small businesses to raise funds from diverse investors. Republic allows investments as low as $10 for company equity, StartEngine offers investment opportunities across industries, and Wefunder has helped over 600 companies raise over $200 million, empowering anyone to invest in startups they support.\n\n3.3.1.4 Cross-border payment\n\nCross-border financial institutions enable payments between countries with different currencies. However, economic fluctuations resulting from events such as the 2001-2002 Argentine financial crisis, the 2008 global financial crisis, the 2014-2016 Russian financial crisis, the 2018-2020 US-China trade war, and the Covid-19 pandemic have disrupted cross-border payments.55 The Society of Worldwide Interbank Financial Telecommunications (SWIFT) is a prominent organization in this space but its centralized nature results in prolonged transaction times and unclear operational fees.55\n\nRipple, a blockchain-based project, addresses these issues through a decentralized peer-to-peer network for faster transactions and reduced fees compared to SWIFT.56 Ripple also uses its own consensus algorithm called Unique Node List (UNL), where node operators select a list of “unique” nodes that they approve of. Nodes within the UNL are considered valid only if they have approval from other “unique” nodes, protecting the network from external attacks and preventing a majority vote from compromising nodes within the UNL.57\n\n3.3.1.5 Stablecoin\n\nStablecoins are a type of digital currency designed to maintain a stable value by pegging it to another asset, such as gold or fiat money.58 Unlike other cryptocurrencies, which can exhibit significant price volatility, stablecoins provide a more predictable and reliable means of exchanging and storing value. Their development reflects market demand for a stable digital currency that emulates fiat money, which is typically controlled by regulators or central authorities.\n\nWhile cryptocurrencies like Bitcoin exemplify blockchain technology, their high volatility and susceptibility to regulatory and informational influences have raised investor concerns.59 In contrast, stablecoins exhibit low volatility and are increasingly used as an alternative to fiat currency in digital markets.58 There are three primary categories of stablecoins based on their stabilization methods60:\n\n1. Asset-backed: Stablecoins pegged to and backed by assets held by private banks. Tether, for example, is an asset-backed stablecoin with its value pegged to the USD fiat.\n\n2. Crypto-collateralized: Stablecoins whose value is pegged to other cryptocurrencies. The value of the collateralized cryptocurrencies exceeds the issued crypto-collateralized ones. DAI is an example, as its value is backed by USD and other cryptocurrencies like ETH (Ethereum’s cryptocurrency).\n\n3. Algorithmic: This category of stablecoins does not rely on another asset for support. Instead, it uses oracle price feeds, algorithmic stabilization, and user participation (trading) to maintain its peg. LUNA, developed by Terra, a community-based blockchain platform, is an example of an algorithmic stablecoin. However, algorithmic stablecoins are often considered failures due to their remaining volatility, lack of widespread adoption, and vulnerability to unexpected events that disrupt supply and demand.\n\n3.3.1.6 Asset management\n\nThe asset management firm’s objective is to record and transfer ownership of an asset based on a contractual agreement.61 By establishing a decentralized system, blockchain facilitates asset transactions and maintains asset registries. This decentralized asset management system enables faster asset settlement processes, as there is no need for central authority validation, and it provides greater asset transparency as monitoring is performed through the Smart Contract. Asset management manages two kinds of assets62:\n\n1. Fungible. An asset can be exchanged with any other object, such as currency. For example, ten one-dollar bills are equal in value to a ten-dollar bill.\n\n2. Non-fungible. It refers to a singular asset that possesses unique characteristics despite being identical to others. For instance, diamonds are classified according to their clarity, cut, color, carat, and certification. The diamond may differ from one to another, despite being referred to as “diamonds”.\n\nAsset management firms can use permissioned or permissionless blockchains or both to improve their business operations.63 Government officials can maintain the permissioned blockchain to verify the asset’s registration to prevent double-spending and ensure the legality of traded assets. In contrast, the permissionless blockchain represents the marketplace of traded assets. Asset management firms should consider using a permissioned blockchain to prioritize scalability and security. Meanwhile, if they plan to emphasize decentralization and accessibility, they may choose to use a permissionless blockchain.\n\nThere are three examples of decentralized asset management platforms in this paper. The first is Melon Protocol, which is a decentralized asset management platform that allows anyone to create, manage, and invest in digital asset portfolios. The platform uses smart contracts to ensure that assets are managed securely and transparently. The second example is called Balancer. Balancer is a decentralized asset management platform that allows users to create custom portfolios of cryptocurrencies. The platform uses an automated market maker algorithm to ensure that the portfolio’s value remains balanced. The last example is Set Protocol. It is a decentralized asset management platform that allows anyone to create, manage, and invest in tokenized portfolios of cryptocurrencies. The platform uses smart contracts to automate portfolio management tasks and ensure the portfolio complies with them.\n\n3.3.1.7 Insurance\n\nFraud has been a significant concern in the conventional insurance sector. The FBI estimates losses in the United States alone to exceed $40 billion (about $120 per person in the US), or about $120 per person. This issue, combined with several drawbacks in the insurance industry, such as lack of customization, bureaucratic complications, limited transparency, and customer dissatisfaction, calls for innovation. Blockchain technology has the potential to enhance the efficiency of the insurance industry in numerous ways.\n\n1. Fraud elimination: Companies like Everledger utilize the blockchain to create a global registry for items like gemstones, making fraudulent transactions more difficult.\n\n2. Automated claim management process: Integrating claim management data enhances visibility for insurers, brokers, and reinsurers.\n\n3. Reinsurance: Smart Contracts facilitate clear and open systems between reinsurers and insurers.\n\n4. Transparency: Blockchain improves claim tracking, product verification, and service authentication transparency.\n\n5. Enhanced consumer management: Blockchain enables personalized insurance products catering to specific customer needs.\n\n6. Data analysis: Insurance companies can make better business decisions by analyzing customer data within the blockchain network, such as credit information, policy details, and accident environmental data.\n\nThree examples of blockchain-based insurance platforms include Nexus Mutual, a decentralized insurance firm offering coverage for smart contract failures on the Ethereum network; Etherisc, a decentralized insurance platform allowing individuals and businesses to create and purchase insurance products using smart contracts, covering various needs like flight delay and crop insurance; and InsurAce, a decentralized insurance platform providing coverage for a range of DeFi products and services, using a mix of on-chain and off-chain data for policy pricing and claim assessment.\n\nNotwithstanding the substantial advancements in the financial sector, blockchain technology remains encumbered by certain limitations that warrant attention. Inadequate management of these limitations may result in unfavorable repercussions for organizations that adopt this technology. It is crucial to examine the blockchain trilemma when discussing this subject matter. Figure 4 presents a graphical depiction of the blockchain trilemma for elucidation purposes:\n\nThe trilemma theorizes that a blockchain implementation is challenging to cover all three attributes.64 The attributes consist of decentralization, security, and scalability. Decentralization refers to the distribution of the network among numerous nodes and is not centralized. Security means that the network is resistant to tampering and attack. The scalability attribute refers to the situation where the network can handle lots of transactions in a short period of time. Currently, a blockchain network is only able to cover two of the attributes. It challenges the developers to establish a balance between those three attributes to the specific needs of a product/service. We have identified five threats associated with implementing blockchain in the financial industry. The threats are listed as follows.\n\n3.4.1 Scalability and speed\n\nScalability and speed are two interrelated threats in blockchain utilization. Scalability refers to the blockchain’s ability to handle the increased amount of workload. Speed is the amount of time a system requires to conduct a certain task. Those threats are related since a system is addressed as scalable if it can handle a workload increase within a specific amount of time. In several cases, blockchain networks may be unable to handle the increased workload, thus slowing the whole network. As more transactions are added to the blockchain network, the slower it gets. Fortunately, researchers and platform developers are developing solutions to address these threats. It aims to make blockchain more practical and efficient to face the increased workload.\n\n3.4.2 Security\n\nSeveral factors contribute to the risk of security threats in the digital realm. One such factor is the susceptibility of consensus algorithms, like Proof of Work (PoW), to manipulation. Attackers can gain control over the system by amassing 51% of its computational power, which enables them to dictate their own rules. However, this level of control is challenging to achieve due to the vast number of network participants. Phishing is another security threat, where scammers deceive victims into investing in counterfeit cryptocurrency wallets. Once victims share their information with the fraudulent wallet, they cannot access their funds without the private key. Lastly, a Sybil attack poses a significant security threat by creating numerous false identities to seize network control. If successful, the attacker can exploit the network with impunity.\n\n3.4.3 Cost\n\nAlthough blockchain can potentially reduce transaction costs, users in FinTech must pay service fees to miners rather than a financial institution, with variable costs depending on the effort required and traffic. Fees incentivize miners to include transactions in the next block, with the amount dependent on the demand and supply of block space. High demand leads to increased fees, which contribute to rising costs. Hardware prices, bandwidth requirements, and network synchronization complexities are also cost factors. These factors have hindered widespread adoption, however newer innovations like Layer 2 (L2) mechanisms offer a faster and more affordable implementation.\n\n3.4.4 Regulation\n\nInsufficient regulations can negatively impact the establishment of new products, leading to disorder and increased criminal activities. Therefore, it is important to strike a balance between regulation and innovation. It is also important to note that the level of regulation may differ among countries, and weak regulations and limited user knowledge regarding blockchain can make it easier for criminals to carry out illegal activities. Regulators must play a vital role in establishing regulations regarding blockchain-based digital assets to prevent negative consequences. If authorities fail to regulate blockchain, it could lead to various negative outcomes. Firstly, it could facilitate money-laundering activities due to the anonymity provided by blockchain transactions, allowing criminals to obscure their funds’ origin. Secondly, customers may be vulnerable to blockchain scams due to the technology’s complexity and lack of protection. Therefore, regulators should establish appropriate rules to safeguard citizens. Lastly, the lack of standardization and regulation could result in interoperability issues between different blockchain networks, hindering or even preventing transactions between companies. The regulations of blockchain technologies vary among developed and developing countries. Developed countries tend to have a clearer legal framework for blockchain and a higher level of blockchain adoption than developing countries. Also, developed countries tend to have clearer tax regulations, whereas developing countries may still determine the tax procedure.\n\n3.4.5 Environment and energy\n\nThe energy consumption of blockchain technology, specifically the PoW mechanism, has raised concerns about its negative environmental impact. In fact, a single Bitcoin transaction can consume as much as 1,499 kWh of electricity due to the intense competition between miners to solve computational problems and earn rewards.65 This increased demand for electricity has led to more fossil fuel consumption, contributing to increased carbon emissions and pollution. The widespread use of PoW as a consensus mechanism in cryptocurrencies has further compounded these environmental issues, necessitating alternative consensus algorithms promoting environmental sustainability. Additionally, the issue of hardware waste has significantly affected environmental sustainability, as blockchain companies often require the continuous procurement of new hardware with a limited lifespan. Furthermore, the high energy requirements for mining activities have led to a concentration of mining activities in regions with low energy costs or favorable tax policies, leading to centralization, contrary to the decentralized philosophy underpinning blockchain technology. Therefore, it is crucial to address these environmental concerns to ensure blockchain technology’s sustainable growth and development.\n\n\n4. Threat solutions\n\nNumerous researchers have proposed potential solutions to mitigate the threats described in the preceding section (subsection 3.4). It is worth noting, however, that these solutions are not the only viable means of addressing these threats. Financial institutions can implement the suggested solutions or explore superior alternatives that may emerge in the future. Therefore, it is critical for financial institutions to remain vigilant and flexible in their approach to security, ensuring they effectively tackle the constantly evolving nature of these threats. Financial institutions must continuously assess their security measures and invest in innovative approaches that provide the best possible protection against cybersecurity threats. This proactive approach will ensure they remain ahead of the curve in the ongoing battle against cybercriminals. By prioritizing cybersecurity, financial institutions can better safeguard their customers’ sensitive information and maintain their reputation for trust and reliability.\n\nResearchers have proposed solutions to address scalability and speed issues in blockchain systems, particularly Layer 1 (L1) platforms like Bitcoin and Ethereum, which cannot be easily modified. A solution called Layer 2 (L2) has been developed to overcome these limitations, which involves aggregating transactions before writing them to L1. Several techniques have been developed for L2, including Simplified Payment Verification (SPV), which reduces data usage compared to traditional methods, Lightning Network (LN), which uses micropayment channels to update balances continuously,66 and sharding, a technique that partitions data among multiple nodes.67 Sharding divides the network into smaller shards, each responsible for processing a subset of transactions, reducing the burden on individual nodes and increasing transaction processing speed. Additionally, sharding offers benefits such as sublinear communication, higher resiliency, rapid committee consensus, secure configuration, fast cross-shard verification, and decentralized bootstrapping. Notably, Rapidchain and Ethereum 2.0 are among the leading platforms that have adopted sharding.\n\nTo mitigate the risk of a 51% attack, various consensus algorithms such as PoS, Unique Node List (UNL), Proof of History (PoH), and Proof of Authority (PoA) can be used instead of the traditional PoW. PoS, for example, reduces the possibility of a malicious entity taking over the network by making it almost impossible to perform a 51% attack. Peercoin is an example of a blockchain product that utilizes the PoS mechanism.68 UNL is another solution that protects the network from external attacks by preventing malicious entities from entering the network without being recognized as the node operator. PoH is a consensus algorithm proposed by Solana, where every transaction has a unique hash and count, serving as a real-time record that miners can use to reconstruct transactions based on their historical records, increasing resilience against possible attacks.69 PoA is another type of consensus where miners stake their reputation, rather than coins, to be recognized as a validator.70 This means they are not anonymously operated, unlike in PoW and PoS, making it easier to detect conspiring parties and increasing resistance to 51% of attacks.\n\nHowever, security threats may also arise from the lack of user awareness, rather than the system. Therefore, there are several solutions to prevent attacks. The first is to avoid suspicious financial investments and invest in registered financial institutions, which are less likely to conduct scams. Raising awareness of various scamming methods, such as phishing, pop-ups, and spoofing, is another solution to increase user awareness and prevent attacks.23\n\nOver the course of several years, the Financial Action Task Force (FTAF) has implemented various changes to its policies, ultimately resulting in the release of Recommendation No. 15. This recommendation mandates that cryptocurrencies and their affiliated financial institutions disclose information about the entities and recipients involved in digital asset transactions, which is commonly referred to as the travel rule.71 However, Virtual Asset Service Providers (VASPs) - as financial institutions - have encountered obstacles when attempting to apply the travel rule to blockchain-based digital assets. The core issue is that VASPs struggle to manage the cryptographic keys associated with their customers, as digital assets on a blockchain are directly controlled through a private-public key mechanism. To address these challenges, Figure 5 outlines two potential approaches68:\n\n1. Non-custodian: This approach utilizes a secure method where the parties involved in the asset transfer - the originators and beneficiaries - hold both private and public keys. At the same time, the VASP only has access to their public keys. This ensures that the VASP’s involvement is limited to monitoring the transaction and does not involve intermediation. By complying with the travel rule, this approach empowers financial institutions to validate and verify transactions before they are executed, thus enhancing the security and soundness of the financial system.\n\n2. Custodian: This refers to a custody-based approach, where the VASP assumes responsibility for the secure storage of both the public and private keys, and neither the originator nor the beneficiary has direct ownership of the keys. This method enables financial institutions to manage the transfer of their clients’ assets and is commonly used by blockchain-based exchanges such as Binance, Coinbase, and Uphold. By employing a robust custody mechanism, financial institutions can ensure their clients’ assets are secure and safeguarded against potential threats or loss.\n\nEthereum 2.0 provides a viable solution to address the high costs associated with blockchain technology. Through the use of PoS and sharding, Ethereum 2.0 reduces the computational requirements of blockchain transactions, thereby lowering transaction costs.69 Integrating the Beacon Chain, a new type of consensus layer, with the existing PoW layer in Ethereum 2.0 represents a unique approach that eliminates the need for traditional PoW consensus, resulting in faster processing times and significantly reduced transaction costs.70 Miners can optimize gas usage to reduce costs by improving code efficiency and consolidating multiple transactions into a single batch. However, addressing the cost-related challenges in the blockchain industry requires a multifaceted approach that involves technological solutions and market reforms. As blockchain innovation continues to evolve, it presents opportunities for new platforms to emerge with lower costs than existing ones, making the industry more accessible and widely adopted. The birth of various new blockchain platforms is motivated by the need for cost reduction, most of which are L2 solutions, as we mentioned in subsection 4.1.\n\nRegulating blockchain technology is a multifaceted issue that presents challenges due to the diverse regulatory landscape across jurisdictions. Nonetheless, several potential solutions could be implemented globally to address this challenge. The first solution involves governments prioritizing the development of blockchain regulations that promote data privacy, anti-money laundering, and consumer protection. Through such regulations, governments can ensure blockchain operations align with legal frameworks and safeguard stakeholder interests. Secondly, creating regulatory sandboxes offers a controlled environment for blockchain companies to experiment with regulatory approaches in collaboration with regulators. This approach enables a balance between innovation and regulation.72 Thirdly, international cooperation among countries is essential, given the global nature of blockchain technology. Governments can collaborate to establish global standards and coordinate regulatory efforts, promoting innovation, accountability, and consumer protection. Finally, adopting CBDC represents a potential solution for regulating blockchain technology in the financial industry. By issuing a regulated form of cryptocurrency, central banks can monitor and enforce compliance with regulations while enhancing transaction transparency and preventing threats such as money laundering. However, it is important to balance innovation and regulation to mitigate potential risks and promote the industry’s growth.\n\nSeveral methods can be utilized to address environmental and energy issues associated with blockchain technology. The first method is the implementation of the PoS algorithm, which lowers the mining difficulty for each node and increases the speed of the mining process based on the number and duration of coins held by the node,7 resulting in fewer participating nodes than PoW. The second method involves the use of permissioned blockchains, which limit the number of parties in the network, ultimately reducing energy consumption. Transitioning mining operations to renewable energy sources such as solar, water, and wind can also be a potential solution to reduce the carbon footprint of the mining process. In addition, blockchain-as-a-service (BaaS) can be leveraged as a means of reducing energy consumption, as it allows companies to outsource their blockchain networks to third-party providers, thereby reducing the need for companies to establish and maintain their own energy-intensive blockchain networks. Finally, raising awareness and education about the impact of blockchain on the environment and energy sustainability is essential. Individuals and organizations can take steps to reduce their environmental impact and promote energy sustainability through their use of blockchain technology. By adopting a multifaceted approach that integrates technological and social solutions, we can mitigate the negative impact of blockchain on the environment and energy sustainability.\n\n\n5. Discussion\n\nBlockchain technology has gained significant attention recently, particularly in the financial industry. This is due to its potential benefits, such as low-cost financial services, high security and privacy, efficient financial transactions, high return on investment, and transparency. Two key drivers of blockchain technology are Smart Contracts and DLT, which are essential for establishing a decentralized system. The decentralized nature of blockchain technology has the potential to promote financial inclusion by providing low-cost financial services to the unbanked and underbanked populations. This has the potential to revolutionize how financial services are offered, particularly in developing countries where traditional financial services may be costly and inaccessible.\n\nFurthermore, blockchain technology can offer high security and privacy, protecting users’ sensitive financial information. Efficient financial transactions, such as remittances, can also be facilitated using blockchain technology. Blockchain-based solutions can offer faster transaction processing times and lower transaction fees than traditional financial institutions. Additionally, the programmable nature of blockchain technology allows for the creation of programmable assets and currencies, which can support new financial instruments and business models.\n\nDespite its potential benefits, the adoption of blockchain technology in the financial industry faces several challenges. One of the significant issues is the complexity of the blockchain system, which requires significant technical expertise to implement and maintain. For example, how to transform the business process into the blockchainable one.73 The lack of standardization and regulation also presents a challenge, as it can hinder the technology’s adoption in the industry. Other prominent issues that we already mentioned and have been discussed extensively in the section threat and its solution, including cost, speed, and scalability issues.\n\nTo overcome these challenges, there is a need for education and awareness programs to provide human resources with the necessary knowledge and skills to implement and maintain blockchain technology. Standardization and regulation efforts can ensure that blockchain technology is governed within a legal framework protecting all parties involved. It is important to note that the problems and solutions discussed in this context cannot be universally applied. Each country may have its own rules and regulations for governing blockchain technology within its jurisdiction. However, as blockchain technology continues to grow and expand beyond borders, there may be a need for regulation that spans multiple countries. It is crucial that regulators must find a balance that ensures the safety and security of all parties involved to prevent any negative outcomes from arising.\n\n\n6. Conclusion\n\nWe have carefully crafted a taxonomy based on four dimensions, which we believe are essential in understanding and mapping the blockchain-based financial industry. We have provided detailed explanations of each dimension, including the key drivers, benefits, products, and threats associated with blockchain technology. We have also analyzed the interdependence between each dimension to understand better how they can impact one another. It is important to note that our taxonomy’s dimensions may not be exhaustive, as the blockchain-based financial industry is constantly evolving. However, our paper provides a comprehensive overview of the conditions at the time of writing. We have made a conscious effort to highlight the most significant aspects of blockchain technology in finance.\n\nOne of the key advantages of blockchain is its potential to increase business process efficiency and drive innovation in the financial industry. However, establishing adaptive regulations is crucial to ensure that users and financial institutions utilize blockchain technology securely and responsibly. It is possible that our paper may not have captured all dimensions of the blockchain-based financial industry, given the rapidly evolving nature of this technology. Therefore, future research could delve deeper into exploring the gaps to gain a more profound understanding of blockchain’s role in FinTech companies. Overall, our paper aims to provide valuable insights into the blockchain-based financial industry and its potential for disrupting traditional financial systems.\n\n\nAuthor contributions\n\nConceptualization: A.A., Data Curation: S.S. and A.A., Formal Analysis: A.A. and S.S., Methodology: A.A., Resources: S.S., Supervision: A.A., Validation: A.A. and S.S., Visualization: S.S., Writing – Original Draft Preparation: S.S., Writing – Review & Editing: A.A. and S.S.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nMarket cap of top 100 banks globally 2022\|Statista. (accessed Jul. 19, 2022). Reference Source\n\nPuschmann T: Fintech.2017; 59(1): 69–76. Publisher Full Text\n\nGomber P, Koch JA, Siering M: Digital Finance and FinTech: current research and future research directions. J. Bus. Econ. 2017; 87(5): 537–580. Publisher Full Text\n\nZhang R, Xue R, Liu L: Security and privacy on blockchain. ACM Comput. Surv. 2019; 52(3): 1–34. 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Publisher Full Text" }	[ { "id": "171680", "date": "22 May 2023", "name": "Giulio Caldarelli", "expertise": [ "Reviewer Expertise Blockchain", "Oracles", "and Decentralized Finance." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Author,\nThanks for submitting your manuscript to F1000Research. As you know, the journal is reputable and indexed in the main scholarly databases.\nThe manuscript you submitted concerns a taxonomical analysis of Blockchain based applications in the financial sector. It is undoubtedly a useful resource for scholars and practitioners working in the field.\nAlthough I believe it is an interesting contribution, some changes are necessary, in my opinion, for the article to be understandable to a broader audience. Please accept some suggestions to improve the paper.\nIntroduction\nIn the introduction, some words are closed in quotation marks (“ “) and others are not. I’m referring to “internal, provider oriented and customer-oriented digitalization”. Please consider a consistent use of quotation marks for all of them.\n\n“but first we need to explain what blockchain is”. Consider removing this sentence. It is more appropriate for a blog article than an academic paper. If you believe you need to explain blockchain, go ahead and explain it directly. By the way, I believe the ledger is made of blocks and is secured by cryptographic proofs.\n\nThe revolution brought by blockchain to the organizational structure can be heterogeneous and not only due to the DAOs. I believe you need to specify also the organizational structure of what type of company. Did you mean the financial ones?\n\n“Blockchain is the technology behind Bitcoin”. I heard this sentence a lot, but I don’t think is very accurate. There are many technologies behind Bitcoin. Blockchain sometimes is used as a synonym for Bitcoin. We cannot say that blockchain is a technology. It is more a concept thanks to which we refer to bitcoin-like ecosystems. Consider removing the sentence\n\n“Another blockchain product in the financial sector is Centralized Finance (CeFi)”. Its often used as synonymous with Traditional Finance (TradFi). I hardly hear CeFi as a goal of blockchain implementation. So please specify what you wish to intend here.\n\nA critical part that is missing in the Introduction is the significance of the study. Do you believe that among all the published papers on DeFi, there is still a need for a review? I truly read many, many review papers on Decentralized Finance. Why do you believe your research is fundamental at this stage? What are you offering that other published papers have not? This is a critical point also to understand the motives behind the paper type you have selected. Is a classic review appropriate for the contribution you are proposing?\nLiterature Review\nThe idea consists in a review of papers which is coherent with the scope of the paper, I believe. What I cannot understand is the practical method, thanks to which you took the articles. You said that you picked 73 articles from some publishers, but how? Why those publishers? What is the ratio? What is the academic approach? Where did you put the mentioned keywords? Have you queried some academic databases? You say that you gathered information from crypto projects. Why did you add data from them? Was the data retrieved insufficient? How did you find them? What are the criteria? What is the source? Why is the source selected? Is there any filtering? It is true that this article is intended to be a simple review paper, but what you are proposing here is probably more consistent with a systematic review. Being a paper that tries to clarify and harmonize the taxonomy, it probably requires a well-written and explained methodology. Do you know other taxonomical paper that use a simple review explained in that way?\nA paper that can be of inspiration for what you are writing here is the following one: Tasca P., Tessone C.J., “A Taxonomy of Blockchain Technologies: Principles of Identification and Classification “ https://ledger.pitt.edu/ojs/ledger/article/view/140\nAlthough they are not using a systematic review, they give a specific contextualization of their approach.\nTherefore, my suggestion is to remove the literature review paragraph and write a section that clearly describes how you organized your research on taxonomy. Explain thoroughly and carefully how you got the articles, sources, and those interviews you mentioned in the abstract. Again, since you also mentioned interviews, a simple review paper type feels inappropriate. Consider giving all possible details on this data. If possible, provide a link to a repository. Explain your research idea extensively, the gap you are covering, and how methodologically you are going to cover it. Build on previous research articles and be inspired by other reviews in the field. Although not required for simple review, it would be better if what you achieve is replicable.\nThe Taxonomy\nThis section is interesting. However, it really needs to be extensively explained and well-linked to the methodology section. Otherwise, it is not even clear how you made the graphical word map.\nDiscussion\nThe discussion appears to be just sketched. Given the length and heterogeneity of the information provided, readers probably expect some more elaboration from the authors.\nUnfortunately, without a thorough methodological explanation, I cannot continue the review process properly. Therefore, I must suggest rewriting the methodological part so that the rest of the content can be evaluated. Of course, it is vital to explain in advance the significance of the paper and the reason why at this stage of research and for this specific goal, a simple review paper is selected.\nGood luck with your research!\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? No\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? No", "responses": [ { "c_id": "9906", "date": "18 Jul 2023", "name": "Andry Alamsyah", "role": "Author Response", "response": "Introduction 1. Thank you for pointing out the inconsistencies; we decide to remove the quotation marks (“ “) and modify the sentence accordingly. 2. Thank you for the suggestion; we have modified the statement to follow the formality of the academic paper. We also alter the misleading statement into “… consists of a chain of block secured by cryptographic proof to secure its integrity.” 3. Thank you for the critical opinion on DAO usage. We have stated to limit only the organization structure; thus, mentioning the DAO conceptual approach is relevant here. What we meant here is the usage DAO conceptual approach, which is decentralized and autonomous to generate/spark innovation. To make matters clear, we have modified the text in the 3rd paragraph as follows “…The revolution brought by blockchain to the organizational structure is through Decentralized Autonomous Organization (DAO) idea. The DAO concept offers a decentralized approach rather than a pyramid hierarchy, often used in conventional institutions, including the financial industry. The decentralization and autonomous concept also drive the innovation of numerous new products, eliminating intermediaries’ functions. For instance, a digital cryptocurrency operated on a decentralized peer-to-peer network, called bitcoin..” 4. Thank you for the critics. We have removed the “blockchain is the technology behind the bitcoin” statement. 5. Thank you for the correction; we have added TradFi to the CeFi term. 6. Thank you for the constructive critics. We have found several precedent articles regarding blockchain in the financial industry and DeFi taxonomy—notably a publication from Puschman and Huang-Sui. We have mentioned these publications in the 5th paragraph of the introduction section. We explained in detail the difference between our paper and the previous article in scope, control, financial instruments, interoperability, risk, and regulation. We underline that since blockchain in the financial industry is still nascent, the public would benefit from different approaches and diverse literature views. Literature review 1. We have modified the previous section 2 about the literature review section into the methodology and literature review section. Subsequently, we divided this section into subsections 2.1 Methodology and 2.2 Literature Review. In the methodology, we clarify that we do not choose specific publishers to construct the taxonomy construction. The idea is to collect information from scholars, industry, and regulators using related keywords such as blockchain technology, financial industry, decentralized finance, token economy, application, implementation, and blockchain for business processes. Several important questions are asked and explored to clarify the scope further to construct the taxonomy. The questions are shown in the 2nd paragraph of subsection 2.1. Keywords and questions become the fundamental idea of taxonomy construction. We add Table 2 to describe the academic publication source and its ratio. Also, we categorize the academic publication into 3 categories, which we explain in 3rd paragraph of subsection 2.1. Thus, the publication category is shown in Table 3. We also explain clearly the role of literature resources from the industry, including several DeFi projects and the regulator (CBDC and BIS). 2. Thank you for the constructive suggestion. We have altered section 2 into the research methodology and literature review to cover your suggestion regarding how we achieve this research and provide the necessary coverage for the literature review. We also decided to remove the expert interview sections since the majority of our sources come from the literature. Initially, we planned to use domain expert input to strengthen our result. However, we found, it is sufficient from the available literature review. Taxonomy Thank you for the valuable suggestion. We have added the methodological section, in line with research motivation, literature research criteria through keywords and essential questions, and publication categorization. We hope the explanation can justify the taxonomy construction." } ] }, { "id": "171682", "date": "22 May 2023", "name": "Wisnu Uriawan", "expertise": [ "Reviewer Expertise The blockchain 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 paper describes The Taxonomy of Blockchain-based Technology in the Financial Industry. The taxonomy of this context is interesting, and it is worth to be investigated.\nStill, the paper seems more like a presentation of a theory report than a research paper. In the present form, the manuscript appears more like a white paper.\nIn particular, I have the following significant comments:\nThe advantages and disadvantages of adopting blockchain technology must be better described than other types of blockchain or other solutions not using the blockchain. There is a concise analysis for each section, but more is needed.\n\nI recommend the authors create a specific section to analyse the advantages and disadvantages of adopting blockchain technology in this context.\n\nThe potential risk and vulnerabilities of the proposed approach should be discussed more. The principal vulnerabilities of the proposed system should be described together with the related countermeasures.\n\nA new section could be created, or vulnerabilities and countermeasures could be discussed.\n\nIt would be interesting to link the DeFi concepts in the marketplace with the design description and how the taxonomy could be enhanced using blockchain technology and its records history.\n\nIt would be helpful to provide more details in Section 4 on the potential standards and protocols that could be used to implement the proposed approach.\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": "9907", "date": "18 Jul 2023", "name": "Andry Alamsyah", "role": "Author Response", "response": "1. The advantages and disadvantages of adopting blockchain technology must be better described than other types of blockchain or other solutions not using the blockchain. There is a concise analysis for each section, but more is needed. Thank you for the suggestion. After we describe the advantages and disadvantages of financial industry blockchain implementation in subsection 2.2, we add a concise summarization in Table 4. However, it is worth noting that we only focus on the key features related to the financial industry; thus, it might not include all aspects. 2. I recommend the authors create a specific section to analyse the advantages and disadvantages of adopting blockchain technology in this context. Thank you for the advice. Since our primary objective is focusing on the business processes and products/services in the financial industry, adding a specific section for blockchain technology will devise the focus more on the technological side. Moreover, adding the requested explanation in Table 4 is already sufficient to support the paper's objective. We will consider this recommendation in the future taxonomy development focusing on technological aspects, which we write in the future research suggestion in the conclusion section. 3. The potential risk and vulnerabilities of the proposed approach should be discussed more. The principal vulnerabilities of the proposed system should be described together with the related countermeasures. We have dedicated section 4 specifically to discuss potential risks/vulnerabilities of blockchain technology usage. Each subsection discusses the state of the idea of how to resolve the problem and how to mitigate the risks in practice. 4. A new section could be created, or vulnerabilities and countermeasures could be discussed. The threat solutions section is intended to complement the main idea of taxonomy creation. It is not the main idea of the paper. Using Table 4 and the discussion on threats solutions section is enough for the complementary discussion. Nevertheless, we thank the reviewer for pointing out this idea; we will consider writing a new taxonomy paper specifically for the technological aspects. 5. It would be interesting to link the DeFi concepts in the marketplace with the design description and how the taxonomy could be enhanced using blockchain technology and its records history. The purpose of the study is to construct the taxonomy for a higher general purpose (audience) which has no or little prior knowledge about blockchain technology and how this technology can achieve several abstractions that were impossible to be implemented before, such as peer-to-peer transactions, transparency, and automation (smart contract). This new perspective will inspire creativity that sparks many crypto industry marketplaces today where most of them in the form of DeFi and GameFi. For the discussion to add future taxonomy enhancement, we have added the following suggestion in the conclusion section \"Therefore, future research could delve deeper into exploring the gaps to gain a more profound understanding of blockchain's role in FinTech companies. Another approach is to develop the taxonomy based on blockchain technical aspect exploration.\" 6. It would be helpful to provide more details in Section 4 on the potential standards and protocols that could be used to implement the proposed approach. Thank you for the suggestion, we have mentioned the trade-off of blockchain protocol choice based on the blockchain trilemma in section 4. The practical use case might differ between implementations, so we would prefer to underline the standard principle in resolving threats in the blockchain trilemma concept: speed/scalability, cost, and security. We avoid mentioning the blockchain protocol choice since we can not keep up with the dynamic development of blockchain protocols. For example, today, the fastest blockchain protocol is Solana at the rate of 50000 transactions per second, but it might soon change with the emergence of new blockchain protocols." } ] } ]	1	https://f1000research.com/articles/12-457
https://f1000research.com/articles/12-843/v1	18 Jul 23	{ "type": "Research Article", "title": "Implementing a quality improvement initiative for reducing intravenous antihypertensive utilization in the hospital setting: Improving patient outcomes without prolonging hospital stay", "authors": [ "Moez Alnazeer", "Jessica Jones", "David Ficklen", "Jessica Jones", "David Ficklen" ], "abstract": "Background: This project aimed to implement a quality improvement initiative to reduce the utilization of non-indicated intravenous (IV) antihypertensive medications in the hospital setting and evaluate its impact on hospital length of stay. Methods: A quality improvement initiative was conducted at a 500-bed regional hospital to improve management of inpatients with asymptomatic severe hypertension. An algorithm was developed to guide management to minimize the inappropriate use of IV antihypertensives. Educational sessions were conducted with medical providers and nursing staff to promote adherence to the algorithm. Pharmacy records were reviewed to assess the utilization of IV antihypertensive medications. Aggregated length of hospital stay before and after the intervention were compared. Statistical analysis was performed using paired t-tests. Results: The utilization of IV antihypertensive medications was reduced by 47.6% after the intervention, as measured by days of therapy per 1000 patient days (p <0.001). However, the average length of hospital stay did not show a significant difference before and after the intervention (p = 0.094). Conclusions: The implementation of a quality improvement initiative, including an algorithm and education for healthcare staff, successfully reduced the utilization of non-indicated IV antihypertensive medications in the hospital setting. This approach has the potential to improve patient safety and reduce healthcare costs. Further research is needed to explore the long-term effectiveness of this intervention and its impact on patient outcomes.", "keywords": [ "quality improvement initiative", "IV antihypertensive medications", "hospital setting", "length of stay", "patient safety", "healthcare costs" ], "content": "Introduction\n\nHypertension is a common condition seen in hospitalized patients. Aggressive management with intravenous (IV) antihypertensive medications is often inappropriately utilized for asymptomatic patients with severe hypertension.1 However, there is a lack of evidence to support the routine use of IV antihypertensive medications in this population.2 Studies have shown an increased risk of complications, such as acute kidney injury, cerebral vascular accident, myocardial infarction, dizziness, and falls, associated with this practice.3–5 In addition to the potential harm to patients, this approach also leads to increased healthcare costs.\n\nTo address this issue, an algorithm was developed (Figure 1) to guide nursing and medical staff in the management of asymptomatic patients with severe hypertension with the goal of reducing the blood pressure moderately and slowly using oral medications when appropriate. The primary objective of this project was to evaluate the effect of this intervention on the utilization rates of IV antihypertensive medications after providing education on the flowchart pathway to nursing and medical staff. The secondary objective was to assess the impact of the intervention on length of stay.\n\n\nMethods\n\nThe project involved reviewing aggregate pharmacy data that were de-identified. No patient records were accessed and the project involved minimal risks. Quality improvement initiatives do not require IRB approval per our institutional guidelines and the US Department of Health Services Regulations. An informed consent form was used to obtain consent from the participants of this project.\n\nThis project was conducted at a 500-bed community hospital, College Station, Texas. Patients in the Emergency Department, Intensive Care Unit and Stroke Unit were excluded based on the appropriate need for IV antihypertensive medications in these areas.\n\nAggregated hospital inpatient pharmacy data regarding the utilization of intravenous (IV) antihypertensive medications was extracted for the months of July 2022 through March 2023.6 This data identified the types of IV antihypertensive medications utilized during the project period. Hydralazine and labetalol represented over 90% of the IV antihypertensive doses given during the project period. Therefore, this project focused on these two drugs. The data were collected and recorded in a secure electronic database for analysis. Overall length of stay data were obtained from case management department data.\n\nThe primary outcome measure for this project was the difference in average monthly utilization of IV antihypertensive medications between the four-month period before and the four-month period after the intervention. The utilization was measured using the standardized “days of therapy per 1000 patient days (DOT/1000)” to account for the potential differences in patient volume and length of stay during the project period. The secondary outcome was the effect of this intervention on the average length of stay of the patient population studied.\n\nAn algorithm that outlined the appropriate management of severe asymptomatic hypertension in the hospital setting was created based on current evidence-based guidelines and local hospital protocols (Figure 1). This was reviewed and approved by the hospital’s Pharmacy and Therapeutics Committee.\n\nSeveral educational sessions were conducted with the medical staff, nursing staff, and pharmacists to discuss the management of severe asymptomatic hypertension and utilization of the suggested algorithm. These educational sessions included presentations, case discussions, and interactive discussions to promote understanding and adherence to the recommended pathway. These sessions were facilitated by a multidisciplinary team which included clinical pharmacists, clinical nurse educators, and physician champions.\n\nAfter the completion of the educational sessions, the utilization of IV antihypertensive medications was monitored over the subsequent four-month period to assess the impact of the intervention. The utilization data were collected from the pharmacy records and recorded in the electronic database for analysis.\n\nDescriptive statistics, including mean, median, standard deviation, and frequency distributions, were used to summarize the utilization of IV antihypertensive medications during the project period. The changes in utilization and length of stay before and after the intervention were compared using paired t-tests. A p-value of less than 0.05 was considered statistically significant. The Microsoft Excel 365 data analysis tool was used to conduct statistical analyses.\n\n\nResults\n\nAggregate pharmacy data on the usage of IV antihypertensive medications were reviewed for the duration of July 2022 to March 2023 (Table 1). The primary outcome was the impact on utilization of IV antihypertensives using DOT/1000. This measure showed a significant decrease in the four-month period after the intervention 25.24 (SD = 3.05) compared to the four-month interval before the intervention 48.21 (SD = 3.06). After the intervention, the utilization rate decrease was maintained for four consecutive months measured. For the secondary outcome, the average length of stay in days for patients hospitalized did not demonstrate any statistically significant change. The average length of stay before the intervention was 4.15 (SD = 0.12), whereas after the intervention, the average length of stay was 4.375 (SD = 0.12). The average length of stay before the intervention in July, August, September, and October was 4.1, 4.3, 4.2, and 4, respectively. After the intervention, the average length of stay increased in December (4.3) and January (4.6) and decreased in February (4.4) and March (4.2) (Figure 2).\n\nDefinitions: Days of therapy (DOT): Presents administrations of a specific medication on the calendar day. Days present: Number of patients present in the hospital for any portion of a calendar day. DOT/1000 patient days: DOT*1000/Days present.\n\nThe data were analyzed using a paired t-test to compare the mean utilization rate before and after the intervention. The results showed a significant difference between the means (t(6) = 8.65, p < 0.001). The effect size was large (Cohen’s d = 3.54). For the average length of stay in days for patients hospitalized, the data were analyzed using a paired t-test to compare the mean length of stay before and after the intervention. The results showed no significant difference between the means (t(6) = -1.99, p = 0.094). The effect size was small (Cohen’s d = 0.61).\n\n\nDiscussion\n\nIn this project, we implemented a quality improvement initiative to reduce the utilization of non-indicated intravenous (IV) antihypertensive medications in the hospital setting. Our results showed that the implementation of an algorithm and educational sessions successfully decreased the utilization of IV antihypertensives, as measured by days of therapy per 1000 patient days. The reduction in IV antihypertensive utilization is important for patient safety and cost saving. By shifting the management approach towards oral medications, we can minimize the potential harm and increased healthcare costs associated with unnecessary IV antihypertensive use. While the intervention significantly reduced IV antihypertensive utilization, there was no significant difference in the average length of hospital stay before and after the intervention. This indicates that slowly lowering blood pressure with oral medications does not necessarily increase hospital length of stay.\n\nThere are several limitations to this project. First, the project was conducted in a single community hospital, which may limit the generalizability of the findings to other settings. Second, the project relied on pharmacy records for data collection, which may be subject to inaccuracies or missing data. Third, the project was conducted over a relatively short time frame of four months. This may not capture long-term changes in utilization patterns. Finally, the project did not assess the impact of the intervention on patient outcomes, such as blood pressure control or adverse events, which may provide further insights into the effectiveness of the intervention.\n\n\nConclusions\n\nA quality improvement initiative introducing an algorithm with education for nursing and medical staff, significantly reduced the utilization of IV antihypertensives using DOT/1000 but did not significantly affect the average length of stay in days for patients hospitalized. This project has shown the potential to improve patient safety by reducing the risk of complications associated with unnecessary IV antihypertensive medication use and also has the potential to reduce healthcare costs. Further research is warranted to explore the potential clinical implications of these findings and to evaluate the long-term effectiveness of the intervention in optimizing antihypertensive medication usage in this patient population.\n\n\nConsent\n\nWritten informed consent for publication of the participants’ details was obtained from the participants.", "appendix": "Data availability\n\nFigshare: Underlying data for ‘Implementing a quality improvement initiative for reducing intravenous antihypertensive utilization in the hospital setting improving patient safety without prolonging hospital stay’. https://doi.org/10.6084/m9.figshare.23523708.v1. 6\n\nThis project contains the following underlying data:\n\n• Implementing a Quality Improvement Initiative for Reducing Intravenous Antihypertensive Utilization in the Hospital Setting Improving Patient Safety Without Prolonging Hospital Stay.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\nCherney D, Straus S: Management of patients with hypertensive urgencies and emergencies: a systematic review of the literature. Gen. Intern. Med. 2002; 17(12): 937–945. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKitiyakara C, Guzman N: Malignant hypertension and hypertensive emergencies. J. Am. Soc. Nephrol. 1998; 9: 133–142. Publisher Full Text\n\nO’Mailia JJ, Sander GE, Giles TD: Nifedipine-associated myocardial ischemia or infarction in the treatment of hypertensive urgencies. Ann. Intern. Med. 1987; 107(2): 185. Publisher Full Text\n\nGrossman E, Messerli FH, Grodzicki T, et al.: Should a moratorium be placed on sublingual nifedipine capsules given for hypertensive emergencies and pseudoemergencies. JAMA. 1996; 276(16): 1328–1331. PubMed Abstract \| Publisher Full Text\n\nZeller KR, Von Kuhnert L, Matthews C: Rapid reduction of severe asymptomatic hypertension: a prospective, controlled trial. Arch. Intern. Med. 1989; 149(10): 2186–2189. PubMed Abstract \| Publisher Full Text\n\nAlnazeer M: Implementing a Quality Improvement Initiative for Reducing Intravenous Antihypertensive Utilization in The Hospital Setting Improving Patient Safety Without Prolonging Hospital Stay. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "213669", "date": "18 Oct 2023", "name": "Zachary G. Jacobs", "expertise": [ "Reviewer Expertise Inpatient hypertension" ], "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 research article, the authors describe a quality improvement (QI) initiative aimed at reducing the unnecessary use of intravenous (IV) antihypertensive medications at a 500-bed community hospital in Texas. The QI intervention was comprised of an educational campaign targeting medical staff, nursing staff, and pharmacists, which took place sometime in November 2022. The primary outcome was the monthly utilization of IV antihypertensives, which was calculated as the number of days of therapy (DOT) per 1000 patient days (DOT/1000) per month. The secondary outcome was average length of stay per month. The outcomes were compared pre- (Jul 2022 – Oct 2022) and post-intervention (Dec 2022 – Mar 2023).\nThis is an important topic and I commend the authors for their work on this initiative. There is a growing body of evidence demonstrating the potential harms of overtreating severe asymptomatic hypertension. This study adds to several other recent QI initiatives with similar goals, which have utilized educational campaigns (1), informatics (2), or a combination of the two (3,4). I also applaud the authors’ use of an educational campaign, which can take significant effort to develop and implement.\nIn terms of results, the authors report a 47.6% reduction in the average utilization of IV antihypertensives in the four-month post-intervention period compared to the four-month pre-intervention period; however, as discussed in my feedback below, there are potential errors in the reported data and calculations. I do believe this is important work and adds to the body of existing literature. It could be appropriate for publication once these data inconsistencies, and some other issues, are addressed, but given the fundamental way these inconsistencies impact the interpretation of the results and the subsequent conclusions, it is not appropriate for acceptance prior to crucial revisions.\n\nMajor Feedback\nIntroduction: the references provided by the authors are out of date, with the most recent one being more than two decades old. I recommend adding more timely citations, as there have been several relevant studies published in the last few years that would better support their claims (e.g., 5-7).\n\nAlgorithm: I commend the authors for creating an easy-to-follow educational algorithm to aid in their educational efforts. Regarding the content, I have several recommendations. Obviously, the educational campaign for their initiative has already taken place and cannot be changed, but I would advocate for revising the algorithm prior to future use or publication. Specifically,\nAssessing for symptoms should be the first step of the algorithm, not the second, as treatment of hypertensive emergency should not be delayed for 30 minutes. Further, more accurate language would be to assess for “symptoms suggestive of hypertension-mediated end-organ damage”.\n\nIn step 3 of the algorithm, consider adding other common contributing factors for hospitalized patients, including nausea, drug withdrawal, drug or alcohol intoxication, volume status, and medication side effect (e.g., corticosteroids).\n\nIn the final step of the algorithm, I would caution against stating that gradually reducing the blood pressure “is indicated” in this setting. There is growing evidence to suggest that treating severe asymptomatic hypertension in the hospital even with oral agents may lead to harm (e.g., 6,7) and that intensification of home antihypertensive regimens on discharge may result in serious adverse events, especially among the elderly (8). At most, I would state that gradual blood pressure reduction may be indicated in certain circumstances, but this is a nuanced decision.\n\nResults: I note several potential errors:\nThe results presented in Table 1 are inconsistent with the data shared in the supplementary material. Specifically, in the first column, the DOTs for October and March are reported in the table as 247 and 117, respectively, whereas in the supplement they are reported as 274 and 177, respectively. In the second column, the “Days present” for September is reported in the table as 5732, whereas in the supplement it reads 5749. Lastly, in the third column, the DOT/1000 for September and March are reported as 45.88 and 20.18, respectively, whereas in the supplement they are reported as 45.75 and 30.53, respectively. This last error with the DOT/1000 for March is of particular concern, as it appears to demonstrate an upward trend in rates of IV antihypertensive use following the initial decrease after the intervention. The authors should explain and/or correct these inconsistencies, and address the finding of the upward trend in March in their discussion.\n\nIn the text of the Results section, the authors state “The primary outcome was the impact on utilization of IV antihypertensives using DOT/1000. This measure showed a significant decrease in the four-month period after the intervention 25.24 (SD=3.05) compared to the four-month interval before the intervention 48.21 (SD=3.06)”. The syntax of this second sentence is confusing and it is unclear what ”this measure” is referring to. I believe the authors are comparing the average DOT/1000 for the four-month pre- and post-intervention periods, but I cannot completely replicate their calculations, regardless of whether I use the DOT/1000 values from the table, or those in from supplement. The authors should elaborate on how these values for their primary outcome were calculated (perhaps I am misunderstanding the calculation) and ensure that the math is correct.\n\nOn the following page, under Statistical analysis, the authors report t values from a paired t-test. I would be interested to know the reasoning behind selecting a paired t-test rather than an unpaired one, as the pre/post intervention data seem independent. I tried to replicate the t-test results using the data provided but was unable to get the same values as those reported here. I do note 6 degrees of freedom listed with the t statistic, which would seem to fit more with an unpaired test.\n\nDiscussion: The authors state that “the intervention significantly reduced IV antihypertensive utilization…”. I hesitate to draw this conclusion without a) knowing the exact timing of the educational campaign, as the DOT/1000 in November was already lower than the preintervention average, and b) addressing the inconsistencies in the data, which may include a discussion of the fact that the DOT/1000 appears to have been trending back upward again as of March (assuming the data in the supplement are correct).\n\nDiscussion: there are several other limitations that should be added. First, if the initiative was comprised only of a single month of education, that the impact of the intervention would be expected to be transient. Second, the DOT/1000 calculation does not take into account the number of doses or number of patients treated on a given day, compared to measuring the number of medications orders, as done by Krouss et al. and Pasik et al. (2,3)\n\nMinor Feedback\nMethods, Ethical Considerations: The authors state “An informed consent form was used to obtain consent from participants of this project”. It is unclear who these participants were or why they were consented given that IRB approval was not needed. Please elaborate.\n\nMethods, Project Setting: The authors mention one exclusion criteria (ED, ICU, or stroke unit), but additional inclusion/exclusion criteria would be helpful. For example, were these only adult patients?\n\nMethods, Plan of Action: The authors state that, in addition to local hospital protocols, their algorithm was created based on “current evidence-based guidelines”. To my knowledge, while there are consensus statements from various organizations about severe asymptomatic hypertension in general (e.g., ACC/AHA), there are no evidence-based guidelines per se, especially pertaining to the management of hospitalized patients in particular. I recommend modify this statement to more accurately reflect this and add a citation to the consensus statement(s) you are referencing.\n\nMethods, Educational sessions: More information about the educational sessions would be helpful, including when exactly they happed. Reading between the lines, they appear to have taken place sometime in November, but knowing the dates and cadence is important for interpreting the results, since, as mentioned above, the DOT/1000 for November was already lower than the preintervention average. Please also specify how the educational algorithm was used. Was this simply discussed during the educational sessions, or was it distributed and/or made accessible in some way afterward? Lastly, how will these educational efforts be carried forward in the future? If this is a one-off campaign, the impact is likely to be highly transitory and this should be addressed in the limitations section, as mentioned above.\n\nResults, Statistical analysis: the first sentence of this section describing how the statistical analysis was conducted should appear in the Methods section, not Results.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "223799", "date": "15 Dec 2023", "name": "Ingrid Prkacin", "expertise": [ "Reviewer Expertise Arterial Hypertension", "Chronic Kidney Disease", "Emergency Medicine", "Nephrology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article describes the results of a quality improvement project focusing on the reduction of intravenous antihypertensive medication use following the creation of an algorithm for the management of severe (grade III) hypertension in the emergency department and staff education. While the topic is interesting and important, there are several questions that require answering before the article is ready for publication. 1. In the \"Ethical considerations\" part of the \"Methods\" section, it is stated that the project involved the review of de-identified pharmacy data and that no patient records were accessed. It also states that an informed consent form was used to obtain consent from the participants. Who were the participants that were required to give consent if no patient records were accessed, and the study was based on aggregated, de-identified pharmacy data? 2. In the \"Plan of action\" part of the \"Methods\" section, the authors mention that the algorithm was created based on current evidence-based guidelines and local hospital protocols but cites no such guidelines. Which guidelines were used and from what societies? Please also provide citations for these guidelines. 3. The \"Educational sessions\" part of the \"Methods\" section should be expanded and explained in more detail, outlining the curriculum used, number of sessions, topics of each session etc. (this can be provided as an Appendix or Supplemental Material) in order to make the intervention replicable in other interested institutions. 4. In \"Table 1\" of the \"Results\" section, it is stated that the DOT/1000 for March 2023 was 20.18, while in the \"Underlying material\" data, page 6, it is stated that the DOT/1000 for March 2023 was 30.53. Please explain this discrepancy. 5. More citations should be added, especially to the \"Discussion\" section, which contains none. 6. Which oral antihypertensive medications were used in place of the intravenous ones? There should be pharmaceutical data on the usage of those. Is there a trend of an increase in the use of oral antihypertensive medications in the observed period following the implementation of the algorithm? 7. The references should be of a more recent date. Also, similar interventions implemented by other authors should be discussed and presented in the \"Discussion\" section (for example, the study by Grassi et al. cited below).\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-843
https://f1000research.com/articles/12-842/v1	18 Jul 23	{ "type": "Study Protocol", "title": "Outcome analysis of posterior cruciate ligament injuries", "authors": [ "Anmol Suneja", "Sanjay Deshpande", "Vivek Jadawala", "Sachin Goel", "Sanjay Deshpande", "Vivek Jadawala", "Sachin Goel" ], "abstract": "Background - The posterior cruciate ligament (PCL), a major stabiliser of the knee, restrains the posterior translation of tibia over femur. Injury to the two bundles of this ligament is usually seen in a motor vehicle accident, followed by dashboard injury. Methods - Non-operative management post posterior cruciate ligament tears includes non-steroidal anti-inflammatory drugs and rehabilitation. Common surgical procedures include trans-tibial tunnel or tibial inlay technique of graft reconstruction, single bundle or double bundle reconstruction. Literature on outcomes of posterior cruciate ligament injuries managed with either of the methods is sparse; we therefore aim to conduct an interventional study to analyse the patients’ functional status and satisfaction post treatment. Conclusions - Lysholm knee scoring scale and IKDC knee scoring system will be used as outcome measures. The follow up scores are taken 6, 12, 15 and 24 months after the treatment. CTRI registration: REF/2023/06/068422", "keywords": [ "Posterior Cruciate Ligament", "Autologous Tendon Graft", "Posterior Drawer Test", "Outcome Analysis" ], "content": "Introduction\n\nIn the knee joint complex, cruciate ligaments are of great importance as they provide maximal restrain to the translation of tibia over the femur.1 The posterior cruciate ligament with its attachment at the antero-lateral aspect of medial condyle of femur proximally and distally at the tibial plateau, gives primary restrain to posterior translation of tibia over femur.2 It, to some extent, also works to resist the valgus and varus forces.3 Injury to this ligament occurs less often than to the other cruciate ligament of the knee complex. It has a cross sectional area of 11-13 mm2, making it twice as thick as the anterior cruciate ligament and a tensile strength of 739 to 1627 Newton.4\n\nA posteriorly directed strong force is required to damage both the postero-medial and antero-lateral bundles of the posterior cruciate ligament (PCL) and this usually occurs with knee in flexion.5 Dashboard injuries following motor vehicle accidents are the most common causative factors.6 Additionally, falling forward onto a flexed knee might result in PCL damage. In baseball, football, skiing and rugby, PCL injuries are the most frequent sports-related injuries. Less frequently, harm to the knee joint might result from a rotational hyperextension injury.7,8\n\nInjury to this ligament accounts for only 20% of the ligament injuries of the knee. PCL sprains or tears usually occur with the involvement of other ligaments, making isolated PCL injuries a rare occurrence.9 A study conducted in 2003 stated that motor vehicle accidents and sport injuries account for 45% and 40% of PCL injuries respectively, with the average age of receiving these injuries being 27 years old. Falls on a flexed knee with foot plantar flexed accounted for 24%.10,11\n\nThe ligament is further divided into two parts: the antero-lateral bundle, making up 65% of the ligament, and the postero-medial bundle, making up 35%.12 The postero-medial bundle is taut with knee in extension and the anterolateral bundle is taut in knee flexion.13 It provides greatest restrain between 30-90 degrees of knee flexion.14 Since injuries to the flexion are more common, the anterolateral bundle is more susceptible to sprains and tears,15 although literature on pure isolated injuries of the two bundles is scarce.16 The middle geniculate artery supplies blood to the PCL, which also is innervated by the tibial nerve.17 At 90 degrees, 95% of the posterior translational forces are absorbed by the PCL.18 The postero-lateral joint capsule, popliteus, medial collateral ligament, and posterior oblique ligament also helps to prevent posterior translation of tibia over femur.19\n\nManagement for grade I and II sprains where only a proportion of fibres are involved includes rehabilitation and non-steroidal anti-inflammatory drugs. Surgical treatment includes ligament reconstruction using either hamstring, peroneus or bone patellar tendon bone graft.20–22\n\nThe primary objective of the study is to assess the functional, clinical and radiological outcome of posterior cruciate ligament injuries managed surgically. The secondary objectives of the study are to study the aetiology of posterior cruciate ligament injuries, and to assess any complications associated with management modalities.\n\n\nProtocol\n\nThis trial has been registered with CTRI (REF/2023/06/068422).\n\nThis is a single group type of trial with participants being surgically managed for PCL injuries. The framework of the trial is superiority and exploratory. This is a hospital-based experimental study.\n\nThe study will be conducted in Department of Orthopaedics, Jawaharlal Nehru Medical College (JNMC) and Acharya Vinoba Bhave Rural Hospital (AVBRH), Wardha, Maharashtra, India. Included in the study will be all skeletally matured patients of age 25 years and above, both male and female, with symptoms and traumatic PCL injuries planned for surgical management. Exclusion criteria will be patients with injuries to the PCL who will be managed conservatively, injuries to the PCL that have infectious foci, tumour conditions, osteoarthritic changes, and congenital and metabolic disorders.\n\nA pre-intervention assessment will be done, taking detailed clinical history with assessment pro-forma, clinical examination, and radiological tests such as X-ray and magnetic resonance imaging, as well as all routine examination like complete blood count, liver function tests, kidney function test, random blood sugar, chest X-ray, electrocardiogram and with functional parameters. Pre-anaesthetic check-up, part preparation and physician fitness will be obtained for each patient. Arthroscopic PCL reconstruction with double-bundle graft23 surgery will be performed, and the expected duration of the surgery will be two to three hours. Patients will be arranged supine on the operating table. Under all aseptic precautions and antibiotic prophylaxis, the site to be operated on will be prepared thoroughly keeping the knee joint in flexion. A tourniquet applied around the proximal thigh will be inflated. Arthroscopic portals will be placed and a scope inserted to visualise the PCL tear. Regarding the type of graft used (auto-graft), if the patient has a PCL avulsion fracture then interference cc screw will be used; if they have a single PCL injury then a hamstring graft, i.e. semitendinosus and semimembranosus graft will be used, and if they have a multi ligament injury then a peroneus tertius graft will be used. Similar considerations will be given to the anaesthesia used: if the participant has an avulsion and single ligament injury then spinal anaesthesia will be given, and if they have a multi ligament injury then spinal and epidural anaesthesia will be given. Arthroscopic tunnels will be positioned with graft in place using endobutton loop and fixed with interference screw or suture disc. A thorough wash will be given, closure to be done in layers with sterile dressing in situ and long knee brace21 will be applied before moving the patient to the recovery ward for observation. Pre and intra-operative discontinuation or modifications will be considered as per the participant’s request and possible improvement or worsening of their condition. Post-intervention, all assessments will be repeated using clinical examination, pro-forma, radiological findings and with functional parameters. Post-operatively Mass General Brigham rehabilitation protocol for PCL reconstruction will be followed. Clinical, radiological and functional results of PCL injuries will help to investigate the causes and to evaluate any problems related to treatment options and any complications associated with it. The participants enrolled in the study will be followed up for post-operative assessment at intervals of 1 month, 3 months, 6 months and then 2 years.\n\nPrimary outcome measures\n\n1. Lysholm knee scoring scale24 (Figure 1)\n\nThis will be administrated to evaluate functional status, specifically instability post knee ligament surgeries. It consists of eight items: limp, support, locking, pain, and swelling, instability, climbing stairs and squatting. An arbitrary score with a decreasing value for each item is given. The sum of each score for the 8 items is recorded. A maximum possible score of 100 indicates no symptom and disability and a score of less than 64 indicates poor status.\n\n2. IKDC knee scoring system25 (Figure 2)\n\nThis is a knee specific, patient reported outcome measure that assesses an individual’s knee related symptoms (7 items), functions (2 items) and sports activities (2 items). Scores range from 0 points (lowest level of function or highest level of symptoms) to 100 points (highest level of function and lowest level of symptoms).\n\nSecondary outcome measures\n\n1. Visual examination\n\nThis includes gait examination, instability and any abnormal swelling. Additionally, the Sag test will be conducted to compare the affected and non-affected side.\n\n2. Muscular strength and range of motion\n\nMuscle strength and range of motion assessment will be done using a muscle strength grading system, and range of motion assessment will be done using a goniometer assessment.\n\n3. Additional tests\n\nThese include scoring and measurements from the posterior drawer test, varus and valgus tests, and dial test.\n\n4. Radiological findings\n\nThese include X-ray and MRI of the knee joint.\n\nThe sample size formula (Daniel, 1999) is used,26 which is\n\nIf the population is more than 10,000 where,\n\nZ = statistic for a level of confidence. (For the level of confidence of 95%, which is conventional, Z value is 1.96).\n\nP = expected prevalence or proportion i.e. prevalence of PCL injuries in India = 2.76% = 0.0276.27\n\nd = precision or desired error of margin = 7% = 0.07\n\nStatistical methods: Student’s t-test, one way ANOVA and Pearson’s correlation coefficient.\n\nA total of 25 participants will be enrolled in the study who meet the inclusion criteria. All the participants will be educated about the purpose of the research, will then undergo the pre-study assessment and will complete clinical and radiological tests as described above. They will also undergo the Lysholm knee scoring scale and the IKDC knee scoring system, and the baseline data will be noted for each participant. The participants will be followed up for a minimum of 6 months and a maximum of 2 years from the treatment, as is suitable for the patient and the researcher. On every follow up, complications, if any, will be noted and managed appropriately. All the relevant statistical data will be collected pre, intra, and post-operatively along with follow up data which will be recorded for each of the outcome measures (Figure 3). The obtained data will then be tabulated in an Excel sheet and a master chart will be created, and later be used for statistical analysis. To carry out the statistical analysis, SPSS version 27 software will be used. The analysis will be done considering the desired error of margin and confidence interval of 95%.\n\nThis protocol is addressed in accordance with SPIRIT reporting guidelines.28\n\nThis study will be published in indexed journal.\n\nData collection has not yet started.\n\n\nDiscussion\n\nThe main aim of this study is to produce an outcome analysis of the participants’ PCL injuries. This is a clinical trial protocol carried out in the Department of Orthopaedics in Jawaharlal Nehru Medical College, Wardha, Maharashtra, India. As the prevalence and occurrence of PCL injuries are now increasing, and there are various treatment options available, it is necessary to investigate the outcome analysis of PCL injuries.23,29,30\n\nThe Lysholm knee scoring scale and the IKDC knee scoring system have different domains for the assessment of quality and function of the knee joint. The scales include items on the patient’s satisfaction and expectation with functional parameters related to the knee joint health. Assessment using these scales will tell us about success of the performed PCL surgeries.31,32\n\nUsing the data obtained from the measurement of pre and post-study scoring scales, we will perform statistical analysis and compare the analyses for different PCL outcomes.33,34\n\nLimitations of this study include small sample size, single centre study, and short duration of study.\n\nThis research protocol received approval from the institutional ethical committee of the Datta Meghe Institute of Higher Education and Research (approval number ECR/440/Inst/MH/2013/RR-2019) on 18/07/2022.\n\nAll participants will be educated about the purpose of the research. Written and verbal informed consent will be obtained from all the participants by the principal investigator prior to the intervention. Procedures in this study will be conducted in accordance with the Helsinki Declaration of 1975, as referenced in 2008.\n\nThe study material will be considered to be confidential documents and will be safely stored with access only to the principal investigator.", "appendix": "Data availability\n\nNo underlying data are associated with this protocol.\n\nZenodo: Outcome analysis of Posterior Cruciate Ligament injuries. https://doi.org/10.5281/zenodo.8050632\n\nThis project contains the following extended data:\n\n- Study flow design.docx\n\n- Informed consent (English and Marathi).docx\n\n- IKDC knee scoring system.docx\n\n- Lysholm Knee scoring scale.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo: SPIRIT checklist for ‘Outcome analysis of posterior cruciate ligament injuries’, https://doi.org/10.5281/zenodo.8050632.\n\n\nAcknowledgements\n\nI express my gratitude to Dr. Swapnil Date for his indespensible role in my better understanding of the subject. His knowledge, expertise and constant moral support throughout helped me tremendously. I am grateful for his help in the final corrections and editing of my protocol.\n\nThe author also expresses gratitude to all personnel at the department of orthopaedics in JNMC, AVBRH, Sawangi, Wardha, Maharashtra, India for their assistance.\n\n\nReferences\n\nFreychet B, Desai VS, Sanders TL, et al.: All-inside posterior cruciate ligament reconstruction: surgical technique and outcome. Clin. Sports Med. 2019 Apr 1; 38(2): 285–295. Publisher Full Text\n\nHopper GP, Heusdens CH, Dossche L, et al.: Posterior cruciate ligament repair with suture tape augmentation. Arthrosc. Tech. 2019 Jan 1; 8(1): e7–e10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStrauss MJ, Varatojo R, Boutefnouchet T, et al.: The use of allograft tissue in posterior cruciate, collateral and multi-ligament knee reconstruction. Knee Surg. Sports Traumatol. Arthrosc. 2019 Jun 1; 27: 1791–1809. Publisher Full Text\n\nRaj MA, Mabrouk A, Varacallo M: Posterior Cruciate Ligament Knee Injuries. StatPearls. StatPearls Publishing; 2021 Aug 14.\n\nVincent HK, Bruner M, Obermayer C, et al.: Musculoskeletal pain in lacrosse officials impacts function on the field. Res. Sports Med. 2021 Sep 3; 29(5): 486–497. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPache S, Aman ZS, Kennedy M, et al.: Posterior cruciate ligament: current concepts review. Arch. Bone Jt. Surg. 2018 Jan; 6(1): 8.\n\nFanelli GC: Knee dislocation and multiple ligament injuries of the knee. Sports Med. Arthrosc. Rev. 2018 Dec 1; 26(4): 150–152. PubMed Abstract \| Publisher Full Text\n\nLogterman SL, Wydra FB, Frank RM: Posterior cruciate ligament: anatomy and biomechanics. Curr. Rev. Musculoskelet. Med. 2018 Sep; 11: 510–514. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLee BK, Nam SW: Rupture of posterior cruciate ligament: diagnosis and treatment principles. Knee Surg. Relat. 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Arthroscopy. 2005 Nov 1; 21(11): 1354–1361. PubMed Abstract \| Publisher Full Text\n\nWang D, Graziano J, Williams RJ, et al.: Nonoperative treatment of PCL injuries: goals of rehabilitation and the natural history of conservative care. Curr. Rev. Musculoskelet. Med. 2018 Jun; 11: 290–297. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBedi A, Musahl V, Cowan JB: Management of posterior cruciate ligament injuries: an evidence-based review. J. Am. Acad. Orthop. Surg. 2016 May 1; 24(5): 277–289. Publisher Full Text\n\nJacobi M, Reischl N, Wahl P, et al.: Acute isolated injury of the posterior cruciate ligament treated by a dynamic anterior drawer brace: a preliminary report. The Journal of Bone and Joint Surgery. British Volume. 2010 Oct; 92-B(10): 1381–1384. Publisher Full Text\n\nChandrasekaran S, Ma D, Scarvell JM, et al.: A review of the anatomical, biomechanical and kinematic findings of posterior cruciate ligament injury with respect to non-operative management. Knee. 2012 Dec 1; 19(6): 738–745. PubMed Abstract \| Publisher Full Text\n\nShelbourne KD, Muthukaruppan Y: Subjective results of nonoperatively treated, acute, isolated posterior cruciate ligament injuries. Arthroscopy. 2005 Apr 1; 21(4): 457–461. PubMed Abstract \| Publisher Full Text\n\nShelbourne KD, Clark M, Gray T: Minimum 10-year follow-up of patients after an acute, isolated posterior cruciate ligament injury treated nonoperatively. Am. J. Sports Med. 2013 Jul; 41(7): 1526–1533. PubMed Abstract \| Publisher Full Text\n\nMontgomery SR, Johnson JS, McAllister DR, et al.: Surgical management of PCL injuries: indications, techniques, and outcomes. Curr. Rev. Musculoskelet. Med. 2013 Jun; 6: 115–123. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJansson KS, Costello KE, O’Brien L, et al.: A historical perspective of PCL bracing. Knee Surg. Sports Traumatol. Arthrosc. 2013 May; 21: 1064–1070. PubMed Abstract \| Publisher Full Text\n\nMeleiro SA, Mendes VT, Kaleka CC, et al.: Treatment of isolated lesions of the posterior cruciate ligament. Rev. Assoc. Med. Bras. 2015 Mar; 61: 102–107. Publisher Full Text\n\nRace A, Amis AA: PCL reconstruction: in vitro biomechanical comparison of ‘isometric’versus single and double-bundled ‘anatomic’grafts. The Journal of Bone and Joint Surgery. British Volume. 1998 Jan; 80(1): 173–179.\n\nLysholm J, Tegner Y: Knee injury rating scales. Acta Orthop. 2007 Jan 1; 78(4): 445–453. Publisher Full Text\n\nCollins NJ, Misra D, Felson DT, et al.: Measures of knee function: international knee documentation committee (IKDC) subjective knee evaluation form, knee injury and osteoarthritis outcome score (KOOS), knee injury and osteoarthritis outcome score physical function short form (KOOS-PS), knee outcome survey activities of daily living scale (KOS-ADL), Lysholm Knee Scoring Scale, Oxford Knee Score (OKS), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), Activity Rating Scale (ARS), and Tegner Activity Score (TAS). Arthritis Care Res. 2011 Nov; 63(S11): S208–S228. Publisher Full Text\n\nDaniel WW: The Fisher exact test. Daniel WW. Biostatistics: a foundation for analysis in the health sciences. 7th ed.New York: John Wiley and Sons; 1999; pp. 606–611.\n\nJohn R, Dhillon MS, Syam K, et al.: Epidemiological profile of sports-related knee injuries in northern India: an observational study at a tertiary care centre. J. Clin. Orthop. Trauma. 2016 Jul 1; 7(3): 207–211. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChan AW, Tetzlaff JM, Gøtzsche PC, et al.: SPIRIT 2013 explanation and elaboration: guidance for protocols of clinical trials. BMJ. 2013 Jan 9; 346: 346. Publisher Full Text\n\nPierce CM, O’Brien L, Griffin LW, et al.: Posterior cruciate ligament tears: functional and postoperative rehabilitation. Knee Surg. Sports Traumatol. Arthrosc. 2013 May; 21: 1071–1084. PubMed Abstract \| Publisher Full Text\n\nWijdicks CA, Kennedy NI, Goldsmith MT, et al.: Kinematic analysis of the posterior cruciate ligament, part 2: a comparison of anatomic single-versus double-bundle reconstruction. Am. J. Sports Med. 2013 Dec; 41(12): 2839–2848. PubMed Abstract \| Publisher Full Text\n\nKennedy NI, Wijdicks CA, Goldsmith MT, et al.: Kinematic analysis of the posterior cruciate ligament, part 1: the individual and collective function of the anterolateral and posteromedial bundles. Am. J. Sports Med. 2013 Dec; 41(12): 2828–2838. PubMed Abstract \| Publisher Full Text\n\nSpiridonov SI, Slinkard NJ, LaPrade RF: Isolated and combined grade-III posterior cruciate ligament tears treated with double-bundle reconstruction with use of endoscopically placed femoral tunnels and grafts: operative technique and clinical outcomes. JBJS. 2011 Oct 5; 93(19): 1773–1780. PubMed Abstract \| Publisher Full Text\n\nPanchal HB, Sekiya JK: Open tibial inlay versus arthroscopic transtibial posterior cruciate ligament reconstructions. Arthroscopy. 2011 Sep 1; 27(9): 1289–1295. Publisher Full Text\n\nMarkolf KL, Zemanovic JR, McAllister DR: Cyclic loading of posterior cruciate ligament replacements fixed with tibial tunnel and tibial inlay methods. JBJS. 2002 Apr 1; 84(4): 518–524. PubMed Abstract \| Publisher Full Text" }	[ { "id": "210698", "date": "10 Nov 2023", "name": "Si Heng Sharon Tan", "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 a well-written protocol for the analysis of outcomes following surgical management for posterior cruciate ligament injuries. It is a protocol for a single-arm study, and the sample size calculated is also for a single-arm study, therefore while it is sufficient for a case series, it would not be sufficient for a comparative study. Specific to the sample size calculation, may I ask why a 0.07 error of margin was chosen?\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": "10974", "date": "22 Mar 2024", "name": "Anmol Suneja", "role": "Author Response", "response": "This is a single arm study to find the difference in outcomes for pre & post evaluation after operative procedure. The cases that we are taking are having lesser prevalance, so this study can be done in case series format also. We are taking estimation error at 7% for lesser prevalence of study cases." } ] } ]	1	https://f1000research.com/articles/12-842
https://f1000research.com/articles/12-837/v1	17 Jul 23	{ "type": "Opinion Article", "title": "The metaverse and Islamic financial contracts: The case of Ijarah", "authors": [ "Auwal Adam Saad", "Raja Rehan", "Abubakar Abukakar Usman", "Adnan Opeyemi Salaudeen", "Raja Rehan", "Abubakar Abukakar Usman", "Adnan Opeyemi Salaudeen" ], "abstract": "The metaverse is a virtual world that exists alongside the actual world. While the actual world refers to the real, physical world, the metaverse is a digital world that is accessed through technology. Evidently, several international brands have integrated their businesses with the virtual metaverse providing business opportunities. However, there are currently several gaps in the sector of Shariah finance that need to be addressed in order to take full advantage of the potential of the metaverse. For instance, rare studies enlighten the concept of Ijarah, a substitute for conventional leasing in the metaverse virtual world. Undoubtedly, the metaverse has the potential to revolutionize the Shariah finance industry by providing new opportunities for financial inclusion and innovation. Therefore, for the readiness of Islamic finance institutions, this study is an attempt to explore the possibility of executing Shariah principles that could be utilized in the metaverse. More specifically, this study is an endeavor to explore and discuss how Shariah-based leasing i.e., Ijarah integrates with the recent metaverse technologies. Additionally, this study also discusses the metaverse evolution and its integration into international business brands, the metaverse virtual assets ownership, the metaverse virtual leasing, non-fungible tokens (NFTs), and virtual real estate in the metaverse. Indeed, this study is a novel addition to the Shariah finance literature, which helps policymakers to generate new strategies that guide the execution of Ijarah contracts in the virtual universe of the metaverse.", "keywords": [ "Metaverse", "Islamic Finance", "Shariah Contracts", "Ijarah", "Virtual Real Estate", "NFTs" ], "content": "Introduction\n\nThe “metaverse” is a blend of two dissimilar words that are “meta”, which means beyond, and the “universe”. Hence, the metaverse has been identified as a post-reality universe that merges physical reality with a virtual digital world (Mystakidis, 2022). Interestingly, this incredible technology, the metaverse, which is also termed as the next internet advancement, is the blend of diverse technologies that allows multisensory interactions with virtual environments, people and digital objects such as virtual and augmented reality (Njoku et al., 2022). Technically, the metaverse is an inter-connected web of social network environments that enables seamless embodied user communication in real-time and dynamic interactions with digital artifacts (Wiles, 2022). Hence, in the metaverse, everything could potentially be under one roof, as users would have access to a wide range of virtual environments, experiences, and services. This could include virtual storefronts for shopping, virtual classrooms for education, virtual offices for work, virtual social spaces for entertainment, and much more (Cruz et al., 2023). Typically, the metaverse is a fully virtual interactive space, where users can generate their own avatars and interact with other users, contributing to numerous virtual activities, such as real estate, gaming, shopping, and attending academic events, as well as professional meetings.\n\nThe metaverse is generating several business opportunities for industries. Evidently, by using metaverse advancements, companies are altering their ways of functioning and able to offer their services and products, organize their day-to-day operations and increase collaboration with customers, etc. (Sundaram, Sachdev and Pokhriyal, 2023). Also, in 2021, one of the social media giants, Facebook owner Mark Zuckerberg, announced the rebranding of Facebook to “Meta” (Huynh-The et al., 2023). Considering these advancements, it is predicted that by 2026 almost 25% of the world’s population will start spending at least one hour a day in a metaverse-generated virtual world for their meetings, education, business contracts, shopping, and entertainment (Julian, Chung and Wang, 2023). The metaverse has the potential to create a new digital economy with a wide range of business opportunities for businesses of all sizes and industries (Yemenici, 2022). Therefore, many tech businesses and financial institutions are currently capitalizing on the growth of the metaverse, thus, it is anticipated to become a substantial part of our virtual and digital lives in forthcoming years. Remarkably, one of the most noticeable uses of metaverse technology is virtual branches of banks (Zainurin et al., 2023).\n\nFundamentally, banks play a key role in the financial industry. They act as intermediaries among borrowers and savers, offering financial products to individuals and businesses. Thus, the use of the metaverse in the banking sector is one of the most tremendous growths in the banking industry (Sarkar, 2023). Technically, a virtual bank in the metaverse is a digital financial institution that functions within a simulated world or virtual atmosphere. These banks provide services and products which are similar to those of conventional banks, counting deposits, long and short-term loans, and various types of investment opportunities, but wholly in a digital format. Remarkably, in most Muslim nations, there are typically two types of banking systems in operation: the conventional banking system and the Islamic banking system which are functioning in parallel. This is recognized as a dual banking system. Interestingly, several Islamic banks have also introduced their virtual branches, for instance, the first Islamic bank in the world is Kuwait’s Warba Bank, which first declared its entry into the metaverse’s virtual world (Tamano, 2022). Notably, virtual Islamic banking in the metaverse is aligned with Islamic banking principles and adheres to the rules and regulations which are set by multiple Shariah finance scholars and regulatory bodies (Riyadi, 2022). This development shows how technology is moving very fast to change how financial institutions interact with people, customers, and communities via the highest technological innovation.\n\nVisibly, the metaverse is still at a nascent stage, thus, the formerly available literature that explains how Shariah finance integrates with recent technologies is rare. More specifically, clear guidelines for Ijarah are not available for the metaverse technology. Technically, Ijarah is a concept in Islamic finance that refers to a type of interest-free leasing agreement in which one party, known as the lessor, agrees to lease a tangible asset or property to another party, known as the lessee, in exchange for rental payments (Zafar, 2012). Also, the lessor retains ownership of the asset while the lessee has the right to use the asset for a specified period of time. Ijarah is a popular financing tool in Islamic Finance and is often used for financing business equipment, real estate, and other assets. Islamic Finance is considered a permissible alternative to traditional interest-based loans, as it does not involve charging interest on rental payments (Ghuddah, 1998). Likewise, Ijarah in the metaverse would refer to the application of Islamic finance principles to lease contracts within a metaverse environment (Munadi, 2023). In view of the above discussion, this research endeavored to explore and look at the possibilities of taking advantage of economic opportunities to apply Shariah leasing principles i.e., Ijarah in transactions in the metaverse.\n\nFigure 1 above explains key metaverse technologies. Visibly, the virtual technologies that permit this vision of the metaverse are still growing, however, seven central technologies that are expected to be important include; virtual reality, augmented reality, blockchain, artificial intelligence, 3D modeling and animation, cloud computing and edge computing.\n\nAs per the authors’ knowledge, there are currently no established standards or guidelines for applying Shariah leasing principles to metaverse transactions, as the metaverse is a relatively new and rapidly evolving area. Further, this article presents a new addition to the Islamic finance literature which helps policymakers deliver a framework that guides the procedure to generate Ijarah-based contracts in the virtual sphere of the metaverse.\n\nAs discussed, the metaverse is generating several opportunities for businesses in the virtual world. The next section of this study highlights the evolution of metaverse technologies and their integration with the core international business brands.\n\n\nThe evolution and integration of metaverse technologies by international brands\n\nThe metaverse is rapidly gaining attention and changing how customers and businesses interact (Google Trends, 2022). However, the globally increased value of the metaverse has raised questions regarding its existence and overall scope (Barrera and Shah, 2023). Technically, the metaverse is a new enhancement of the Internet which possesses a simulated and physical world and it utilizes avatars, digital platforms, virtual reality (VR) headsets, and blockchain technologies for users to interact (Lee et al., 2021). Thus, the metaverse is a digital hyper-connected platform committed to reshaping and changing brands, industries, and customer interactions (The Verge, 2021).\n\nVisibly, the notion of the metaverse is really not a new one and it has existed since the last century. The term metaverse was first coined in 1992 by the writer Neal Stephenson in the sci-fi book named Snow Crash which discussed reality-based web technologies (Stephenson, 1992). However, the metaverse technology has swiftly risen during the recent Covid-19 pandemic. During the quarantine, internet-based social media facilitated people to get in touch with each other, however, it was really not enough. The thirst to feel everything and the need to go out to explore and see things has always been present. Precisely, that was the time when the metaverse evolution started and began to reach its height (LearnTek, 2022). According to Market Research Future (MRFR, 2022), the value of the metaverse market in 2022 was $7.91 billion. The metaverse market is anticipated to increase from USD 11.47 billion in 2023 to USD 107.79 billion by 2030, at a compound annual growth rate (CAGR) of 45.2%. Clearly, the anticipation for the significant growth of metaverse technology is due to its global recognition, adoption, and execution in businesses (Mileva, 2022).\n\nUniversally, it has been witnessed how the metaverse formed its place in the gaming industry and social media. For instance, in 2021 Facebook announced Meta as a new brand name for its application (Kraus et al., 2022). Subsequently, NIKE launched its interactive brand, NIKELAND, which was introduced on Roblox (global virtual gaming platform) and developed by using metaverse technology (Hollensen, Kotler and Opresnik, 2022). NIKELAND used the metaverse platform to offer its new athletic brand where users are allowed to enter virtually to play games. Later, NIKE also attained RTFKT studio (pronounced “Artefact”), the latest technology of the metaverse in digital fashion, blockchain verification, and increased reality to create digital objects. Likewise, RTFKT also focuses on crypto-based projects to integrate blockchain with sneakers and fashion. Furthermore, via adopting metaverse technology NIKE also presented a new platform, Web3, which is also called Swoosh to expand the visibility of its products (Longshak, 2023). to expand the visibility of its products (Longshak, 2023).\n\nIn the same vein, Hyundai, which generally targets tech-savvy inhabitants start-ups, created a partnership with Roblox to develop new products using metaverse technology. Lately, Samsung, also known as a technology giant, launched its first store to offer metaverse products. Also, Coca-Cola, originally a beverage firm, joined the metaverse race and introduced its collection of non-fungible Tokens (NTFs) with Opensea (Mileva, 2022). NFTs are blockchain-based cryptographic assets with metadata that has separate identification codes from each other (Wang, Wang and Chen, 2021). Evidently, during the Covid-19 pandemic lockdowns the tourism industry suffered vast losses but Sentosa, an island resort off Singapore’s southern coast, continued with the tourism market for the people who were stuck at home. In 2020, Sentosa launched a virtual island in its gaming product ‘Animal Crossing’. Similarly, following the footprints of other international brands Walking Dead, Louis Vuitton, Adidas and Gucci integrated their products with metaverse-based technologies.\n\nUndoubtedly, with the flourishing of NFT-based platforms, metaverse is now the most thriving virtual platform around the globe (Wang, Yu and Li, 2022). Moreover, the metaverse has presented an innovative business model for industries and financial markets (Chen, 2022). Considering the benefits attained from adopting metaverse technology, numerous international brands integrated their businesses with metaverse technologies and started functioning on several top platforms of a metaverse in order to maintain sustainable financial growth (Lee, 2021). Thus, now the actual business world is rapidly connecting with the virtual world by adopting metaverse transformation and integration, therefore, expectations from metaverse technology are hyping and rising. Remarkably, metaverse platforms are online virtual environments that permit clients to interact with other individuals in a seamless way. These simulated platforms are often constructed using virtual or augmented reality technologies and offer users the facility of creating, customizing, and experiencing digital and simulated content in a shared space in the metaverse’s virtual world.\n\nTable 1 below displays the top virtual metaverse platforms which are graded according to their monthly regular users. Also, in the Islamic finance industry, the use of the metaverse potentially opens up new opportunities. Nevertheless, it is essential to note that any use of a metaverse in Islamic finance must be in accordance with the principles of Shariah, which prohibits all those activities which are forbidden in Islam such as riba (interest) and Gharar (uncertainty). Notably, for Shariah following investors, the evolution of the metaverse represents an extensive challenge indicating the lack of Shariah financing guidelines for the rapidly evolving metaverse technologies (Ishak and Billah, 2022).\n\n\nMetaverse in banking and finance\n\nIn the banking context, the metaverse has the potential to modernize how financial services are delivered and implemented (Dubey et al., 2022). Technically, in the banking industry the metaverse is taken as a concept that refers to the use of virtual and augmented technology for the creation of a sort of digital universe in which financial services and their customers can interact in a much more engaging and immersive way (Zainurin et al., 2023). Metaverse banking is, therefore, actualized by integrating the metaverse and online banking services using various advanced technologies. Moreover, metaverse banking and financing also provides customers with synchronous banking and financing services through integration of metaverse and online banking services, facilitated by a combination of numerous advanced technologies, that provides customers with synchronous banking services accompanied by 3D virtual world experiences. (Koohang et al., 2023).\n\nNotably, there are many aspects in metaverse banking which include virtual financial advisors, virtual branches, virtual product demonstrations, and so on. Thus, the essence of using the metaverse in banking is that it is a potential way of improving customer engagement, satisfaction, and more importantly accessibility to financial services for customers, particularly those in remote or underserved areas (Sarkar, 2023). Besides, by adopting virtual banking, several banks create virtual branches that are available 24/7, offering clients the accessibility to interact with their accounts and make transactions from anywhere in the globe. Likewise, another use of the metaverse in the banking and finance industry is the construction of virtual economies. Banks maintain simulated currencies such as crypto that are traded within the metaverse virtual world, permitting customers to earn rewards for completing tasks or attaining goals. In addition to banking, the metaverse has also been introduced to finance as virtual reality and other digital technologies are employed to create a shared, immersive digital space that can serve as a platform for people to interact, transact, and engage in other forms of financial services (Gadekallu et al., 2022).\n\nVisibly, the metaverse offers several virtual products to the financial industry such as virtual banks, virtual stock exchanges, virtual insurance companies, virtual trading floors, virtual financial education centers, as well as virtual financial planning tools (Morgan, 2022). Hence, it is anticipated that introducing more advancements of the metaverse to the finance industry will help in granting the clients more access to important financial services and offer new opportunities for more cutting-edge innovations in the financial industry (Cho, Dieck and Jung, 2022). Thus, the metaverse is altering the banking and financial industry in a positive and effective manner by augmenting performance and offering innovative experiences to customers (Ding, Kou and Wu, 2023; Seth, Gupta and Singh, 2022). Evidently, various banking and financial institutions have already adopted opportunities afforded by the use of similar metaverse technologies in banking and finance. For instance, Mastercard made a partnership agreement with a virtual reality company to create a metaverse for the company’s financial and banking services. Likewise, BBVA also launched a virtual branch in the metaverse of the video game known as Entropia Universe (Turi, 2023). Similarly, the Singapore Exchange (SGX) announced that it agreed to work with a virtual reality company (Singapore Exchange, 2021). The reason giant banking and financial institutions are becoming increasingly interested in metaverse banking and financing is because of the new avenues of opportunities it opens for businesses and better and more effective customer service. It is, therefore, not only a more modern way of banking and financing but also more sustainable than the existing alternatives (Lee, 2021).\n\nThe metaverse provides a platform for reaching a bigger audience and presents the opportunity to develop novel strategies for delivering virtual financial services that adhere to Shariah principles while avoiding speculation. In other words, the metaverse enables the development of new and more accessible ways of offering Islamic financial and banking services in a virtual environment that adheres to Shariah principles (Katterbauer, Hassan and Cleenewerck, 2022). Thus, the metaverse presents opportunities and challenges in equal measure for the application of Islamic banking principles. As the metaverse continues to evolve, it is likely that Islamic financial institutions will need to adapt and develop innovative solutions to meet the needs of this emerging virtual economy.\n\n\nVirtual ownership in the metaverse\n\nAfter the recent evolution of metaverse technologies, it seems that our indulgence in the economy, money, assets and possessions, businesses, and their ownerships have dramatically converted into the virtual and digital world (Kim, 2021). Ownership of virtual assets such as homes, books, farms, furniture, and vehicles is established in the metaverse economy by the proof of their digital presence. Possession of these assets is essentially determined by the confirmation of their virtual presence in the metaverse, rather than physical possession in the real world. Individuals and businesses can now own and trade virtual assets that exist entirely in the metaverse economy, opening up new avenues for virtual commerce and asset ownership. The key component which is required for the validation of virtual assets and possessions in the metaverse economy is NFTs which are underpinned by the technology of blockchain. Technically, the blockchain serves as a form of publicly opened transparent owner registration where every virtual asset transfer can be tracked. Whereas NFT is a unique type of cryptographic token that is used to confirm the ownership of certain virtual assets (Far et al., 2022). Typically, every NFT is protected by a cryptographic identification key that is not erasable, copied, or damaged and provides decentralized and robust verification. This verification process is essential for each digital and virtual identity in the metaverse economic society. Also, this cryptographic-based identification procedure is helpful for the differentiation and interaction of one metaverse-based society with another (Xu et al., 2022). Thus, unique digital assets recognized as metaverse NFTs such as simulated homes, businesses, video game possessions and virtual banks are present inside the metaverse’s offered virtual world.\n\nFundamentally, the asset possession in the metaverse digital world is not dissimilar from the prevailing virtual zones of different gaming platforms such as Roblox, Second Life, etc. The virtual and digital assets in these metaverses are NFT, meaning they are unique and not interchangeable. Also, these virtual assets are available on the blockchain and their verification can easily be done outside the meta premises (Nakavachara and Saengchote, 2022). In view of these aspects, numerous brands such as Samsung and Mcdonald’s have acquired their possessions in the metaverse virtual world. Remarkably, Samsung is operating its own metaverse display centers. In the same way, Mcdonald’s is running its virtual restaurant which is delivering food to the physical world. Likewise, virtual land possession is another important aspect of the metaverse world (Sant, 2022).\n\nMetaverse real estate prices are rapidly increasing. In several cases, the metaverse land prices deliver 100% profit to its proprietors. Typically, the metaverse has divided its available space into several areas and then distributes and allocates those areas into several virtual plots. The users can simply purchase and sell these parcels of land using cryptocurrency and exchange it as NFTs. Interestingly, the cost of metaverse property increased by 700% in 2021, bringing the market to almost $500 million. The market is expected to double to around $1 billion by 2022 (Sensorium, 2022). The user can purchase available space on the metaverse, or they can adopt a secondary market to acquire land that is a NFT based platform such as OpenSea or Binance NFT. As virtual metaverse land is purchased and sold as NFT, in order to secure the transaction, the ownership deed is always etched and available on the blockchain (Kiong, 2022). Thus, the key important aspect of the metaverse land parcel is that it is an NFT-based transaction, thus, the purchase, sale, and possession of land are considered secure. Interestingly, the Shariah-based principles do not clearly explain the notion of virtual ownership. Nevertheless, several scholars indicate that the ownership principles of Shariah finance can also be applicable to virtual assets such as NFTs and real estate (Chong, 2021).\n\n\nVirtual leasing in the metaverse\n\nVirtual leasing in the metaverse mentions the rent of simulated properties such as land, buildings, vehicles, and other objects in a simulated world. The Covid lockdowns increased awareness among people to have their own simulated spaces. Thus, as recovery starts following the pandemic shock, the latest variety of real estate leasing, i.e., metaverse virtual land leasing, has rapidly gripped the real estate market and is rated as one of the top virtual investment venues in 2021 (Mulia, 2022). This trend continued into 2022, and sales of metaverse virtual land surpassed USD 500 million and is also anticipated to have doubled by the end of 2022 (Frank, 2022). Importantly, it is also projected that between 2021 and 2026, investments in the metaverse real estate market will rise by USD 5.37 billion with an annual compound growth rate (CAGR) of 61.74% (Garcha et al., 2022).\n\nTypically, the metaverse assigns its free space into several areas available for purchasing, and owners are allowed to offer it for leasing. The virtual land leasing procedure in the metaverse is simpler and cheaper than its counterpart, real-world land leasing. The virtual land price started rising after the funds were launched by Everyrealm (formerly Republic Realm), a company that specializes in investing in and managing virtual real estate in the metaverse. Everyrealm is considered a leader in metaverse real estate in acquiring a virtual parcel of land in the metaverse. These allocated funds are used to acquire metaverse land and convert it into online stores, buildings, hotels, etc. (Narin, 2021). Recently, Sandbox, Somnium, Decentraland, and Cryptovoxels (Voxels) are the four big platforms that are dealing in sales of metaverse virtual land (Coelho, 2022). Technically, each platform has a limited number of virtual plots, for instance, Sandbox acquired 166,654 virtual plots of land parcels (Ibrahim, 2022). Notably, firms that are dealing in sales of metaverse virtual land also offer NFT-based proof of ownership to landowners (Saengchote, 2022). Thus, NFT-based ownership not only secures ownership but also provides a way to earn revenue without selling possessed virtual land. This leads to an upsurge in the value of these virtual land properties among its clients (Narin, 2021).\n\nFrom an Islamic finance perspective, metaverse simulated leasing should be organized to comply with Islamic principles. Also, the conditions of the lease contract must be clear and unmistakable, with no room for ambiguity or uncertainty (Morshed, 2022).\n\n\nVirtual ownership of NFTs, real estate and vehicles in Islam\n\nIn the metaverse all users are allowed to conduct free transactions for buying and selling (Ishak and Billah, 2022). Fundamentally, this is because of NFTs and blockchain (Guidi and Michienzi, 2022). In the virtual world of the metaverse, NFTs provide the ownership facilities of land, merchandise, avatars, etc. (Raman and Raj, 2021). Thus, the use of NFTs in the metaverse is to support secure asset exchange, transaction, and trailing that removes security-related issues for consumers (Zainab et al., 2022). Virtual ownership is a relatively new concept, thus, there is not a clear consensus among Islamic scholars on its permissibility (Schuijers, 2023; Wang et al., 2022). The concept of virtual ownership in the context of Islamic finance could be referred to as intangible asset ownership in Islamic law. In Islam, the notion of ownership is founded on the principle that every person has a right to own, control, and use the property as long as it is attained through lawful means (Daneshfar et al., 2023). This includes the concept of virtual ownership, which refers to the ownership of virtual assets such as NFTs. Thus, non-fungibles that are created to improve people’s lives are authorized in Islam (Adam, 2021).\n\nIslamic scholars generally recognize the ownership of intangible assets, such as intellectual property, and this can be extended to virtual real estate and other virtual assets that have real-world economic activity and utility (Alhabshi et al., 2018; Bouheraoua et al., 2015). For instance, real estate in a virtual world that is used for legitimate purposes such as gaming or social interaction may be recognized as a form of ownership. In addition, the concept of virtual ownership of real estate in Islam is subject to the same rules and principles that govern traditional ownership. This includes requiring real estate property to be acquired through lawful means and not through fraud, theft, or other illegal activities (Fauzi et al., 2021; Faishal and Eng, 2008).\n\nIn the context of the metaverse real estate, Ijarah can be applied to simulated properties and assets. In the metaverse, a virtual property developer could own a virtual building or land and lease it to users through an Ijarah contract (Wang, 2022). The users could pay rent for the use of the virtual property, while the developer retains ownership of the asset. However, Ijarah contracts for real estate in the metaverse would have to comply with Islamic principles, such as ensuring that the rent charged is fair and not exploitative and that the asset being leased out is not used for any unethical or prohibited purposes (Maksalmina, 2022). Noticeably, virtual ownership of NFTs, real estate, and other assets must also be used for the greater good and not solely for personal gain. Thus, several scholars (see for example, Wang, Wang and Chen, 2021; Laldin and Djafri, 2019) argue that the ownership of NFTs and virtual real estate assets can be permissible in Islamic finance as long as the underlying assets are halal and the transactions are done without riba i.e., interest (Qamar, Anwar and Afzal, 2023).\n\nVisibly, in the next few years, the metaverse will unquestionably mark the major tipping point in the history of the vehicle industry. Notably, the first retail car sale in the metaverse is to be carried out by Germain Toyota (Guerra, 2022). Like other virtual assets, the notion of virtual possession of vehicles in a metaverse presents new challenges and queries from an Islamic viewpoint. This would mean that the ownership of these virtual vehicles would be subjected to the same rules and restrictions as other virtual assets, including the prohibition of interest (riba) and the requirement for assets to be permissible (halal in accordance with Shariah law), and has a valuable usufruct for Ijarah purposes. Remarkably, implementing these Islamic finance principles in the context of virtual assets is still a topic of debate among Islamic scholars (see Samad and Hasan, 2022; Kamdzhalov, 2020). Hence, Islamic finance’s principles of ownership and possession can be applied to virtual assets such as NFTs, real estate, and vehicles. Additionally, lack of physicality, high volatility, lack of stability and tangibility, limited Shariah rulings and studies are some challenges that hinder virtual ownership in Islam (Adam, 2022).\n\n\nIjarah of virtual properties in Islam\n\nIn the context of virtual properties, Ijarah is used to structure transactions involving the ownership and use of virtual assets without charging interest (Toraman, 2022). In this case, the owner of the virtual property, the lessor, would lease the property to another party, the lessee, for a specified period, and in return, the lessee would pay the lessor a rental fee (Usmani, 2001). Typically, Ijarah can be applied to virtual properties such as land, real estate, virtual reality platforms, and other virtual assets (Rabbani et al., 2020). Thus, Ijarah as a concept is permissible in Islamic finance for virtual properties as long as it adheres to the principles of fairness and justice. Principally, the concept of fairness and justice explains that the lessee should not be charged more than the fair value of the property, and both parties should agree upon the lease period, thus, the same would be applicable on virtual properties (Daly and Frikha, 2016). Importantly, the lessee should not be able to make any changes to the virtual property that would harm the lessor’s interests (Alam, Gupta, and Zameni, 2019).\n\nTypically, the Ijarah notion for virtual properties can be a valuable tool for Islamic finance as it offers a way to structure transactions involving virtual assets in a way that is compliant with Islamic principles. Besides, it can also provide an alternative to traditional forms of financing, such as interest-based loans, which are not permissible in Islamic finance (Katterbauer et al., 2022). However, it is essential to note that there have not been issued any specific guidelines or rulings so far on the Ijarah of virtual properties within Islamic law. It would ultimately depend on the details and circumstances of the virtual property (Maksalmina, 2022). Therefore, for Islamic scholars it is warranted to clear the rules for the usage of Ijarah contracts in recent metaverse technology, as in several Muslim nations Shariah tagged businesses cover a major portion of the market: for instance, in Malaysia where 80% of the market is covered by Shariah based firms (Rehan and Abdul Hadi, 2019; Rehan, Abdul Hadi and Hussain, 2019; Abdul Hadi et al., 2018).\n\nThus, the Ijarah of virtual properties is a way to structure transactions involving virtual assets in compliance with Islamic principles. However, since it is a new area of research, it would depend on the specific details and circumstances of the virtual property in question. Considering this, several scholars (see Maksalmina, 2022; Adam, 2021; Laldin and Djafri, 2019) argue that Ijarah can be applied to virtual assets as long as the assets are halal, the transactions are done without riba (interest), and the lessee has the right of possession and usufruct of the assets during the lease period.\n\nIn the context of the metaverse, the concept of virtual properties is relatively new, and the legal and regulatory frameworks surrounding it are still yet to be developed. This could make it challenging to create contracts and agreements for virtual properties that are legally bound and enforceable. Likewise, evaluation of virtual properties is also a significant challenge in the metaverse, where determining the value of these properties within the metaverse may be challenging as the value of digital assets can fluctuate rapidly and may not have a clear market value (Watson, 2022). However, in the case where the market value of an asset on metaverse is clear and there is no excessive risk then it will be okay according to the general Shariah rules.\n\n\nVirtual Ijarah in the metaverse space\n\nIn the metaverse context, the concept of virtual Ijarah is applied to facilitate the leasing of simulated assets such as buildings, land, vehicles and other dissimilar types of virtual goods (Riyadi, 2022). This enables individuals and businesses to attain virtual assets for a definite period of time without making large upfront payments or taking on the risks connected with possessing simulated assets. Notably, Ijarah in the metaverse for virtual properties is still a relatively new area in Shariah finance and there are opposing opinions and clarifications among scholars. For instance, Ishak and Billah, (2022) postulate that the rental transaction of an Ijarah contract is not considered secure in the metaverse virtual environment. Hence, the volatile price of Crypto and NFTs in the metaverse poses a serious threat to people and all these sorts of transactions which cover Gharar, (uncertainty and speculation) must be avoided since they are dubious and do not serve the goals of Islamic law. In Islamic finance, Gharar mentions the existence of risk, speculation or uncertainty in a transaction (Dewi, 2023). Therefore, it is advisable to seek the guidance of a qualified Islamic scholar or advisor before entering into any meta-Ijarah contract for virtual properties.\n\nVisibly, the metaverse concept for virtual Ijarah, has not yet been fully explored in an Islamic context. However, it is possible that the principles of Islamic finance, such as the prohibition of interest and the promotion of shared risk (Abdul Hadi et al., 2019), could be applied to the development of virtual assets in the metaverse (Riyadi, 2022). For instance, Islamic finance could be used to fund the development of virtual assets, such as virtual real estate, and leasing models like Ijarah could allow users to access and use these assets without owning them outright. Hence, the principles of Shariah compliance and transparency could be applied to the governance and management of the metaverse Ijarah to ensure that it aligns with Islamic values (Belk, Humayun, and Brouard, 2022). Moreover, looking into the general principles of Ijarah, if the virtual asset in the metaverse is a Shariah compliant asset and has a valuable usufruct then it has fulfilled the requirement of Ijarah.\n\nTherefore, it is possible to argue that the Ijarah principles can be applied to virtual assets in the metaverse as long as the underlying assets are halal, have value and usufruct and the transactions are done without riba i.e., interest. It can also be argued that using blockchain technology in the virtual metaverse Ijarah transactions are consistent with the principles of transparency and accountability in Islamic finance (Elasrag, 2019). Thus, in the metaverse Ijarah lease contract, the financial institution buys the virtual asset and then leases it to the individual or company for an agreed time period. Technically, throughout the total lease period, the individual or company pays agreed rent to the owner i.e., the financial institution. Notably, the agreed rent is settled based on the actual cost of the virtual asset and the total rental period of the lease. At the end, the individual or business has the choice to buy the virtual asset from the financial institution at an agreed rate (Katterbauer et al., 2022). Figure 2 below explains the Ijarah leasing process in the metaverse.\n\n(Source: Katterbauer et al., 2022).\n\nIn view of the above discussion, it is clear that Ijarah in the metaverse is still in its nascent phase, thus there has been growing attention in this zone by investors to gain capital. However, for Shariah-based financial investors, the metaverse virtual land leasing specifies a sustainable challenge and indicates a gap in the existing Shariah financing models. In the case of Shariah finance, the Ijarah incorporates a digital-based asset concept but the important question that arises is whether this virtual land platform integrates the mechanism of Gharar (El-Gamal, 2001). Clearly, the upsurge of metaverse-based virtual land leasing also exposes several threats. Moreover, selected academics claim that ownership and possession principles of Shariah finance also apply to virtual assets such as virtual real estate, virtual leasing, and NFTs (Lajis, 2019). Thus, the metaverse virtual transactions fulfill the perspectives of Shariah Muamalah (Islamic laws of transactions), hence, are permissible. Likewise, according to the 2021 Ijtima Ulama MUI (Majelis Ulama Indonesia - Indonesian Council of Islamic Scholars) fatwa, transactions that are done among intangible assets such as crypto and virtual land purchasing and leasing, can be classified as assets and commodities if they meet the requirements (Maksalmina, 2022).\n\n\nConclusion\n\nMetaverse is a new buzzword in the technological space. It is a notion that describes a virtual world where users can interact with each other and digital objects. Technically, NFTs, which are underpinned by the technology of blockchain, offer a way to represent virtual assets ownership in the metaverse. These unique digital assets, also recognized as metaverse NFTs include virtual real estate, businesses, video game possessions, banks, vehicles, etc. which are present inside the metaverse’s virtual world. Evidently, the metaverse has revolutionized the entire financial industry and introduced numerous financial products and services, such as a simulated environment where users are able to make virtual businesses, exchange virtual currency, and can also access banking facilities inside the simulated world. In the banking industry, numerous banks including several Islamic banks opened their virtual branches in the metaverse simulated world. Visibly, Islamic finance products are developed and integrated into the metaverse as it grows and evolves. Though, until now, no specific guidance or regulation exists that clarifies the application of Shariah finance principles for the metaverse virtual world. The concept of virtual Ijarah and virtual ownership is one of them. The virtual Ijarah and ownership is referred to as the rental of simulated properties such as buildings, land, intangible assets or objects in a metaverse virtual world. Importantly, Islamic finance principles require that transactions be based on real assets and that speculative transactions be avoided. However, multiple scholars have argued that intangible assets are allowed and can be treated like tangible assets if they represent real economic value and are used for productive purposes. Also, virtual assets treated like tangible assets must not be used for any activities forbidden in Islam such as riba (interest, gambling etc.). Therefore, the application of the concept of Ijarah on virtual properties and assets such as NFTs, real estate, and vehicles in the metaverse could be seen from this angle. Hence, virtual Ijarah is permissible in Islamic finance as long as the underlying assets are halal, have valuable usufruct and are free from Gharar (risk). Notably, the use of blockchain technology in virtual transactions is also considered consistent with the principles of transparency and accountability in Islamic finance. This comprehensive discussion is a fresh addition to the Islamic finance literature which helps policymakers produce a new policy that guides the implementation of Ijarah contracts in the simulated metaverse universe. Visibly, several challenges may arise when implementing virtual Ijarah contracts in the metaverse space such as there may be some overlap with the principles of Shariah finance. Thus, there is still a need for more research and in-depth discussions to establish clear standards for the virtual Ijarah contracts in the metaverse space.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAbdul Hadi AR, Rehan R, Zainudin Z, et al.: Capital structure determinants of Shariah and Non-Shariah companies at Bursa Malaysia. Opcion. 2018; 34(16): 678–695.\n\nAbdul Hadi AR, Hussain HI, Zainudin Z, et al.: Analyzing Performance of Shariah and Non-Shariah Portfolios during the Global Financial Crisis 2007-2008: Malaysia’s Experience. 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International Conference on Islamic Studies (ICIS). 2022; pp. 765–777.\n\nMileva G: 20 Brands Leaping into the Metaverse.2022. (Accessed on 15. Jan. 2023). Reference Source\n\nMorgan JP: Opportunities in the metaverse.2022. Reference Source\n\nMorshed A: Comparative Analysis of Accounting Treatments Between the IFRS’s and AAOIFI for The Islamic Financial Leasing Provided by Islamic Banks (Doctoral dissertation, soe).2022.\n\nMRFR: Metaverse Market.2022. (Accessed on 15 Jan 2023). Reference Source\n\nMulia MA: Leasing In The Metaverse, Ingram.2022. (Accessed on 20 Jan 2022). Reference Source\n\nMunadi M: Al-Ijarah: Understanding, legal basis and problems of contemporary practices in Sharia business. International Journal of Humanities, Social Sciences and Business (INJOSS). 2023; 2(1): 11–20.\n\nMystakidis S: Metaverse. Encyclopedia. 2022; 2(1): 486–497. Publisher Full Text\n\nNakavachara V, Saengchote K: Is Metaverse LAND a good investment? It depends on your unit of account!. arXiv preprint arXiv:2202.03081.2022.\n\nNarin NG: A Content Analysis of the Metaverse Articles. Journal of Metaverse. 2021; 1(1): 17–24.\n\nNjoku JN, Nwakanma CI, Amaizu GC, et al.: Prospects and challenges of Metaverse application in data-driven intelligent transportation systems. IET Intelligent Transport Systems. 2022; 17(1): 1–21. Publisher Full Text\n\nQamar S, Anwar Z, Afzal M: A systematic threat analysis and defense strategies for the metaverse and extended reality systems. Computer Security. 2023; 128: 103127. Publisher Full Text\n\nRabbani MR, Khan S, Thalassinos EI: FinTech, blockchain and Islamic finance: An extensive literature review. International Journal of Economics and Business Administration. 2020; 8(2): 65–86. Publisher Full Text\n\nRaman R, Raj BE: The world of NFTs (non-fungible tokens): the future of blockchain and asset ownership. Enabling blockchain technology for secure networking and communications. IGI Global; 2021; pp. 89–108.\n\nRehan R, Abdul Hadi AR: Capital structure determinants of Shariah and non-Shariah companies at Bursa Malaysia–dynamic approach. International Journal of Innovation, Creativity and Change. 2019; 6(8): 334–345.\n\nRehan R, Abdul HAR, Hussain HI: Sectorial-specific capital structure determinants-evidence from Bursa Malaysia. International Journal of Innovation, Creativity and Change. 2019; 6(8): 346–357.\n\nRiyadi S: Penerapan Teknologi Metaverse Pada Bank Syari’ah. ISLAMIC BUSINESS and FINANCE. 2022; 3(1).\n\nSaengchote K: Cryptocurrency bubbles, the wealth effect, and non-fungible token prices: Evidence from metaverse LAND. arXiv preprint arXiv:2209.04385.2022.\n\nSamad TFD, Hasan N: Women entrepreneurs in the era of metaverse: An Islamic economic perspective. Review of Islamic Social Finance and Entrepreneurship. 2022; pp. 131–140. Publisher Full Text\n\nSant H: How to Buy Land in The Metaverse on These 7 Platforms, Geekflare.2022. 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Handbook of Research on the Interplay Between Service Quality and Customer Delight. IGI Global; 2023; pp. 133–150.\n\nTamano N: Islamic bank ventures into the metaverse, IFNFintech.2022. (Accessed on 15-April-23). Reference Source\n\nThe Verge: Mark in the Metaverse.2021. (Accessed on 15 Jan 2023). Reference Source\n\nToraman Y: Interest-Free Finance Model by Using Blockchain-Based Company Tokens: Research on Digital Turkish Lira (DTL) and Borsa Istanbul with Technology Acceptance Model (TAM). EMAJ: Emerging Markets Journal. 2022; 12(2): 56–66. Publisher Full Text\n\nUsmani MT: Ijarah. An Introduction to Islamic Finance. Brill; 2001; (pp. 69–82).\n\nWang L: Non-fungible token real estate, IFN Correspondent Report: Islamic fintech.2022. (Accessed on 15 April 2023). Reference Source\n\nWang C, Yu C, Li Y: Toward Understanding Attention Economy in Metaverse: A Case Study of NFT Value. IEEE Transactions on Computational Social Systems. 2022; IEEE Publication; pp. 1–12. Publisher Full Text\n\nWang Q, Li R, Wang Q, et al.: Non-fungible token (NFT): Overview, evaluation, opportunities and challenges. arXiv preprint arXiv:2105.07447.2021.\n\nWang FY, Qin R, Wang X, et al.: Metasocieties in metaverse: metaeconomics and metamanagement for metaenterprises and metacities. IEEE Transactions on Computational Social Systems. 2022; 9(1): 2–7. Publisher Full Text\n\nWatson R: The virtual economy of the metaverse: Computer vision and deep learning algorithms, customer engagement tools, and behavioral predictive analytics. Linguistic and Philosophical Investigations. 2022; 21: 41–56.\n\nWiles J: What Is a Metaverse? And Should You Be Buying In? Gartner.2022. (Accessed on: 26-Feb-23). Reference Source\n\nXu H, Li Z, Li Z, et al.: Metaverse Native Communication: A Blockchain and Spectrum Prospective. arXiv preprint arXiv:2203.08355.2022.\n\nYemenici AD: Entrepreneurship in the world of Metaverse: Virtual or real? Journal of Metaverse. 2022; 2(2): 71–82. Publisher Full Text\n\nZafar F: Ijarah contract: a practical dilemma. Journal of Islamic Accounting and Business Research. 2012; 3(1): 67–69. Publisher Full Text\n\nZainab HE, Bawany NZ, Imran J, et al.: Virtual Dimension—A Primer to Metaverse. IT Professional. 2022; 24(6): 27–33. Publisher Full Text\n\nZainurin MZL, Haji Masri M, Besar MHA, et al.: Towards an understanding of metaverse banking: a conceptual paper. Journal of Financial Reporting and Accounting. 2023; 21: 178–190. Publisher Full Text" }	[ { "id": "190675", "date": "03 Aug 2023", "name": "Sherin Kunhibava", "expertise": [ "Reviewer Expertise Islamic banking and finance", "Fintech and blockchain governance", "commercial law" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 need to define digital banks - in the real world under digital banking license by regulators and 'digital/virtual banks' in the metaverse. Is there a regulator in the Metaverse?\n\nWhat Islamic banks are in the metaverse - give reference to the bank.\n\nState the objective of paper and methodology in the introduction.\n\nExplain NFT in greater detail and how it is used in the metaverse.\n\nExplain why metaverse banking and finance is more sustainable than the existing alternatives.\n\nDifferent opinions of scholars on the validity of virtual assets in the metaverse should be included\n\nExplain how rent is paid in the metaverse?\n\nConsider whether there is a usufruct for virtual assets and thus would ijara be possible in the metaverse? Authors need to consider and explain this.\n\nAlso consider whether 'virtaul land' which has no prospect of having physical structure is recognised as an asset or commodity or good in Shariah for which consideration can be given.\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? Partly\n\nAre arguments sufficiently supported by evidence from the published literature? Partly\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Partly", "responses": [] }, { "id": "219009", "date": "13 Nov 2023", "name": "Muhammad Maksum", "expertise": [ "Reviewer Expertise Islamic economic law", "Islamic Law", "Islamic Business contract", "Islamic banking law", "and" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article presents an intriguing perspective, introducing a novel discussion on ijarah financing, particularly its application through the ijarah contract within the realm of virtual assets, encompassing real estate, vehicles, and other non-physical entities. Despite the nascent concept of the metaverse, the ijarah contract embodies Sharia principles adaptable across various domains, including the metaverse, provided that these principles are rigorously observed.\nAn imperative aspect for this article involves a comprehensive elucidation of the business mechanisms within the metaverse to facilitate the appropriate application of Sharia principles in this evolving landscape. Historically, ijarah pertained predominantly to tangible assets. Nevertheless, the evolution of Islamic financing has led to the conception of ijarah financing, extending its purview to digital assets like digital gold and non-physical yet substantial assets such as trademarks and franchise businesses.\nConsequently, the article ought to explicate the manifestation of ijarah in two distinct forms: ijarah assets and ijarah services, delineating their adaptation to the diverse spectrum of assets. Additionally, a thorough exploration of the viewpoints of Islamic scholars (faqih) is imperative. This exploration should encompass the categorization of tangible and intangible assets, inclusive of property rights, benefits, and other abstract entities that may be subject to rental agreements within the framework of Islamic principles.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-837
https://f1000research.com/articles/11-484/v1	03 May 22	{ "type": "Research Article", "title": "Potential impact of great lockdown on students’ knowledge, attitude and practices towards the COVID-19 outbreak", "authors": [ "Mahmoud Berekaa", "Eltigani Omer", "Munthir Almoslem", "Khaled Alsahli", "Mohammed Aljassim", "Eltigani Omer", "Munthir Almoslem", "Khaled Alsahli", "Mohammed Aljassim" ], "abstract": "Background: Despite variation in the types of COVID-19 vaccines and genetic variation in the SARS-CoV-2 genome, using preventive measures remains the first choice to reduce risks associated with COVID-19 infection. Methods: This cross-sectional study highlights students’ knowledge, attitudes, and practices toward SARS-CoV-2 infection during the lockdown. The study was conducted at the Imam Abdulrahman Bin Faisal University (IAU), Eastern Province, Saudi Arabia. Data was collected from 43 male preparatory students via an online self-structured questionnaire. Knowledge level was determined using mean scores, while chi-square and t-tests were performed to detect significant differences between groups. Results: Males aged 17–20 displayed better knowledge regarding COVID-19 than other groups (t = 2.03, p = 0.049). Most participants recognized the typical symptoms and transmission routes; 93% indicated they viewed social distancing as a crucial preventive measure. Following lockdown, a 1.7-fold increase in the number of participants who believed that mask-wearing was an effective preventive measure was observed; however, 37.2% did not trust this practice. There was a 2.2-fold increase in the number of participants who took part in awareness programs during lockdown. Students’ knowledge increased from 73.2% to 81.5% following the lockdown. Specifically, mean knowledge regarding the role of contaminated tools in disease transmission increased from 33.7% to 75.5%. After lockdown, 58.1% of participants were anxious and afraid of having contact with their colleagues, while 39.5% missed their classes due to anxiety. Two sources of information impacted students’ knowledge following the lockdown: university studies (t = 2.149, p = 0.038) and friends (t = 2.6, p = 0.013). Conclusions: The findings suggest that IAU preparatory-year students have acceptable knowledge, awareness, and attitudes towards COVID-19 infection. This reflects the impact of media on the improvement in preventive measure uptake. Knowledge of the pandemic may increase if health education programs are designed to target students.", "keywords": [ "COVID-19 pandemic", "preparatory-year students", "perception", "non-pharmaceutical intervention", "Knowledge", "attitudes", "behavior", "preventive measures", "IAU students" ], "content": "Introduction\n\nThe emergence of the novel COVID-19 coronavirus disease has become a global health concern. COVID-19, caused by SARS-CoV-2, was first detected in Wuhan city, China.1–4 The most significant risk associated with COVID-19 is its potential to cause a severe acute response that may result in death. Epidemiological studies have revealed that the virus is spread, transmitted, and gains host entry by various means.2,5–8 COVID-19 has directly impacted numerous sectors, such as public health, the economy, and education. During the early stages of the outbreak, higher education institutions responded in different ways, with some having strong reactions that disproportionally impacted students who experience anxiety. For example, students from the Imam Abdulrahman Bin Faisal University (IAU) responded to the unprecedented preventive measures that were enforced by the Saudi Arabian government to control the spread of COVID-19. However, students’ responses to non-therapeutic protective measures are significantly influenced by their knowledge, behavior, and attitude toward the disease. While poor understanding and risk perception of COVID-19 among community sectors, such as educational institutes and healthcare providers, may significantly increase disease spread and infection levels,9–11 high knowledge and awareness levels among students can limit the disease spread.12 Baloran13 reported that non-therapeutic interventions should be highly effective during a pandemic. In a study conducted during the MERS-CoV pandemic, Al-Mohaissen14 reported that most Saudi Arabian university communities were aware of the disease’s epidemiology and symptoms; however, there was less awareness regarding the preventive measures that could limit its spread. Olaimat15 reported that university students in Jordan had adequate knowledge regarding COVID-19 infection, with significant levels of knowledge observed among postgraduate students using the internet, social media, and mass media as sources of COVID-19 information.\n\nIn early March 2020, Saudi Arabia announced its first COVID-19 case. Subsequently, all on-premise educational activities, including at IAU, were suspended, with all activities becoming virtual.16 Several studies have been conducted on medical and non-medical university students in Saudi Arabia, including during the lockdown period, to explore their knowledge, awareness, and attitudes towards COVID-19.17–20 On a community level, major precautions to combat the spread of the virus were taken by several countries, including Saudi Arabia. Several researchers have attempted to monitor the citizens’ knowledge levels and behaviors during lockdown periods.21–27\n\nThis research aims to determine the impact of the lockdown on IAU students’ knowledge regarding COVID-19’s transmission methods and symptoms and their attitudes and practices regarding preventive measures during their study. Emphasis was placed on the impact of social media and family as sources of COVID-19 knowledge and awareness. Furthermore, this study documents the behavior changes of IAU students during the lockdown period, particularly their interaction with infected or individuals suspected of being infected, with a focus on student anxiety.\n\n\nMethods\n\nThe study involved preparatory year students from IAU, Eastern Province, Saudi Arabia. The study took place before and after the lockdown period associated with COVID-19, which was between the second academic semester in March 2020 and the first academic semester in October 2020.\n\nThe study population primarily consisted of 43 randomly selected preparatory male students enrolled in health specialties. The sample size was calculated using Cochran’s formula.28 Baseline data pertaining to the participants’ pre-lockdown COVID-19 awareness and practices was gathered. Following lockdown, another sample of male students was randomly selected, and the impacts of lockdown on their awareness of COVID-19 were measured. A randomization policy was used to avoid bias in the selection of the study units.\n\nThe IAU QuestionPro platform was used for data collection. A pre-validated structured online questionnaire was constructed, generated, and randomly distributed to the students. The same questionnaire was used to assess knowledge levels and attitudes both pre- and post-lockdown.\n\nThe data was processed and analyzed using the SPSS19.0 program (SPSS Inc., Chicago, IL, USA). A descriptive and mean difference analysis questionnaire was conducted, with the percentage of responses to each section calculated. A statistical test was used to determine the presence of significant changes in the knowledge and attitudes of the students toward COVID-19. All variables were matched during the analysis to remove any confounding variables.\n\nEthical permission was obtained from the Institutional Review Board (IRB) of IAU Dammam, Saudi Arabia (IRB-2021-03-020). Written and verbal consent was obtained from all participants.\n\n\nResults\n\nDemographic data indicated that, before lockdown, participants aged 17–20 years and 21–23 years made up 69.8% and 20.9% of the sample, respectively. After lockdown, those same age groups made up 88.4% and 11.6% of the sample, respectively. The number of household members each participant had was measured before lockdown, with 3–5, 6–8, and 9 or more household members making up 27.9%, 48.8%, and 14% of the sample, respectively.\n\nTable 1 demonstrates the differences in participants’ COVID-19 knowledge with regard to their demographic characteristics. There are no statistically significant differences between knowledge level and age group in the period before the lockdown. However, a statistically significant difference in knowledge and age group was seen after lockdown. Participants aged 17–20 demonstrated greater knowledge than other groups (t = 2.03, p = 0.049). Regarding the number of household members, there was a statistically significant difference in the participants’ knowledge scores based on the number of household members they had.\n\n* Statistically significant.\n\n^ NA: not available.\n\nExcluding one, all participants had heard about COVID-19 prior to the lockdown; 90.7% of them knew it was a virus and the main causative agent of COVID-19. Following lockdown, 100% of participants had heard of it and knew it as the main causative agent.\n\nRegarding methods of transmission of the COVID-19 (Table 2), the most commonly recognized methods pre-lockdown were sneezing (86%), touching (65.1%), hugging (41.9%), coughing (69.8%), and shaking hands (60.5%). Post-lockdown, improvement in knowledge levels around transmission methods was observed, with 97.7%, 95.3%, 79.1%, 97.7%, and 97.7% of participants recognizing the aforementioned methods, respectively. Additionally, the average knowledge regarding contaminated tools, doorknobs, money, and mobile phone as methods of disease transmission increased from 33.73% to 75.48%, pre- and post-lockdown, respectively.\n\nKnowledge levels about the major sources of COVID-19 infection are depicted in Table 3. The correct answers were air and person-to-person contact. Pre-lockdown, 41.9% of students correctly identified air as an infection source, while 81.4% correctly identified person-to-person contact. However, 55.8% wrongly considered contaminated meat to be a source of infection, and 32.6% considered domestic animals to be. Furthermore, some students incorrectly identified water, soil, cross-contamination with camels, and seafood as infection sources.\n\nRecognition of air and person-to-person contact as infection sources greatly improved following lockdown, with 53.5% of students correctly identifying air as an infection source and 97.7% identifying person-to-person contact. However, some students did still cite other incorrect infection sources in their answers.\n\nTable 4 displays the participants’ knowledge regarding the main COVID-19 symptoms. The correct symptoms were fever, cough, shortness of breath, and headaches. Pre-lockdown, many students correctly identified fever (79.1%), cough (76.7%), and shortness of breath (72.1%) as COVID-19 symptoms. However, just over a third (34.9%) of the students considered headaches a symptom, while other methods, such as runny nose, diarrhea, and pain, were identified incorrectly.\n\nAfter lockdown, all students correctly identified fever and shortness of breath as symptoms, and 97.7% correctly identified a cough as a symptom. Additionally, headaches were recognized as a symptom by 65.1% of students. However, runny nose, joint pain, and diarrhea were mentioned by some participants still.\n\nTable 5 demonstrates participants’ knowledge regarding COVID-19 protection methods. Before lockdown, a low level of knowledge regarding the correct protection methods was observed among participants. However, this increased following the lockdown. For example, 79.1% of students correctly identified “avoid contact with infected persons” as a protection method pre-lockdown, while 100% identified it post-lockdown. Furthermore, despite mask-wearing being an effective preventive measure, only 37.2% trusted this practice pre-lockdown. However, this increased to 62.8% following lockdown. Moreover, fewer students identified the incorrect statement “avoid contact with domestic animals” as a protection method following lockdown, with the proportion of responses decreasing from 25.6% to 14%.\n\nFigure 1 demonstrates participants’ knowledge levels regarding COVID-19 pre- and post-lockdown. Pre-lockdown, the mean knowledge score was 73.2%. Post-lockdown, this increased to 81.5%.\n\nFigure 2a and 2b show the distribution of the participants who received information about COVID-19. Pre-lockdown, 23.3% of participants had received information on the disease. Post-lockdown, this increased to 51.2%.\n\nFigure 3a and 3b depict the sources of information used by students regarding COVID-19. All sources of information increased in use post-lockdown except for newspaper. University studies contributed to the awareness of16.3% of students pre-lockdown and 44.2% post-lockdown.\n\nRegarding information sources and their effects on participants’ knowledge, Table 6 shows no statistically significant differences between knowledge and any information sources pre-lockdown. However, two sources of information significantly affected participants’ knowledge post-lockdown; university studies (t = 2.149, p = 0.038) and friends (t = 2.6, p = 0.013).\n\n* Significant at p<0.05.\n\nParticipants’ knowledge regarding the COVID-19 vaccine revealed that pre-lockdown, 11.6% were aware of the vaccination, while 27.9% and 60.5% responded with “no” and “I don’t know,” respectively. In contrast, post-lockdown, 14% responded with “yes,” while 60.5% and 25.6% responded with “no” and “I don’t know,” respectively. Moreover, regarding knowledge about the presence of a COVID-19 drug, pre-lockdown, only 23.3% of the participants were aware of its presence, while 27.9% and 48.8% responded with “no” and “I don’t know,” respectively. Post-lockdown, 41.9% responded with “yes,” while 44.2% and 14% responded with “no” and “I don’t know,” respectively.\n\nTable 7 demonstrates participants’ attitudes toward COVID-19. Pre-lockdown, 39.5% of participants were anxious and afraid of coming into contact with their IAU colleagues due to the disease. However, only one was absent from class due to anxiety. Post-lockdown, 58.1% of participants were anxious and afraid of coming into contact with their colleagues, and 39.5% missed classes due to anxiety.\n\nTable 8 shows participants’ practices regarding COVID-19, with the incorrect answers being “avoid contact and offer no help” and “help with no concern for safety measures.” The participants showed increased levels of correct practice post-lockdown. Regarding the practice of helping a suspected or infected person while using safety measures, the percentage of correct responses increased from 53.5% pre-lockdown to 76.7% post-lockdown. Likewise, correct responses toward sticking with the strict protection measures increased from 53.5% to 90.7%, while contacting the relevant organizations increased from 65.1% to 90.7%. Regarding the incorrect practice statements, most students responded correctly with “no” post-lockdown.\n\n\nDiscussion\n\nProtection against a highly contagious disease, such as COVID-19, requires strict adherence to guidelines and rules, particularly regarding non-therapeutic interventions. Application of such measures requires adequate knowledge, attitudes, and practices on an individual and community level.12,17,23 The present study assessed the influence of lockdowns on IAU students’ awareness levels during the COVID-19 pandemic. The majority of the participants, who were preparatory year students, were aged between 17–20 and 21–23 years old. As young students are considered to be typically asymptomatic carriers and tend to have more social lifestyles, they may play a significant role in the dissemination of the disease, particularly among their colleagues, family, and friends.8,12\n\nAssessment of participants’COVID-19 knowledge indicated that knowledge regarding different methods of COVID-19 disease transmission (e.g., sneezing, touching, and coughing) greatly improved following lockdown. The role of coughing and sneezing in disseminating the virus has been reported by several health agencies and organizations.29,30 This increase in knowledge demonstrates the crucial role played by Saudi authorities in disseminating this knowledge during lockdown.23\n\nThe participants in this study showed a good understanding that water, soil, meat, contact with domestic animals, camels, and seafood are not involved in the infection process. However, misconceptions about the cause of COVID-19 have been reported among other students.29,30,12 All participants acknowledged that good personal hygiene and regular handwashing were important ways to protect themselves from COVID-19. Khasawneh et al.31 indicated that maintaining good personal hygiene and regular handwashing are the first lines of defense against COVID-19. IAU students demonstrated increased awareness levels regarding social distancing, avoiding hugging, wearing masks, and limiting person-to-person contact and increased knowledge of COVID-19 symptoms post-lockdown, supporting the international regulations and national precaution preventive measures that were put in place during lockdown.1,2,7,12,30,32–34 In a study assessing COVID-19 knowledge, attitude, and practices among the public of Saudi Arabia, approximately half of the respondents were unaware that COVID-19 could spread from person to person via aerosols.23 However, a study in Qassim found that 90.1% of participants were aware of person-to-person transmission.18 Moreover, in other studies, 90% of undergraduate students in China and 79% of undergraduate students in Indonesia acknowledged the role of respiratory droplets in disease transmission and increased infection risk.3,35\n\nIn the current study, the participants demonstrated significant knowledge levels regarding the three major COVID-19 symptoms. Post-lockdown, fever and shortness of breath were correctly identified by all participants, while cough was identified by almost all. Similar results have been observed among the Saudi Arabian public, Saudi Arabian medical interns, Chinese undergraduate students, and in the Qassim region, with 94.75%, 96%, 98.6%, and 97.4% of respondents in these groups correctly identifying coughing as a symptom.18,19,23,35 Additionally,89.7% Indonesian undergraduate students correctly identified cough and fever as COVID-19 symptoms.3\n\nKnowledge regarding COVID-19 drugs and vaccines was satisfactory among the current study participants; only a small number believed there was a vaccine against the infectious agent. Similarly, 96% of the Saudi Arabian public knew there was no clinically approved treatment for COVID-19.23 Unfortunately, during the time of the current study, Singh et al.12 reported that 92% of students were aware that no vaccine exists for COVID-19.\n\nSocial media and TV programs demonstrated significant impacts on the dissemination of knowledge and information regarding COVID-19 infection post-lockdown. Furthermore, the influence of social relationships with family and friends in providing COVID-19 information increased improved by 2.3-fold and 1.5-fold, respectively, post-lockdown. The influence of friends was particularly significant among 17–20-year-olds. Similarly, the role of IAU in improving students’ knowledge increased 2.7-fold, particularly among 17–20-year-olds. As expected, newspapers were not significantly used as sources of information pre- or post-lockdown.\n\nSimilarly, a cross-sectional study by Sobaih et al.37 cited the impact of social media usage during COVID-19 and its importance in promoting social learning among students from nine public higher education institutions in underdeveloped countries. In a case study, Hashim et al.38 reported that social media, particularly television broadcasts, were viewed as the most trusted source of information among approximately 147 students from a Malaysian technical university. A cross-sectional study analyzing the COVID-19 knowledge, attitudes, and practices of students from the University of Sharjah, United Arab Emirates, reported that the internet and social media were major sources of information for 85.2% of health-related and non-health-related students.39 Khasawneh et al.31 carried out a cross-sectional study involving students from six medical schools in Jordan, revealing that social media (83.4%) and online research engines (84.8%) were the preferred sources of COVID-19 information among the students. The preference of students to share verified COVID-19 information with family and friends via social media, which can be considered a third-party method of information, is an interesting finding.\n\nThe current study’s results indicated that the influence of family and friends in providing COVID-19 information increased following lockdown. However, mutual knowledge exchange between students and their families may occur, particularly regarding COVID-19 information.12 Saud et al.40 noted the importance of social media platforms as ab easy and accessible way to disseminate COVID-19 information between family and friends.\n\nThe current study revealed that IAU students experienced increased levels of anxiety due to COVID-19, particularly around having contact with IAU colleagues. Furthermore, an increased level of absenteeism was observed following lockdown. On the contrary, students in Japan were less anxious due to their adherence to precautionary behaviors.41 The impacts of lockdown on students’ mental health and the need for psychological support have been reported by many researchers.42–48 The assessment of IAU students’ responses toward suspected or infected persons indicated a high level of awareness regarding the importance of following strict safety and protective measures. However, research on how individuals react towards other individuals with COVID-19 is scarce; this is an area that requires further investigation.\n\n\nConclusions\n\nThe frequent variation in the COVID-19 genome has led to the requirement of different vaccine types, reflecting the importance of preventive measures in mitigating the risks associated with COVID-19 infection. Students’ lack of knowledge regarding the nature of the disease and the precautions that should be taken may have increased disease spread. The findings of the current study suggest that IAU preparatory students had acceptable levels of knowledge, awareness, and attitudes toward COVID-19 infection. The results highlight the impact of media on the improvement of preventive measure uptake. Students’ COVID-19 knowledge may be significantly improved if a proactive health education program is designed for them. The work presented in this study can serve as the basis for the construction of awareness programs that can act as efficient non-therapeutic interventions for students with limited basic pandemic knowledge.\n\n\nData availability\n\nFigshare: COVID-19 after.sav. DOI: https://doi.org/10.6084/m9.figshare.1939057149\n\nThis study contains the following underlying data:\n\n- COVID19 After.sav (Two main files; COVID-19 Outbreak.sav and COVID19 After.sav contain participants responses data before and after lockdown period.\n\n- Data comprises; gender, age, family members, college and department, knowledge about the disease, attitudes and practices about the COVID-19 disease).\n\n- All datasets have been de-identified in accordance with Safe Harbour Method.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nBerekaa MM: Insights into the COVID-19 pandemic: Origin, pathogenesis, diagnosis, and therapeutic interventions. Frontiers in Bioscience (Elite Ed) 2021; 13: 17–139.\n\nLi Q, Guan X, Wu P, et al.: Early transmission dynamics in Wuhan, China, of novel coronavirus–infected pneumonia. New England Journal of Medicine 2020; 382: 1199–1207. 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Publisher Full Text\n\nAkdeniz G, Kavakci M, Gozugok M, et al.: A survey of attitudes, anxiety status, and protective behaviors of the university students during the COVID-19 outbreak in Turkey. Frontiers in Psychiatry 2020; 11: 695. PubMed Abstract \| Publisher 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. Chronobiology International 2020; 37(*): 1191–1200. PubMed Abstract \| Publisher Full Text\n\nHakami Z, Khanagar SB, Vishwanathaiah S, et al.: Psychological impact of the coronavirus disease 2019 (COVID-19) pandemic on dental students: A nationwide study. Journal of Dental Education 2021; 85(4): 494–503. PubMed Abstract \| Publisher Full Text\n\nKecojevic A, Basch CH, Sullivan M, et al.: The impact of the COVID-19 epidemic on mental health of undergraduate students in New Jersey, cross-sectional study. PloS One 2020; 15(9): e0239696. PubMed Abstract \| Publisher Full Text\n\nBerekaa M: COVID-19 after.sav. figshare. Dataset. 2022. Publisher Full Text" }	[ { "id": "149902", "date": "13 Sep 2022", "name": "Walyeldin Elfakey", "expertise": [ "Reviewer Expertise Pediatrics and Child Health", "Infectious Diseases", "Medical Education" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe author studied the student's knowledge, attitude and practices (KAP) towards SARS-CoV-2 outbreak. They compared between the KAP before and after the lockdown.\nGenerally, the study is good apart from some points that I highlighted in the following report.\nTitle: Is good and reflects the idea of the study.\nAbstract: Acceptable.\nIntroduction: Concise and summarizes the relevant literature.\nMethods:\n\nBaseline data pertaining to the participants’ pre-lockdown COVID-19 awareness and practices was gathered – what was the method of gathering this baseline data which reflects the awareness and practices pre-lockdown? This point needs clarification.\n\nThe author should describe the method of randomization used.\n\nThe study includes males only, is there any female section in the university, if so why were females not included and there any impact of gender variation in the results? As a report from Saudi Arabia with the largest study that included 3388 participants concluded (However, the results showed that men have less knowledge, less optimistic attitudes, and less good practice toward COVID-19, than women).[Ref-1] Another study from Bangladesh stated (More frequent prevention practice factors were associated with female sex, older age, higher education, family income > 30,000 BDT, urban area residence, and having more positive attitudes).[Ref-2]\nResults:\nThe number of household members were categorized in 3 groups 3-5, 6-8, and more than 9, what was the bases behind these categories and why these numbers, I couldn’t find a justification?\n\nThe author stated (while other methods, such as runny nose, diarrhea, and pain, were identified incorrectly) as this is not correct early reports that describe COVID-19 included these symptoms (see https://www.cdc.gov/coronavirus/2019-ncov/symptoms-testing/symptoms.html).\n\nDiscussion: Good and acceptable.\nConclusion: The opening statement was (The frequent variation in the COVID-19 genome has led to the requirement of different vaccine types, reflecting the importance of preventive measures in mitigating the risks associated with COVID-19 infection). I did not find any relation between this conclusion and this 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? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "155351", "date": "05 Jul 2023", "name": "Alok Atreya", "expertise": [ "Reviewer Expertise Forensic Medicine & Toxicology", "and broad areas of interest are injuries", "violence", "trauma", "abuse", "medical ethics", "medical education", "forensic pathology", "forensic anthropology", "criminal law", "forensic psychiatry", "etc." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript investigates the impact of the COVID-19 lockdown on the knowledge, attitudes, and practices of preparatory-year students at Imam Abdulrahman Bin Faisal University (IAU) in Saudi Arabia. The study aims to assess students' knowledge of COVID-19 transmission methods, symptoms, and preventive measures, as well as their attitudes and practices towards the disease. The findings are presented in a descriptive manner, with statistical analyses conducted to identify significant differences. Overall, the study provides insights into the students' knowledge and behaviors related to COVID-19 and emphasizes the role of media and education programs in improving awareness.\nThe abstract provides a clear overview of the study's background, methods, and findings. Please include years after 17-20 in the results section.\n\nThe introduction effectively presents the significance of studying students' knowledge, attitudes, and practices during the COVID-19 pandemic. It establishes the context and highlights the potential impact of lockdown measures on students' responses to preventive measures.\n\nThe methods section describes the study location, sampling design, data collection, and statistical analysis. However, it lacks details on how the online self-structured questionnaire was developed and validated. Providing information on the questionnaire's content validity and reliability would enhance the rigor of the study. Furthermore, the authors have mentioned that the written informed consent was obtained. For the transparency and reproducibility of the methods authors are requested to provide how the written informed consent was obtained. The authors state that the participants were aged from 17-20 years. The authors need to detail who provided the consent for those less than 18 years.\n\nThe results section presents the findings in a comprehensive manner, using tables and figures to display the participants' knowledge, attitudes, and practices before and after the lockdown.\n\nThe discussion section provides an in-depth interpretation of the findings and relates them to existing literature. It highlights the importance of media, social relationships, and education programs in shaping students' knowledge and behaviors. The authors should provide limitations of the study, such as the small sample size, focus on a single university, exclusion of female participants etc. The study chooses random participants both for pre-lockdown and post-lockdown which would not reflect individual’s Covid-19 knowledge, attitude and practice assessment.\n\nThe manuscript adheres to the IMRAD structure and follows a logical flow from introduction to conclusion. The language is generally clear and concise, although there are occasional grammatical errors that could be addressed during proofreading.\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? 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? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "9875", "date": "17 Jul 2023", "name": "Mahmoud Berekaa", "role": "Author Response", "response": "First, as author of the manuscript, I appreciate valuable comments and suggestions highlighted by the reviewer. Kindly find point-by-point response to reviewer’s comments: 1. The abstract provides a clear overview of the study's background, methods, and findings. Please include years after 17-20 in the results section. Reply: Thanks for your comment, done 2. The introduction effectively presents the significance of studying students' knowledge, attitudes, and practices during the COVID-19 pandemic. It establishes the context and highlights the potential impact of lockdown measures on students' responses to preventive measures. Reply: Thanks for your comment 3. The methods section describes the study location, sampling design, data collection, and statistical analysis. However, it lacks details on how the online self-structured questionnaire was developed and validated. Providing information on the questionnaire's content validity and reliability would enhance the rigor of the study. Furthermore, the authors have mentioned that the written informed consent was obtained. For the transparency and reproducibility of the methods authors are requested to provide how the written informed consent was obtained. The authors state that the participants were aged from 17-20 years. The authors need to detail who provided the consent for those less than 18 years. Reply: As response to the mentioned comments, the following modifications and enrichment data provided: The IAU QuestionPro platform was used for data collection. An Arabic self-structured online questionnaire was developed and subjected to face as well as content validation by three public health experts. Before randomly distributed to students, the reliability of the questionnaire was performed using Cronbach’s alpha test, which was found to be moderate (0.60), but mostly acceptable. The same questionnaire was used to assess knowledge levels and attitudes both pre- and post-lockdown. Eligible students should agree on written and verbal consent before admission of the survey. Others unwilling to participate or unable to understand the content of the questionnaires are excluded and have the right to leave the survey at any time. On the other hand, we consider that preparatory year students in IAU with the age of 17 are targeted during any public health awareness program in IAU and through ministry of health and other governmental agencies especially during the study period. 4. The results section presents the findings in a comprehensive manner, using tables and figures to display the participants' knowledge, attitudes, and practices before and after the lockdown. Reply: Thanks for your comment. 5. The discussion section provides an in-depth interpretation of the findings and relates them to existing literature. It highlights the importance of media, social relationships, and education programs in shaping students' knowledge and behaviors. Reply: Thanks for your comment. 6. The authors should provide limitations of the study, such as the small sample size, focus on a single university, exclusion of female participants etc. Reply: The following paragraph addressing the major limitations that should be considered during interpretation of the results was added. “On the other hand, there are some limitations that should be considered during interpretation of the results. First, the study focuses on small student number from IAU university, thus cannot be generalized. Second, the questionnaire was only available for male students, with exclusion of female participants, therefore there is a potential for participation bias. Finally, the study chooses random participants both for pre-lockdown and post-lockdown which would not reflect individual’s Covid-19 knowledge, attitude, and practice assessment” 7. The manuscript adheres to the IMRAD structure and follows a logical flow from introduction to conclusion. The language is generally clear and concise, although there are occasional grammatical errors that could be addressed during proofreading. Reply: the manuscript subjected to proofreading before submission. Is the work clearly and accurately presented and does it cite the current literature? Yes Reply: thanks Is the study design appropriate and is the work technically sound? Yes Reply: thanks Are sufficient details of methods and analysis provided to allow replication by others? No Reply: more details on methods and analysis section provided to allow replication by others. Are all the source data underlying the results available to ensure full reproducibility? Yes Reply: thanks Are the conclusions drawn adequately supported by the results? Yes Reply: thanks" } ] } ]	1	https://f1000research.com/articles/11-484
https://f1000research.com/articles/12-103/v1	27 Jan 23	{ "type": "Research Article", "title": "Relationships Between Childhood Bullying/Domestic Violence Experience and Insomnia among Employees in Japan", "authors": [ "Kei Muroi", "Mami Ishitsuka", "Daisuke Hori", "Tsukasa Takahashi", "Tomohiko Ikeda", "Tamaki Saito", "Sasahara Shinichiro", "Ichiyo Matsuzaki", "Kei Muroi", "Mami Ishitsuka", "Daisuke Hori", "Tsukasa Takahashi", "Tomohiko Ikeda", "Tamaki Saito", "Ichiyo Matsuzaki" ], "abstract": "Traumatic childhood experiences such as domestic violence and bullying have been reported to be associated with insomnia in adulthood. However, little evidence is available for the long-term effects of childhood adversity on workers’ insomnia worldwide. Our objective was to examine whether childhood experiences of bullying and domestic violence are associated with insomnia in workers in adulthood. We used survey data from a cross-sectional study of the Tsukuba Science City Network in Tsukuba City, Japan. Workers aged 20 to 65 years (4509 men and 2666 women) were targeted. The Binomial Logistic regression analysis with the Athens Insomnia Scale as the objective variable showed that childhood bullying and domestic violence experience of childhood bullying and domestic violence were associated with insomnia. It may be useful to focus on childhood traumatic experiences regarding insomnia in workers.", "keywords": [ "Adverse Childhood Experiences", "Sleep Disturbance", "Athens Insomnia Scale", "Cross-Sectional", "Employees" ], "content": "Introduction\n\nInsomnia is an important public health problem, affecting about 30% of the worldwide population (Bhaskar et al., 2016). Insomnia increases the risk of mental disorders, suicide, and chronic health conditions such as obesity, diabetes, and cardiovascular disease (Sofi et al., 2012; McCall & Black, 2013; Biddle et al., 2018; Cai et al., 2018; Nishitani et al., 2018; Zhang et al., 2019). In Japan, Itani and colleagues conducted a nationwide interview survey and reported that 12.2% of men and 14.6% of women in the country had insomnia symptoms, eg, difficulty initiating sleep, difficulty maintaining sleep, or early morning waking (Itani et al., 2016). The OECD Health Statistics 2019 survey revealed that Japan has the shortest average sleep time among developed countries. Thus, insomnia is one of the most important challenges in Japan (OECD, 2020).\n\nSocioeconomic factors such as low income, low education, divorce, and bereavement have been reported to be associated with insomnia (Lallukka et al., 2012; Kawata et al., 2019). Also, lifestyle factors such as smoking, lack of exercise, and chronic diseases have been reported to be risks for insomnia (Brook et al., 2015; Koyanagi et al., 2015; Kelley & Kelley, 2017). Job stress is considered an occupational risk factor for insomnia, with the evidence showing a suspected relationship between job stress and sleep problems including insomnia (Utsugi et al., 2005; Kim et al., 2011).\n\nAdverse Childhood Experiences (ACEs), defined as physical, psychological, or sexual abuse, bullying victimization, or family dysfunction experienced before age 18, are a public health problem (Anda et al., 2006; Brown et al., 2009; Chapman et al., 2011; McKay et al., 2021). People who experience ACEs are mentally and psychologically vulnerable. It has been suggested that ACEs is a risk factor for sleep disturbance in adulthood (Kajeepeta et al., 2015; Brindle et al., 2018; Sullivan et al., 2019).\n\nLittle evidence is available for the long-term effects of childhood adversity on workers’ insomnia worldwide. Examining the effects of childhood bullying and domestic violence (DV) insomnia in workers can shed light on new causes of worker insomnia that have one unreported until now in addition to job stress.\n\nIn the present study, we investigated whether experiences of bullying/DV are related to insomnia among employees in Japan.\n\n\nMethods\n\nWe conducted a cross-sectional study using data obtained from a survey of the Tsukuba Science City Network in Tsukuba, a city situated about 70 km northeast of Tokyo. The Tsukuba Science City Network is an organization of the city’s research and academic institutes that aims to promote cooperation among its member institutes (MEXT, n.d.). The Tsukuba Science City Network conducts a mental health survey every 5 years of the researchers and engineers from the member institutes in Tsukuba city. From February to March 2017, we conducted the survey via an anonymous web questionnaire entitled The 7th Life Environment and Workplace Stress Survey. The total number of subjects in this study was 19,481 workers at 53 research institutes in Tsukuba City, all of whom were affiliated with the Tsukuba Science City Network. These workers were contacted via e-mail through the general affairs department of each institution and directed to a self-administered questionnaire form via a URL described in the e-mail. Participants were given the option to choose either the Japanese or English version of the questionnaire. All participants remained anonymous, and no data regarding their institute affiliation was obtained. The results of this survey have been published on the Tsukuba Science City Network website, and several studies using this survey have been reported (Hori et al., 2019; Takahashi et al., 2019; Ikeda et al., 2020). The total number of respondents was 7255, yielding a response rate of 37.2%. Sixty participants were excluded due to missing data or no response. The final sample consisted of 7175 participants (average age: 44 years; 4509 men and 2666 women) aged 20 to 65 years who answered the main response items. The detailed protocols are available at protocols.io (DOI: dx.doi.org/10.17504/protocols.io.14egn24nmg5d/v1).\n\nExperiences of bullying/DV\n\nWe collected data about experience of bullying/DV by means of an original questionnaire. The experience of bullying victimization was defined by answering “yes” to the question “Have you ever been bullied by others?” Similarly, the experience of DV victimization was defined by answering “yes” to the question “Have you ever been a victim of violence by a family member?” We observed when the experienced occurred (elementary school, junior high school, high school, or university and after). The respondents were able to select overlapping periods of time when they experienced victimization. They were classified into five groups according to the number of experiences; never experienced at all, experienced one period, experienced two periods, experienced three periods, and experienced four periods. We defined the experience from early childhood through high school years as a childhood experience and the experience from university years and after as a current experience.\n\nTherefore, childhood bullying or DV victimization experiences were divided into four groups; never experienced at all, experienced one period, experienced two periods, and experienced three periods.\n\nAthens Insomnia Scale (AIS)\n\nThe outcome variable analyzed in this study was insomnia, which was measured using the Japanese version of the AIS (Okajima et al., 2013). This self-administered questionnaire assesses insomnia according to the 10th revision of the International Classification of Diseases criteria (Soldatos et al., 2000; Okajima et al., 2013). The Japanese version of the AIS has been validated (Okajima et al., 2013) and is commonly used in epidemiological studies. It consists of 8 items: the first 5 assess difficulties with sleep induction, waking during the night, early-morning waking, total sleep time, and overall sleep quality, while the remaining 3 measure the consequences of insomnia during the day, including problems with sense of well-being, overall functioning, and sleepiness. Respondents were asked to rate their experiences with these symptoms over the past month on a 4-point scale ranging from 0 (“not problematic at all”) to 3 (“extremely problematic”). The total score ranges from 0 to 24. A score of less than 4 indicates no problems, while a score of 4 to 5 suggests that consultation with a physician may be necessary (some suspicion of insomnia). A score greater than 6 indicates that consultation with a physician is necessary (suspected insomnia) (Soldatos et al., 2003). Respondents were then dichotomized into two groups: the insomnia group (AIS total score ≥6) and the no-insomnia group (AIS total score ≤5).\n\nOccupational stress\n\nChronic occupational stress as perceived by the workers was assessed using the Brief Scales for Job Stress (BSJS) (Nishikido N, Kageyama T, Kobayasi T, 2000). The BSJS is a 20-item questionnaire developed by Nishikido and colleagues, based on the job demand-control-support model similar to the Job Content Questionnaire (Karasek et al., 1998). All participants were asked to “select the response that most closely matches your feelings about the descriptions of your current working circumstances”. Responses were rated on a 4-point scale (from 1=“disagree” to 4=“agree”), and the mean scores (range: 1.00–4.00) were calculated for six subscales: “workload,” “mental workload,” “interpersonal relationships,” “job control,” “reward from work,” and “support from colleagues and superiors.” These subscales have sufficient internal consistencies (Nishikido N, Kageyama T, and Kobayasi T, 2000). Workload, mental workload, and interpersonal relationships were defined as job-related stress, while job control, reward from work, and support from colleagues and superiors were defined as buffers against it.\n\nOther covariates\n\nThe covariates were age; sex (man, woman); smoking history (current, former, non-smoker); education (high school, university, graduate university, other school); annual house income (less than 4 million yen, more than 4 million yen and less than 8 million yen, more than 8 million yen and less than 12 million yen, more than 12 million yen); exercise habits (a few times a month, once a week, twice a week, 3 or more times a week); marriage status (unmarried, married, divorced, bereaved); presence of children (yes, no); working years (less than 1 year, more than 1 year and less than 3 years, more than 3 years and less than 5 years, more than 5 years and less than 10 years, more than 10 years); regularly go to a hospital (yes, no); residence (Tsukuba science city, Ibaraki prefecture, Tokyo-metropolitan, other); occupation (research or education, office work, technical job, other); job type (full-time, fixed-term, full-time, part-time, permanent); and type of organization (national, agency, private, corporation).\n\nStatistical analysis\n\nThe AIS rates 5 points or less as no insomnia symptoms, and 6 points or more, as insomnia symptoms. A crosstabulation table was prepared for those with and without insomnia symptoms by AIS, and chi-square and unpaired t-tests were performed.\n\nWe conducted a binomial logistic regression analysis with two groups as the objective variables. We created models with childhood bullying experience and domestic violence experience as explanatory variables and additional inputs of age, gender, smoking habits, family income, education, exercise habits, marital status, presence of children, hospital visits, years of work, place of residence, and BSJS as covariates. The BSJS was entered into a logistic regression model with the mean scores of each of the subscales as quantitative variables. Multicollinearity was checked in each model. Hosmer-Lemeshow tests were conducted to examine the quality of each model. Also, Nagelkerke pseudo R-squared measures was calculated.\n\nAll statistical tests were 2-sided, and probability values below 0.05 were considered to indicate significance. We also calculated the 95% confidence intervals.\n\nEZR version 1.40 (Saitama Medical Center, Jichi Medical University, Saitama, Japan) (Kanda, 2013) were used for the statistical analysis. EZR is a graphical user interface for R (The R Foundation for Statistical Computing, Vienna, Austria). More precisely, it is a modified version of R commander designed to add statistical functions frequently used in biostatistics.\n\nEthical considerations\n\nThe web survey contained clear statements that participation was entirely voluntary, that it was an anonymous survey, that the privacy of the respondent would be respected, and that the data would be strictly controlled. In The 7th Life Environment and Workplace Stress Survey, the respondents were not told in advance that the data would be used for research purposes.\n\nThe consent of the participants was taken when The Tsukuba Science City Network conducted the study. We received permission from The Tsukuba Science City Network to use the data for our research. We published an opt-out notice on our laboratory’s homepage, stating that the data would be used for research purposes without any name on the participants’ names (http://occup-aerospace-psy.org/content/files/7tsukukyov3R1.pdf).\n\nFrom the 8th survey, we will inform respondents in advance that the collected data will be used for research purposes. This research proposal was reviewed and approved by the ethics committee of the University of Tsukuba (approval #1374). All procedures were conducted in accordance with the ethical standards of the national research committee and the Helsinki Declaration.\n\n\nResults\n\nTable 1 and Table 2 show the participants’ characteristics. The insomnia group consisted of 2997 patients (41.8%) and the non-insomnia group consisted of 4178 patients (58.2%). A significant difference was found in the number of individuals in the insomnia and non-insomnia groups between the bullying victim group and the DV victim group (chi-squared test, p<0.001). The insomnia group was also higher on all means of the BSJS subscales (unpaired t-test, all p<0.001).\n\na Unpaired t-test was used.\n\nb Chi-square test was used.\n\nc Vocational school, junior college.\n\na Unpaired t-test was used.\n\nb Chi-square test was used.\n\nTable 3 and Table 4 show the results of a binomial logistic regression analysis. A Hosmer-Lemeshow test was performed on the model and the probability value was less than 0.05, indicating a poor fit (p<0.001). Nagelkerke pseudo R-squared measures was 0.151. Job type and occupation were excluded from the explanatory variables because multicollinearity was obtained (variance inflation factor>10).\n\na Vocational school, junior college.\n\nRegarding childhood bullying experiences, there was a trend toward insomnia in the group that experienced one period of bullying and in the group that experienced three periods of bullying compared to the group that never experienced (OR 1.38, 95%CI 1.19-1.60, OR 1.83, 95%CI 1.19-2.84, respectively). On the other hand, regarding childhood experience of domestic violence, there was a trend toward insomnia in the groups that experienced two periods and three periods compared to the group that never experienced (OR 1.82, 95%CI 1.24-2.68, OR 2.06, 95%CI 1.24-3.43, respectively). In BSJS, workload (OR 1.15, 95%CI 1.06-1.24), mental workload (OR 1.42, 95%CI 1.31-1.55), and interpersonal relationship (OR 1.38, 95%CI 1.28-1.48) were positively associated with insomnia as stress load factors, respectively. Regarding mitigating factors, Support from colleagues and superiors (OR 0.86, 95%CI 0.78-0.94) and Reward from work (OR 0.82, 95%CI 0.76-0.88) were negatively associated with insomnia, but not significantly associated with job control (OR 0.92, 95%CI 0.85-1.00).\n\n\nDiscussion/conclusion\n\nOur aim was to examine whether childhood experiences of bullying and DV were associated with insomnia among workers in adulthood. Childhood experiences of bullying and DV tended to cause statistically significant insomnia in a model that also adjusted for age, gender, lifestyle, income, and occupational factors. As for the experience of DV, the higher the time of experience, the higher the odds ratio of insomnia. Ours is the first large cross-sectional study in Japan to examine the influence of bullying and DV experiences on sleep.\n\nThe detail mechanism by which childhood experiences of domestic violence/bullying lead to insomnia in adulthood is unclear, but two hypotheses have been proposed (Kajeepeta et al., 2015). One possibility is that ACE increases corticotropin-releasing hormone (CRH) reactivity, which may later affect sleep quality; elevated CRH, and subsequent enhancement of the hypothalamic-pituitary-adrenal (HPA) axis, is associated with reduced sleep. However, studies on the relationship between ACE and cortisol are inconclusive. HPA axis responses have been suggested to be under genetic and epigenetic influence, and adverse childhood experiences may also influence HPA axis activity in adulthood (Morris et al., 2019).\n\nEmployees with ACEs are more likely than those without ACEs to seek or need health care services related to the chronic physical and mental health conditions associated with this (Arbesman & Logsdon, 2011). Therefore, occupational health nurses and occupational health physicians are likely to meet with individuals with ACEs. The importance of trauma informed care (TIC) has recently been reported as a care for ACEs (Huang et al., 2014). In employees who complain of insomnia, occupational health workers may also identify and address the risk of ACEs. TIC is a framework for acquiring trauma knowledge and responses and supporting appropriate responses for traumatized individuals. TIC is offered in the community as well as in medical institutions (Mahon, 2022) and can be applied in occupational health settings (Rosemberg et al., 2017), as cognitive behavioral therapy that includes TIC has been reported to improve insomnia in PTSD (Carlson et al., 2022), TIC could be practiced in occupational health settings to improve insomnia in workers with ACEs.\n\nThis study has the following limitations. First, it was a cross-sectional study, so a clear causal relationship was not determined. Second, the response rate of this survey was low—37.2%. There have a been study those voluntary respondents reported better physical and mental health than mandatory respondents. This survey relies on voluntary responses, which may have bias in the results. Because the response rate in this survey was low, ways to increase the response rate in the future must be devised. Moreover, we surveyed mainly past experiences, so remembering past actions and emotions was eventually reduced. Third, to investigate the experiences of bullying/DV, the previously validated Bullying and Friendship Interview Schedule (Wolke et al., 2012)/Adverse Childhood Experiences Questionnaire (Felitti MD et al., 1998) may have yielded more accurate data. Fourth, we used a self-report questionnaire called the AIS to investigate insomnia. Self-reported formulas are known to have recall bias. For example, self-reported sleep duration overestimates objective measures of sleep such as those by polysomnography and actigraphy (Jackson et al., 2018). Moreover, in this study, insomnia was not diagnosed by a doctor. Finally, unmeasured confounding factors (such as drinking habits and history of mental illness) were not eliminated.\n\nIn conclusion, we showed that workers with childhood experience of bullying or DV tend to have insomnia. In the future, objective sleep time and sleep efficiency should be evaluated using an activity meter and other methods to verify the effects of bullying and DV experiences.", "appendix": "Data availability\n\nZenodo: Relationships Between Childhood Bullying/Domestic Violence Experience and Insomnia among Employees in Japan, https://doi.org/10.5281/zenodo.7487997 (Muroi et al., 2022).\n\nThis project contains the following underlying data:\n\n- Tsukuba_Cross_Sectional.sav\n\nZenodo: Relationships Between Childhood Bullying/Domestic Violence Experience and Insomnia among Employees in Japan, https://doi.org/10.5281/zenodo.7487997 (Muroi et al., 2022).\n\nThis project contains the following extended data:\n\n- Original Questionnaire (English).pdf\n\n- Original Questionnaire (Japanese).pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe thank all the participants in this study. This study was funded by a research grant from the Tsukuba Science City Network. We thank Miyamasu Flaminia, Medical English Communications Center, University of Tsukuba Faculty of Medicine, for grammatical revision.\n\n\nReferences\n\nAnda RF, Felitti VJ, Bremner JD, et al.: The enduring effects of abuse and related adverse experiences in childhood. A convergence of evidence from neurobiology and epidemiology. Eur. Arch. Psychiatry Clin. Neurosci. 2006; 256(3): 174–186. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBhaskar S, Hemavathy D, Prasad S: Prevalence of chronic insomnia in adult patients and its correlation with medical comorbidities. J. Family Med. Prim. Care. 2016; 5(4): 780–784. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBiddle DJ, Kelly PJ, Hermens DF, et al.: The association of insomnia with future mental illness: is it just residual symptoms? Sleep Health. 2018; 4(4): 352–359. 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PubMed Abstract \| Publisher Full Text" }	[ { "id": "163521", "date": "22 Mar 2023", "name": "Gerardo Ochoa-Meza", "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\nI have a suggestion about the summary. The article can improve its scientific soundness if a clear, brief and concise conclusion is added in the abstract. The conclusion must be written according to what is mentioned in the Discussion/conclusions of this article.\nIn general, it is an excellent article despite the limitations indicated in the article. I consider that it is a contribution to continue advancing in this line of research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "9808", "date": "20 Jul 2023", "name": "Kei Muroi", "role": "Author Response", "response": "Dear Gerardo Ochoa-Meza, We apologize for the delay in contacting you. Thank you very much for pointing this out. We agree with this proposal and will revise our manuscript abstract. Sincerely yours, Kei Muroi MD" } ] }, { "id": "174528", "date": "26 Jun 2023", "name": "Farizah Mohd Hairi", "expertise": [ "Reviewer Expertise social epidemiology", "care of older persons" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract: This study investigates the association between childhood bullying/domestic violence experience and insomnia among employees in Japan. The research aims to explore the potential long-term effects of early-life adversity on sleep patterns and overall well-being. The study utilizes a cross-sectional design and collects data through self-report questionnaires. The findings suggest a significant positive relationship between childhood bullying/domestic violence experience and insomnia symptoms. The implications of these results highlight the importance of addressing past traumatic experiences when considering insomnia prevention and intervention strategies in the workplace.\nIntroduction: The introduction provides a comprehensive overview of the research topic, highlighting the prevalence of childhood bullying and domestic violence in Japan and its potential impact on individuals' long-term health. It discusses the existing literature on the association between early-life adversity and sleep disturbances, emphasizing the need for further investigation in the context of the Japanese workforce. The section concludes by outlining the research objectives and hypotheses.\nMethods: This section outlines the study design, participants, and data collection procedures. It describes the sample selection process, including inclusion and exclusion criteria. The measurement tools used to assess childhood bullying, domestic violence experience, and insomnia symptoms are described in detail, along with their psychometric properties. Ethical considerations and data analysis methods are also presented.\nResults: The results section presents the findings of the study, organized in a clear and concise manner. It provides descriptive statistics of the sample characteristics, prevalence rates of childhood bullying and domestic violence experience, and the distribution of insomnia symptoms among participants. The main analysis examines the relationship between childhood bullying/domestic violence experience and insomnia, utilizing appropriate statistical tests. The section includes effect sizes and confidence intervals where applicable.\nDiscussion: The discussion interprets the study findings in light of existing literature. It explores the possible mechanisms underlying the relationship between childhood adversity and insomnia symptoms, considering psychological, physiological, and socio-environmental factors. The implications of the findings for occupational health and interventions in the workplace are discussed, emphasizing the importance of addressing early-life trauma in promoting healthy sleep patterns among employees. The limitations of the study are acknowledged, and suggestions for future research are provided.\nConclusion: The conclusion provides a concise summary of the research findings and their implications. It emphasizes the significance of the study in shedding light on the relationship between childhood bullying/domestic violence experience and insomnia among employees in Japan. The section concludes by reiterating the importance of addressing early-life trauma and implementing appropriate interventions to promote healthy sleep and overall well-being in the workplace.\nOverall, the manuscript effectively investigates the relationships between childhood bullying/domestic violence experience and insomnia among employees in Japan. It contributes to the existing literature by highlighting the long-term effects of early-life adversity on sleep patterns and providing insights into potential intervention strategies. The study's rigorous methodology, clear presentation of results, and comprehensive discussion enhance the scientific value of the research. Suggestions for further improvements could include a larger and more diverse sample, longitudinal study design, and consideration of other potential confounding variables.\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/12-103
https://f1000research.com/articles/11-126/v1	31 Jan 22	{ "type": "Software Tool Article", "title": "ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language", "authors": [ "Alex Mas-Sandoval", "Chenyu Jin", "Marco Fracassetti", "Matteo Fumagalli", "Alex Mas-Sandoval", "Chenyu Jin", "Marco Fracassetti" ], "abstract": "A sound analysis of DNA sequencing data is important to extract meaningful information and infer quantities of interest. Sequencing and mapping errors coupled with low and variable coverage hamper the identification of genotypes and variants and the estimation of population genetic parameters. Methods and implementations to estimate population genetic parameters from sequencing data available nowadays either are suitable for the analysis of genomes from model organisms only, require moderate sequencing coverage, or are not easily adaptable to specific applications. To address these issues, we introduce ngsJulia, a collection of templates and functions in Julia language to process short-read sequencing data for population genetic analysis. We further describe two implementations, ngsPool and ngsPloidy, for the analysis of pooled sequencing data and polyploid genomes, respectively. Through simulations, we illustrate the performance of estimating various population genetic parameters using these implementations, using both established and novel statistical methods. These results inform on optimal experimental design and demonstrate the applicabil- ity of methods in ngsJulia to estimate parameters of interest even from low coverage sequencing data. ngsJulia provide users with a flexible and efficient framework for ad hoc analysis of sequencing data.ngsJulia is available from: https://github.com/mfumagalli/ngsJulia", "keywords": [ "high-throughput sequencing data", "population genetics", "genotype likelihoods", "Julia language", "pooled sequencing", "polyploidy", "aneuploidy" ], "content": "Introduction\n\nPopulation genetics, i.e. the study of genetic variation within and between groups, plays a central role in evolutionary inferences. The quantification of genetic diversity serves the basis for the inference of neutral1 and adaptive2 events that characterised the history of different populations. Additionally, the comparison of allele frequencies between groups (i.e. cases and controls) is an important aspect in biomedical and clinical sciences.3\n\nIn the last 20 years, next-generation sequencing (NGS) technologies allowed researchers to generate unprecedented amount of genomic data for a wide range of organisms.4 This revolution transformed population genetics (therefore also labelled as population genomics) to a data-driven discipline. Data produced by short-read sequencing machines (still the most accessible platform worldwide) consists of a collection of relatively short (approx. 100 base pairs) fragments of DNA which are then mapped or de novo assembled to form a contiguous sequence.4 At each genomic position, all observed sequenced reads are used to infer the per-sample genotype (an operation called ‘genotype calling’) and the inter-samples variability, i.e. whether a particular site is polymorphic (an operation called ‘single-nucleotide polymorphism (SNP) calling’).5\n\nTo this end, several software packages have been implemented to perform genotype and SNP calling from NGS data, the most popular ones being samtools/bcftools,6 GATK,7 and freeBayes.8 When, on average, few reads map at each genomic position (a scenario referred to as ‘low-coverage’ or ‘low-depth’), genotypes and SNPs cannot be assigned with confidence due to the high data uncertainty.9,10 Under these circumstances, statistical methods that integrate data uncertainty into genotype likelihoods and propagate it to downstream analyses have been proposed.5 Software packages like ANGSD11 and ngsTools,12 among others reviewed by Lou et al,13 implement a statistical framework to estimate population genetic metrics from low-coverage sequencing data. Similarly, an affordable generation of sequencing data from large sample sizes can be obtained via pooled sequencing experiments, where assignment of individual samples is typically not retained.14 Several new and popular software for the analysis of pooled sequencing have been proposed in recent years.15,16\n\nDespite these advances, most of these implementations are either tuned and suitable for model organisms only (e.g., with haploid or diploid genomes) or not easily adaptable to novel applications. Therefore, an accessible computational framework for building and testing ad hoc population genetic analyses from NGS data is in dire need. Among programming languages, Julia17 has emerged as both a powerful and easy-to-use dynamically typed language that is widely used in many fields of data sciences, including genomics.18 While several Julia packages are currently available for both population genetic and bioinformatic analyses (e.g., BioJulia), to our knowledge, a suitable framework for custom population genetic analysis from NGS data is not available yet.\n\nHere we present ngsJulia, a set of templates and functions in Julia language to process NGS data and create custom analyses in population genetics. To illustrate its applicability, we further introduce two implementations, ngsPool and ngsPloidy, for the analysis of pooled sequencing data and polyploid genomes, respectively. By extensive simulations, we show the performance of several methods implemented in these programs under various experimental conditions. We also introduce novel statistical methods to estimate population genetic parameters from NGS data and demonstrate their applicability and suggest optimal experimental design. We finally discuss further directions and purposes for ngsJulia and bioinformatics for NGS data analysis.\n\n\nMethods\n\nngsJulia was built in Julia language (Julia Programming Language, RRID:SCR_021666) and requires the packages ‘GZip’ and ‘ArgParse’. Auxiliary scripts to process output files were built in R (R Project for Statistical Computing, RRID:SCR_001905) version 3.6.3 and require the package ‘getopt’. ngsJulia receives gzipped mpileup input files which can be generated using samtools.19 Output files are in text file format and can be easily parsed for producing summary plots and for further analyses. Scripts for some downstream analyses are provided in ngsJulia.\n\nngsJulia is compatible with all major operating systems and is maintained at https://github.com/mfumagalli/ngsJulia Documentation and tutorials are available via this GitHub repository and archived at Zenodo20 at the time of writing. All analyses in the manuscript are performed in Julia language and R.\n\nngsJulia implements functions to read and parse gzipped mpileup files and to output gzipped text files on various calculations (e.g., genotype and allele frequency likelihoods) and estimations (e.g., allele frequencies), as requested by the user. ngsJulia also allows for several data filtering options, including on global and per-sample depth, proportion or count of minor allele, and base quality. Finally, several options for SNP and biallelic and triallelic polymorphisms calling are available.\n\nngsJulia provides utilities to calculate nucleotide and genotype likelihoods, i.e. the probability of observed sequencing data given a specific nucleotide or genotype,21 for an arbitrary ploidy level, as in Soraggi et al.22 We now describe how such quantities are calculated in ngsJulia.\n\nFollowing the notation in Soraggi et al,22 for one sample and one site, we let O be the observed NGS data, Y the ploidy, and G the genotype. Therefore, G has values in 01…Y, i.e. the number of derived (or alternate) alleles.\n\nIn the simplest form, genotype likelihoods can be calculated by considering individual base qualities as probabilities of observing an incorrect nucleotide.21 We adopt the calculation of genotype likelihoods for an arbitrary ploidy level POGY as proposed in Soraggi et al.22 From the genotype likelihoods with POGY=1, the two most likely alleles are identified by sorting POGY=1 values after pooling all sequencing reads together across all samples. This operation will restrict the range of possible genotypes to biallelic variation only. Note that this calculation is still valid for monomorphic sites, although the actual assignment of the minor allele is meaningless.\n\nWe now describe how to estimate Fa,n, the frequency of allele a∈ACGT at site n. Similarly to Kim et al,23 the log-likelihood function for Fa,n is given by:\n\nTo perform SNP calling, we implement a likelihood-ratio test (LRT) with one degree of freedom with null hypothesis H0:Fn=0 and alternate hypothesis H1:Fn=F̂n, as described by Kim et al.23 Additionally, we develop a test for a site being biallelic or triallelic. The former can be interpreted as a further evidence of polymorphism, while the latter as a condition not to be met for the site being included in further estimations, as our models assume at most two alleles. The log-likelihood of site n being biallelic is equal to POnGn=ijY=1 while the log-likelihood being triallelic is equal to POnGn=ijzY=1, with i, j, and z being the most, second most, and third most likely allele with Y=1 (i.e. haploid genotype G), respectively. An LRT with one degree of freedom can be conducted to assess whether POnGn=iY=1 is significantly greater than POnGn=ijY=1, or the latter is significantly greater than POnGn=ijzY=1.\n\nSeveral estimation of population parameters from pooled sequencing data are implemented in ngsPool, a separate program which uses functions in ngsJulia. We now describe the statistical framework for the analysis of pooled sequencing data.\n\nIn case of data with unknown sample size, the MLE of the population allele frequency Fn is calculated as in Equation 1 with F∈01. With known sample size, the same equation is used to calculate sample allele frequency likelihoods POnFn=f,24 for instance with f∈01…M×Y for M samples of equal ploidy Y. From these likelihoods, we can calculate both the MLE and the expected value with uniform prior probability as estimators of Fn.\n\nA simple estimator of the site frequency spectrum (SFS) from pooled sequencing data is obtained by counting point-estimates of Fn across all sites. We propose a novel estimator of the SFS implemented in ngsPool. Under the standard coalescent model with infinite sites mutations, we let the probability of derived allele frequency F in a sample of N genomes PF=f to be proportional to 1/fK with f∈1…N−1.25 The parameter K determines whether the population is deviating from a model of constant effective population size. For instance, K=1 is equal to the expected distribution of PF under constant population size, while K>1 models a population shrinking and K<1 population growth.\n\nWe optimise the value of K to minimise the Kullback-Liebrel divergence between the expected distribution of PFK and the observed SFS. The latter can be obtained by either counting F̂n across all sites or by integrating over the sample allele frequency probabilities PFn=fOn∝POnFn=f (i.e. with a uniform prior distribution). A threshold can be set to ignore allele frequencies with low probability to improve computing efficiency and reduce noise. Within this framework, folding spectra can be generated in case of unknown allelic polarisation.\n\nFinally, we introduce a strategy to perform association tests from pooled sequencing data. Similarly to Kim et al,23 we propose an LRT with one degree of freedom for null hypothesis H0:fcases=fcontrols and alternate hypothesis H1:fcases≠fcontrols. The likelihood of each hypothesis is calculated from POnFn=f and, therefore, this strategy avoids the assignment of counts or per-site allele frequencies. A statistically significant LRT with one degree of freedom suggests a difference in allele frequencies between cases and controls, and possible association between the tested phenotype and alleles.\n\nWe now describe the statistical framework implemented in the program ngsPloidy to estimate ploidy levels and test for aneuploidy. When multiple samples are available, two scenarios can be envisaged: (i) all samples have the same ploidy, (ii) each sample can have a different ploidy (aneuploidy).\n\nThe log-likelihood function for a vector of ploidy levels Y→M=Y1=y1Y2=y2…YM=yM for M samples and N sites is defined as:\n\nWith F̂n being the MLE of allele frequency at site n. POnGm,n=iYm=ym is the genotype likelihood while PGm,n=iYm=ymFn=F̂n is the genotype probability given the ploidy and allele frequency at site n.\n\nOnce F̂n is estimated and the inbreeding is known (or under the assumption of Hardy-Weinberg Equilibrium (HWE)), then genotype probabilities are fully defined. Equation 2 is optimised by maximising the marginal likelihood of each sample separately, assuming independence among samples and sites.\n\nWith limited sample size, F̂n is not a good estimator of the population allele frequency and therefore genotype probabilities may not be well defined. In the simplest scenario, genotype probabilities can be set as uniformly distributed, with all genotypes being equally probable. However, the assignment of alleles in into ancestral (e.g., wild-type) and derived (e.g., mutant) states is particularly useful to inform on genotype probabilities. Recalling Equation 2, we can substitute PGm,n=iYm=ymFn=F̂n with PGm,n=iYm=ymFn=EFK), where EFK is the expected allele frequency of PF=fK∝1/fK, as introduced previously. Note that EFK does not depend on the sequencing data for each specific site n.\n\nNote that, in practice, Equation 2 is a composite likelihood function, as samples and sites are not independent observations due to shared population history and linkage disequilibrium, respectively. A solution to circumvent this issue is to perform a bootstrapping procedure, by sampling with replacement segments of the chromosome and estimate ploidy for each bootstrapped chromosome. The distribution of inferred ploidy levels from bootstrapped chromosomes provides a quantitative measurement of confidence in determining the chromosomal ploidy. Moreover, it is not possible to calculate the likelihood of ploidy equal to one after SNP calling, as only putative heterozygous genotypes will be retained. Nevertheless, the identification of haploid genomes from sequencing data is typically trivial, as the observation of polymorphisms should easily rule out the case of Y=1.\n\nSo far, we assumed to know which allele can be assigned to an ancestral state, and which one to a derived state. However, in some cases, such assignment is either not possible or associated with a certain level of uncertainty due to, for instance, ancestral polymorphisms or outgroup sequence genome from a closely related species not being available. Under these circumstances, we extend our formulation by adding a parameter underlying the probability that the assigned ancestral state is incorrectly identified.\n\nLet us define R as the ancestral state and a as any possible allele in ACGT. In practice, a can take only two possible values as we select only the two most likely alleles. We label this set of the two most common alleles as A and we assume that the true ancestral state is included in such set. The log-likelihood function of ploidy for a single sample m under unknown ancestral state is:\n\nWhere PR=a indicates the probability that allele a is the ancestral state, and it is invariant across sites. If PR=a=0.5, then the equation refers to the scenario of folded allele frequencies, where each allele is equally probable to be the ancestral state.\n\nFinally, note that in a sufficiently large sample size, the major allele is more probable to represent the ancestral state. This probability depends on the shape of the site frequency spectrum, and it is equal to the cumulative distribution of PFK evaluated at F=N/2. We can extend Equation 3 to reflect this parameter uncertainty with a being the major allele in PR=a.\n\nWe introduce a novel test for aneuploidy. If all samples have the same ploidy y∈Y, then Yi=Yj=y is true for all ij∈1,2,…,M. We propose an LRT for aneuploidy with null hypothesis H0:supY→=y1=yy2=y…yM=y and alternate hypothesis H1:Y→=Y→MLE A large value of LRT is suggestive of aneuploidy. Statistical significance can be assessed with the LRT and M−1 degrees of freedom.\n\nTo benchmark the performance of methods implemented in ngsJulia, we simulated NGS data following a strategy previously proposed by Fumagalli et al26 available as a stand-alone R script. Briefly, individual genotypes are drawn according to probabilities depending on input parameters. The number of mapped reads at each position is modelled with a Poisson distribution and sequenced bases are sampled with replacement with a probability given by the quality score. As an illustration, the following code\n\nwill simulate 10 diploid genomes (--copy 2x10), 1000 base pairs each (--sites 1000) with an average sequencing depth of 20 and base quality of 20 in Phred score (--depth 20 --qual 20) from pooled sequencing (--pool) with results stored in test.mpileup.gz file.\n\nFor the analysis of pooled sequencing data, we simulated 100,000 independent sites at sample sizes 20, 50, and 100 from a diploid population with constant effective population size of 10,000. We imposed the average per-sample sequencing depth to be 0.5, 1, 2, or 5 with an average base quality of 20 in Phred score. To assess the performance of ngsPool, we calculated bias and root mean squared error (RMSE) between the estimated value of the true value, either from the sample or the whole population. While both metrics measure the distance with the true value, the bias retains the direction of the error (i.e. over- or under-estimation). To quantify the accuracy of SNP calling, we calculated F1 scores (the harmonic mean of precision and recall rates).\n\nTo simulate data for association test, we assumed an equal number of cases and controls (150) and 200 SNPs, either causal or non causal. For non causal sites, cases and controls have the same population allele frequency of 0.10. For causal sites, cases and controls have a population allele frequency of 0.09 and 0.04, respectively. These conditions are derived assuming a high risk allele frequency of 0.1, prevalence of 0.2, genotypic relative risk for the heterozygote of 2, genotypic relative risk for the homozygous state of 4. The sample size simulated guarantees at least 80% power with a false positive rate of 0.10.\n\nTo illustrate the usage of ngsPloidy, we simulated NGS data of genomes with different ploidy (one haploid, eight triploids, one tetraploid) at 1000 sites. NGS data was simulated assuming an average depth of 10 at haploid level. Code and simulated data sets analysed are available in ngsJulia GitHub repository.\n\n\nResults\n\nngsJulia implements data structures and functions for an easy calculation of nucleotide and genotype likelihoods (of arbitrary ploidy) which serve the basis of genotype and SNP calling and for the estimation of allele frequencies and other summary statistics. It is particularly suitable for low-coverage sequencing data and for cases when there is high data uncertainty. To demonstrate the use of ngsJulia, we provide two custom applications from its templates and functions.\n\nWe used ngsJulia to implement a separate program, called ngsPool, to perform population genetic analysis from pooled sequencing data. Specifically, ngsPool implements established and novel statistical methods to estimate allele frequencies and site frequency spectra (SFS) and perform association tests from pooled sequencing data.\n\nngsPool uses functions in ngsJulia to parse mpileup files as input. As an illustration, the following code\n\n\n\nwill parse test.mpileup.gz file and write estimates of allele frequencies in test.out.gz file from unknwon sample size after performing SNP calling with an LRT value of 6.64 (--lrtSnp 6.64, equivalent to a p-value of 0.01).\n\nDepending on the options selected by the user, output files contain, various results are printed on the screen, including\n\n• inferred major allele,\n\n• inferred minor allele,\n\n• LRT statistic for SNP calling,\n\n• LRT for bi- and tri-allelic calling,\n\n• three estimators of the minor allele frequency at each site.\n\nAdditionally, ngsPool can output a file with per-site sample allele frequency likelihoods. The following code\n\n\n\nwill produce estimates of allele frequencies from known sample size (specified by --nChroms 20) and allele frequency likelihoods in test.saf.gz file.\n\nThese files can then be used to estimate the SFS and perform an association test using two scripts provided in ngsPool. For instance, the code\n\n\n\nwill estimate the SFS, while the code\n\n\n\nwill perform an association test assuming two sets of allele frequency likelihood files, one from cases (test.cases.saf.gz) and one from controls (test.controls.saf.gz).\n\nTo illustrate the usage of ngsPool, we estimated allele frequencies based on simulated data at different experimental conditions. We sought to compare the performance among different estimators implemented in the program. If the sample size is not provided, ngsPool provides a simple MLE of the population allele frequency assuming haploidy. Alternatively, if the sample size is provided by the user, ngsPool calculates sample allele frequency likelihoods and returns both the MLE and the expected value of the allele frequency using a uniform prior probability.\n\nResults show that the error of estimating allele frequencies decreases with increasing depth and sample size, as expected (Figure 1). Likewise, the error to estimate the population allele frequency are more pronounced for lower sample sizes. MLE values tend to be less biased than expected values and sample estimates appear to be unbiased even at depth 1 for moderate sample size (Figure 1).\n\nBias and root mean square error against the reference true value from either the population or sample are provided for each value of depth D (the average number of sequenced reads per base pair) and sample size (on column panels) tested. Three estimators of allele frequencies are considered: a population maximum likelihood estimate (MLE) from unknown sample size and the expected value and MLE from known sample size.\n\nFurthermore, we simulated NGS data at fixed population allele frequency and compared the distribution of true sample allele frequencies and estimated values using a MLE approach from known sample size. Figure 2 shows that most of the deviation from the true population allele frequencies occur at intermediate frequencies (F equal to 0.5). This effect is more evident for low depth and low sample size (Figure 2).\n\nTrue sample allele frequencies and maximum likelihood estimates are shown at different fixed population allele frequencies F and sample sizes (on columns, 20 and 50) and depths (the average number of sequenced reads per base pair, on rows, 0.5, 1, 2, and 5).\n\nWe then assessed the effect of low-frequency variants on SNP calling. Specifically, we calculate F1 scores for SNP calling when the population allele frequency is 0 (not a SNP) or greater than 0 (a SNP). Figure 3 shows how the prediction accuracy increases with the population allele frequency (F), sample size, and depth (D). For instance, an F1 score greater than 0.75 is obtained with 20 samples only for F=0.05 and D>0.5. On the other hand, the same F1 score is achieved with 50 samples even with F=0.025 and also at F=0.02 but only if D>1.\n\nF1 scores (harmonic means of precision and recall rates) for predicting either a SNP (true population allele frequency F greater than 0) or not (F=0) are reported are various values of F, sample sizes (on columns, 20 and 50) and depths D (the average number of sequenced reads per base pair).\n\nSNP calling under-performs when there is no variation in the population (F=0), with sequencing errors and sampling statistical uncertainty generating estimate of F greater than 0.\n\nngsPool implements several methods to estimate the SFS from sample allele frequencies. As described in the methods, a simpler estimator is based on assigning the most likely sample allele frequency at each site (labelled count). ngsPool implements novel estimators of SFS from pooled sequencing data as described in the method section. A script implements an algorithm to fit the theoretical SFS to the observed SFS. The latter can be calculated either by assigning per-site MLE of allele frequencies (labelled fit_count) or by integrating the uncertainty across all sample allele frequency likelihoods (labelled fit_afl).\n\nFigure 4 shows the error in estimating either the population or sample SFS at various settings with different methods. The error decreases with increasing depth and sample size. Estimating SFS by fitting the theoretical SFS without assignment of allele frequencies generally outperforms other tested strategies (Figure 4).\n\nRoot mean square error (RMSE) values between true (either population or sample) and estimated SFS are reported at various depths D and sample sizes (on the rows).\n\nNotably, the novel approach implemented in ngsPool to estimate the parameter K of the SFS distribution (see Methods) allow us to directly quantify the error in inferring demographic events. In fact, all simulations assumed constant population size, equivalent to K=1. Figure 5 shows the estimated values of K by either assigning (counting) allele frequencies (fit_count) or by using allele frequency likelihoods (fit_afl). For low-to-moderate depth and sample size, estimates of K tend to suggest population expansion (K<1), possibly due to an over-estimation of the abundance of low-frequency alleles. However, the error is reduced when integrating the data uncertainty with sample allele frequency likelihoods, as estimates of K values tend to be closer to the true simulated value of 1 (Figure 5).\n\nEstimates based on fitting from counted allele frequencies (fit_count) and from allele frequency likelihoods (fit_afl) are reported. Note that the true simulated value of K is 1.\n\nEstimation of minor allele frequencies from pooled sequencing data. Bias and RMSE against the reference true value from either the population or sample are provided for each value of depth D and sample size (on column panels) tested. Three estimators of allele frequencies are considered: a population MLE from unknown sample size and the expected value and MLE from known sample size.\n\nngsPool implements a script to perform association tests from pooled sequencing data. Specifically, the script calculates an LRT statistic, with null hypothesis being that allele frequencies of cases and controls (or any two groups) are the same, as used by Kim et al.23 It uses sample allele frequency likelihoods and, therefore, it maintains data uncertainty and avoids the assignment of counts or per-site allele frequencies. An LRT statistics significantly greater than 0 indicates a difference in allele frequencies between cases and controls.\n\nFigure 6 compares the distribution of LRT statistics between causal and non causal sites at different experimental scenarios. The distribution of LRT at causal SNPs is skewed towards higher values for increasing depth, indicating more support to find phenptype-SNP association. Nevertheless, a clear separation between the distributions of causal and non causal SNPs is observed at low depth (Figure 6).\n\nThe distribution of likelihood-ratio test (LRT) statistics for casual and non causal single-nucleotide polymorphism (SNP) is reported at different depths (the average number of sequenced reads per base pair, on columns).\n\nWe further utilised ngsJulia to implement an additional program, ngsPloidy, for the estimation of ploidy from unknown genotypes. The method implemented is similar to the one proposed by Soraggi et al22 with some notable differences on the calculation of genotype probabilities (see Methods). Additionally, ngsPloidy includes a novel method to test for aneuploidy in the sample. As an illustration, the following code\n\n\n\nwill estimate ploidy levels for 20 genomes (--nSamples 20) from test.mpileup.gz file and return LRT values.\n\nFollowing Equation 2, the genotype probabilities for each tested ploidy are pre-calculated using a script provided in ngsPloidy. This script takes as input the value of parameter K (the shape of the expected SFS), the effective population size, and the probability that the major allele is the ancestral allele. The latter can be either set by the user (e.g., a value of 0.5 would be equivalent to unknown polarisation, as in a folded SFS) or be calculated from the expected population SFS itself. If genotype probabilities are not set, then a uniform distribution is assigned. Further options allow for estimation only on called SNPs and/or genotypes.\n\nngsPloidy uses functions in ngsJulia to parse mpileup files as input. At the end of the computation, various results are printed on the screen, including\n\n• number of analysed sites that passed filtering for each sample,\n\n• a matrix of ploidy log-likelihoods for each sample,\n\n• the log-likelihood and MLE of the ploidy vector (i.e. the individually estimated ploidy for each sample),\n\n• LRT scores for the test of aneuploidy against all tested ploidy levels.\n\nAdditionally, if requested by the user, ngsPloidy can generate output files with several statistics for each site (e.g., estimate allele frequency), and all per-site genotype likelihoods for each sample and tested ploidy.\n\nTo illustrate the usage of ngsPloidy, we deployed it to simulated data of an aneuploid sample consisting of one diploid, eight triploid and one tetraploid genomes. We compared the performance of ploidy and aneuploidy inference among different choices of genotype probabilities. The latter were derived either from the expected folded population site frequency, from the estimated ancestral population allele frequency, or from the calculated sample allele frequency.\n\nIn all tested cases, we inferred the correct vector of marginal ploidy levels. We therefore assessed the confidence in such inference by calculating the LRT statistics of ploidy and aneuploidy inferences. Both were calculated by comparing the most against the second most likely vector of ploidies or the most likely vector of equal ploidies, respectively.\n\nResults show that using the per-site estimate sampled allele frequency yields higher LRT statistics (and therefore confidence) than using expected population allele frequencies (Table 1). We reiterate that for all three cases we correctly identified the patterns of aneuploidy. However, we should caution that with lower sample sizes we do not expect inferences using estimated sample allele frequencies to perform well.\n\nLikelihood-ratio test (LRT) statistics using different methods of incorporating allele frequencies are reported.\n\n\nDiscussion\n\nAnalyses presented here provide further support for the use of genotype and allele frequency likelihoods in the analysis of NGS data.5 Notably, we demonstrated how probabilistic estimates of population genetic parameters can be obtained in case of pooled sequencing data and short-read data from polyploid genomes. Additionally, we motivated the inference of SFS from allele frequency likelihoods as a direct way to infer demography from raw sequencing data.\n\nngsJulia offers new possibilities of software prototyping for custom analyses of NGS data for population genetic applications. Furthermore, it allows for efficient testing of experimental designs and, therefore, would be beneficial for initial planning of any sequencing experiments. Finally, ngsJulia is highly applicable in educational contexts, with accessible documentation and tutorials to educate users on the theory underpinning the implemented methods. We envisage that further improvements in ngsJulia will include the expansion of suitable input formats and data file types, and the compatibility with additional NGS data type, including from long-read sequencing experiments.27\n\n\nConclusions\n\nIn this study, we introduce ngsJulia, a series of templates and functions in Julia language to analyse NGS data for population genetic purposes. We present two implementations for the analysis of pooled sequencing data and polyploid genomes, with the inclusion of novel methods. ngsJulia is a suitable framework for prototyping new software and for custom population genetic analyses from NGS data.\n\n\nData availability\n\nSimulated data and pipeline to reproduce all results presented here are available at https://doi.org/10.5281/zenodo.5886879.20\n\nData are available under the terms of the Creative Commons Attribution 4.0 International Public License.\n\n\nSoftware availability\n\n\n\n• Source code available from: https://github.com/mfumagalli/ngsJulia\n\n• Archived source code at time of publication: https://doi.org/10.5281/zenodo.588687920\n\n• License: Creative Commons Attribution 4.0 International Public License", "appendix": "References\n\nMarchi N, Schlichta F, Excoffier L: Demographic inference. Curr. Biol. 2021; 31(6): R276–R279. 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PubMed Abstract \| Publisher Full Text Reference Source\n\nFumagalli M, Vieira FG, Korneliussen TS, et al.: Quantifying population genetic differentiation from next-generation sequencing data. Genetics. 2013; 195(3): 979–992. PubMed Abstract \| Publisher Full Text Reference Source\n\nLogsdon GA, Vollger MR, Eichler EE: Long-read human genome sequencing and its applications. Nat. Rev. Genet. Oct 2020; 21(10): 597–614. PubMed Abstract \| Publisher Full Text" }	[ { "id": "128232", "date": "13 Apr 2022", "name": "Lindsay Clark", "expertise": [ "Reviewer Expertise Bioinformatics", "polyploidy", "population genetics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript by Mas-Sandoval et al. describes ngsJulia, a collection of functions and scripts in Julia and R for estimating genotype likelihoods from short read DNA sequencing data, as well as estimating allele frequencies in pooled samples, and estimating ploidy where it is unknown. It seems that the goal is also to enable biologists proficient in Julia to develop their own custom genotype calling and population genetic analysis scripts starting with the provided functions for estimating genotype likelihoods. As it is, the manuscript and software suffer from two major flaws: (1) the software and its outputs are not well documented for users or developers, and (2) testing is only performed on simulated data, not empirical data.\nThe software documentation is not very approachable as it currently is. End-to-end tutorials with a real dataset (or something closely resembling a real dataset) are needed for all applications. How are the output files formatted and how might the user further process those files to address biological questions? For example, it seems that one could use ngsJulia to generate a matrix of genotype calls across samples and loci, starting from a set of mpileup files, but from the documentation I have no idea how to accomplish this task.\nThere are eleven different functions for estimating genotype log likelihoods, depending on ploidy, with four different functions for haploids. This strikes me as poor software design. At minimum the eight calcGenoLogLikeX_MajorMinor functions could be collapsed into one, with ploidy as an added argument to the function. Having a single function would make it much easier to update the code and ensure that there aren’t any bugs that prevent it from working consistently across ploidy levels. The hard-coding of tuples for every possible genotype, and the repetitive if-else statements, could be replaced with a more programmatic approach. The programmatic approach with ploidy as a function argument would also enable the software to be used for organisms with ploidy greater than octoploid.\nIf I understand correctly, the SNP calling algorithm only seems to work on haploid samples, which would exclude it from being used in most studies. Please clarify.\nThe estimation of ploidy from sequencing data using the ngsPloidy is a valuable addition. As an author of other software for marker analysis in polyploids, I frequently hear requests for such functionality, so I expect ngsPloidy to get a lot of use. It would be helpful to include a comparison to other tools such as ploidyNGS, ConPADE, and/or SuperMASSA. Additionally, the algorithm is only tested on a simulated dataset, and I would like to see it tested on an empirical dataset (with flow cytometry used as ground truth), both to see how well it scales up to thousands of markers, and how well it deals with potentially messy data.\nThe authors use the term “aneuploidy” incorrectly. Aneuploidy refers to different chromosomes having different copy numbers within one individual. The authors seem to mean different individuals within a population having different ploidies. “Multiploid” is one term for this although depending on the field it is sometimes used as a synonym for “polyploid”.\nHow should the user estimate the shape of the site frequency spectrum and the effective population size, which are required inputs for ngsPloidy?\nI tried “Case A” in the ngsPloidy tutorial. It took me a few minutes to figure out the (undocumented) contents of test.A.txt. I assume that columns 6-25 are the true genotypes, column 5 is the allele frequency, and column 26 is the sample allele frequency. The tutorial otherwise worked. However, I didn’t get anything useful when I added the --callGeno flag.\nSimilarly to ngsPloidy, ngsPool is only tested on simulated data.\nMinor comments:\nThere seems to be a missing right bracket on the left side of equation 2.\n\nThe Figure 2 caption needs to more explicitly define the abbreviations MLE and SAF.\n\nAll of the code to reproduce the analysis in the paper is provided, although there is no documentation explaining the code or indicating which scripts go with which figures.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [ { "c_id": "9050", "date": "29 Nov 2022", "name": "Matteo Fumagalli", "role": "Author Response", "response": "The manuscript by Mas-Sandoval et al. describes ngsJulia, a collection of functions and scripts in Julia and R for estimating genotype likelihoods from short read DNA sequencing data, as well as estimating allele frequencies in pooled samples, and estimating ploidy where it is unknown. It seems that the goal is also to enable biologists proficient in Julia to develop their own custom genotype calling and population genetic analysis scripts starting with the provided functions for estimating genotype likelihoods. As it is, the manuscript and software suffer from two major flaws: (1) the software and its outputs are not well documented for users or developers, and (2) testing is only performed on simulated data, not empirical data. Thank you for reviewing our manuscript. We addressed all concerns by improving the applicability and documentation of our software and by applying it to empirical data. The software documentation is not very approachable as it currently is. End-to-end tutorials with a real dataset (or something closely resembling a real dataset) are needed for all applications. How are the output files formatted and how might the user further process those files to address biological questions? For example, it seems that one could use ngsJulia to generate a matrix of genotype calls across samples and loci, starting from a set of mpileup files, but from the documentation I have no idea how to accomplish this task. We improved the documentation as requested in the specific comments (see below). Examples from simulated mpileup files under various conditions are provided and now clarified. In our response, we clarified that ngsPloidy does not provide a matrix of genotype calls but rather estimates ploidy levels. There are eleven different functions for estimating genotype log likelihoods, depending on ploidy, with four different functions for haploids. This strikes me as poor software design. At minimum the eight calcGenoLogLikeX_MajorMinor functions could be collapsed into one, with ploidy as an added argument to the function. Having a single function would make it much easier to update the code and ensure that there aren’t any bugs that prevent it from working consistently across ploidy levels. The hard-coding of tuples for every possible genotype, and the repetitive if-else statements, could be replaced with a more programmatic approach. The programmatic approach with ploidy as a function argument would also enable the software to be used for organisms with ploidy greater than octoploid. We agree with this comment and we now replace all those functions into a unique one that takes ploidy as input parameter (see calcGenoLike function in file functions.jl). We also replaced all if-else statements with a more programmatic approach which makes ngsPloidy (see file ngsPloidy.jl). If I understand correctly, the SNP calling algorithm only seems to work on haploid samples, which would exclude it from being used in most studies. Please clarify. The SNP calling algorithm relies on either a likelihood ratio test with the null hypothesis being the pooled allele frequency equal to 0 (similar to Kim et al. 2011 Bioinformatics), or from setting a threshold on the estimated pooled allele frequency. Therefore, it is applicable to all ploidy levels. The estimation of ploidy from sequencing data using the ngsPloidy is a valuable addition. As an author of other software for marker analysis in polyploids, I frequently hear requests for such functionality, so I expect ngsPloidy to get a lot of use. It would be helpful to include a comparison to other tools such as ploidyNGS, ConPADE, and/or SuperMASSA. Additionally, the algorithm is only tested on a simulated dataset, and I would like to see it tested on an empirical dataset (with flow cytometry used as ground truth), both to see how well it scales up to thousands of markers, and how well it deals with potentially messy data. This manuscript (submitted as Software Tool Article) aims at proposing a new implementation rather than a new methodology. Additionally, the likelihood function to estimate ploidy levels partly mirrors the approach taken by a parallel study (https://www.biorxiv.org/content/10.1101/2021.06.29.450340) where we provide extensive comparisons with competing algorithms (including ngsPloidy). Therefore, a comprehensive benchmarking of ngsPloidy against alternative software would be outside the scope of this paper. As suggested, we applied ngsPloidy to a real empirical data of isolates from an outbreak of Candida auris (Rhodes et al. 2018). Whilst polyploidy could be associated with multidrug-resistant phenotypes, we inferred haploidy for all samples and contigs, in line with findings from the original study. We added a paragraph on both methods and results sections to describe this new analysis. The authors use the term “aneuploidy” incorrectly. Aneuploidy refers to different chromosomes having different copy numbers within one individual. The authors seem to mean different individuals within a population having different ploidies. “Multiploid” is one term for this although depending on the field it is sometimes used as a synonym for “polyploid”. We replaced all occurrences of “aneuploidy” in the text and documentation with “multiploidy”. How should the user estimate the shape of the site frequency spectrum and the effective population size, which are required inputs for ngsPloidy? The need to specify the shape of the site frequency spectrum and the effective population size is only required when the sample size is too low to have a meaningful estimate of the population allele frequency. Whilst these parameters are not known a prior for nonmodel species, in practice we found that, as long as values are within a reasonable range and the coverage is sufficient, there is not a significant bias associated with inaccurate settings of these parameters. In fact, they simply determine the prior probability of sampling allele frequencies and, for most species and populations, this distribution tends to have more mass at lower frequency values. I tried “Case A” in the ngsPloidy tutorial. It took me a few minutes to figure out the (undocumented) contents of test.A.txt. I assume that columns 6-25 are the true genotypes, column 5 is the allele frequency, and column 26 is the sample allele frequency. The tutorial otherwise worked. However, I didn’t get anything useful when I added the --callGeno flag. We now indicate the contents of all columns of the simulated file. The -callGeno flag does not output called genotypes but rather estimate ploidy by first assigning (calling) genotypes, and thus disabling the integrating over unknown genotypes. This is now clarified in the documentation. Similarly to ngsPloidy, ngsPool is only tested on simulated data. We now also present an application of ngsPool to empirical data. We reanalysed genomic data from Arabidopsis lyrata (Fracassetti et al. 2015). In this study, authors generated data both by genotype-by-sequencing and by pooled-sequencing, with the former providing ground-truth values for genotype and allele calls. We found that estimates of minor allele frequencies using ngsPool yield a lower RMSE (root mean squared error) than estimates from Varscan across all SNPs analysed. We added a paragraph both in the methods and results sections to describe these new analyses. Minor comments: There seems to be a missing right bracket on the left side of equation 2. Fixed. The Figure 2 caption needs to more explicitly define the abbreviations MLE and SAF. We added the acronyms SAF and MLE in the caption. All of the code to reproduce the analysis in the paper is provided, although there is no documentation explaining the code or indicating which scripts go with which figures. In https://github.com/mfumagalli/ngsJulia/tree/master/paper we provide all code to replicate the analyses in the paper. As now indicated, ploidy/do.sh would replicate the simulations and estimation of ploidy variation. We now clarify that in the pool and pool/plots folder each folder/script corresponds to the specific figure in the paper." } ] } ]	1	https://f1000research.com/articles/11-126
https://f1000research.com/articles/12-833/v1	14 Jul 23	{ "type": "Research Article", "title": "Association between dental caries experience and salivary profile among autoimmune thyroid disease subjects - a cross-sectional comparative study", "authors": [ "Aparna K S", "Manjunath P Puranik", "Uma S R", "Manjunath P Puranik", "Uma S R" ], "abstract": "Background: Autoimmune thyroid disease (AITD) is an inflammatory condition that primarily affects women between the ages of 30 and 50. It has been hypothesised that AITD causes salivary glands to produce less saliva due to its endocrine effects. Studies showing the effect of AITD on salivary glands are very scarce. The aim of this study was to compare AITD patients with controls who were of a similar age and gender in terms of salivary metrics and the prevalence of dental caries. Methods: 200 subjects in Bangalore city (100 AITD subjects and 100 healthy subjects as controls) participated in a cross-sectional study. Subjective oral dryness was assessed using Farsi’s criteria. Salivary parameters and caries were assessed using GC Saliva-Check BUFFER kit and WHO caries criteria respectively. Descriptive and analytical statistics were done. Significant data was defined as a p value of <0.05. Results: When compared to controls, the AITD group had substantially more subjective mouth dryness and dental caries. Unstimulated (USFR) and stimulated salivary flow rate (SFR), pH and buffering capacity were reduced in AITD group whereas viscosity was high. There was a significant negative correlation between USFR, SFR, subjective oral dryness and dental caries. In a linear regression, there was no association between age, gender, socioeconomic status (SES), thyroid stimulating hormone (TSH), salivary viscosity, pH, buffering capacity and dental caries. Dental caries, USFR and SFR demonstrated a substantial relationship. Conclusions: The present research may indicate an underlying association between thyroid and salivary gland dysfunction resulting in oral dryness and high dental caries experience.", "keywords": [ "autoimmune thyroid disease", "buffering capacity", "dental caries", "flow rate", "pH", "saliva", "salivary viscosity" ], "content": "Introduction\n\nThe immune system is dysregulated in autoimmune thyroid disease (AITD), which leads to an attack on the thyroid gland. Its two primary clinical symptoms are Graves disease (GD) and Hashimoto’s thyroiditis (HT). An estimated 5% of the general population is thought to be affected by HT and GD. AITD develops when genetically susceptible people lose their tolerance to thyroid antigens in conjunction with environmental factors such altered microbiota. Both symptoms are marked by aberrant thyroid functioning and T and B cell infiltration into the thyroid that is responsive to thyroid antigens.1\n\nAITD is unique to thyroid gland and women are affected 4–10 times more frequently than males.2 The most prevalent forms, Hashimoto’s thyroiditis (HT) and Graves’ disease (GD), have many immune characteristics in common. The primary characteristic of AITD is the emergence of antibodies against thyroid peroxidase (TPO), thyroglobulin (TG), and thyroid stimulating hormone receptor (TSH-R).3\n\nA combination of main and minor salivary gland secretions, gingival crevicular fluid, cellular debris, and bacteria are all present in saliva. Saliva serves a wide range of purposes, including the defence of the mouth cavity, digesting owing to salivary amylase, immunity to microbes, and, most critically, for use in diagnostic activities. The use of saliva in diagnostic procedures is expanding since it is simple, non-invasive, and affordable. Enzymes, hormones, antibodies, antibacterial components, growth factors, and other substances that enter from the blood through the gaps between cells can all be found in saliva. Some of the conditions for which saliva has significant diagnostic potential are oncological, endocrine, cardiovascular, rheumatic, autoimmune, neurological, or viral illnesses.1\n\nDental caries is seen as a complex microbiological illness. It is a multifactorial disease of the teeth that results in a localised loss of tooth structure. It is caused by the interaction of dietary carbohydrates, tooth substrate, and cariogenic bacteria in the dental biofilm, which produces acid after carbohydrate fermentation and causes changes in the pH of the biofilm, which leads to mineral loss (demineralization) as a result of disturbances in the physiologic equilibrium between the biofilm and tooth. Previous studies have discovered an increase in the prevalence of dental caries in people with thyroid dysfunction, either as a result of the disease process itself, as a result of the surgical treatment (thyroidectomy), or as a result of medication taken that worsens oral and dental conditions.4\n\nThe amount and quality of saliva generated are both impacted by AITD, which either directly or tangentially affects salivary gland secretory function. The primary determinants of salivary defence are its composition, buffering ability, pH and flow rate. Saliva production, when reduced, has an impact on mouth health and can cause complications like oral candidiasis, gum disease, tooth cavities, and other pharyngeal and oral disorders.3\n\nPrevious studies have examined the major involvement of the salivary glands in instances with AITD, which suggests that the development of thyroid and salivary gland immunological diseases may have a same mechanism.4 According to animal research, thyroid malfunction alters basal metabolic rate, which may therefore have an impact on the salivary gland’s secretary unit.5\n\nThere are very few studies demonstrating how AITD affects the salivary ducts. Because of this, the following research topic guided the execution of this study: Do AITD participants’ experiences with tooth caries and their salivary characteristics correlate? The link between dental caries history and salivary profile among AITD patients was postulated to exist. The objectives were to evaluate the relationship between tooth caries and salivary profile in AITD individuals and to contrast it with controls who were of a similar age and gender.\n\n\nMethods\n\nIn Bangalore metropolis, a cross-sectional research study involving AITD participants was carried out from June to August (pilot) and August to September (full study) in 2018.\n\nThe Institutional Ethical Committee (GDCRI/IEC-ACM(2)/9/2018-19, dated 21/08/2018) granted their approval for this study. The appropriate approval was received from the hospital’s administrators. The pilot study was conducted prior to ethical approval as this is part of the approval application process. After explicitly outlining the study’s goal and methodology, participants gave their written informed consent. Prior to the commencement of the research, the investigator was trained and calibrated to guarantee reliability (k = 0.80).\n\nThe Farsi oral dryness test, which consists of four queries and answer options, was used.6 During the pilot research, readability and understanding were evaluated. Necessary corrections and modifications were made. Internal consistency (α) was found to be good (0.87).\n\nTo determine the sample number and assess the study’s viability, a pilot study with 10 participants was carried out. The sample size was determined based on the frequency of dental caries using the following formula:\n\n“Where P = Prevalence of reduced unstimulated salivary flow rate i.e., 80.0%, statistical power = 80%, Zα = 1.96 at 95% confidence interval, E = margin of error-10%, Design effect, D = 1”\n\nThe sample size obtained was 96.04 which was rounded up to 100. Hence, 100 AITD subjects and 100 healthy, age- and gender-matched subjects (subjects’ companions) were chosen based on the eligibility criteria.\n\nAITD subjects\n\nInclusion criteria\n\nThe inclusion criteria were subjects aged 18 years and above diagnosed with autoimmune thyroid disease (both hypo and hyper AITD), and subjects with no other systemic illness.\n\nExclusion criteria\n\nThe exclusion criteria were subjects who smoked or drank alcohol, subjects with a history of/undergoing radio-active iodine, and subjects taking any xerogenic medication.\n\nHealthy subjects\n\nInclusion criteria\n\nThe inclusion criteria were those 18 years or older without systemic illness, whose age and gender matched subjects in the AITD group.\n\nExclusion criteria\n\nExcluded from the study were subjects with any habits like smoking and alcohol consumption.\n\nBased on inclusion and exclusion factors, research participants were chosen at random from a hospital that was randomly selected from the list of hospitals in Bangalore.7 The study period was from June to September 2018. Patients who met the eligibility criteria were approached in the hospital based on the medical records and their bystanders were included as the control group. The participants were given an information sheet outlining the purpose of the study, the specifics of the research study, and the processes, after which they consented to participate in the study. Their queries regarding the study were addressed. Written informed consent was acquired. The study’s participants were assured their right to withdraw and were free to leave at any moment. From the data that were accessible from the medical records, thyroid disorders were screened for in all research participants. Among 100 AITD subjects, equal distribution of hyper and hypo AITD were maintained. Most of them were diagnosed within the past year. Data regarding thyroid hormone levels were obtained from the hospital records. Increased blood levels of thyroid stimulating hormone (TSH) > 5mIU/l, low serum free tetraiodothyroxine (FT4) < 0.61 ng/dl, and elevated thyroid peroxidase (TPO) > 34 IU/ml were used to identify autoimmune hypothyroiditis. Based on reduced (TSH) < 0.3 mIU/l, TSH receptor antibody, and elevated FT4 > 2 ng/dl, autoimmune hyperthyroidism was identified.8 Data were gathered by a single calibrated observer using an organised questionnaire, clinical evaluation, and recording by a trained assistant. In addition to demographic information, dentist appointments and oral care routines were logged. Socioeconomic status (SES) was evaluated using an adapted Kuppuswamy categorization system.9\n\nThroughout the research, infection control practises were followed. All the data were collected at one instance from each patient which comprised of demographic details, subjective assessment of saliva using Farsi’s questionnaire, dental caries examination and objective assessment of saliva using GC Saliva-Check BUFFER kit.\n\nDemographic details were first collected by the principal examiner followed by the administration of Farsi’s questionnaire. Oral dryness was assessed using Farsi’s oral dryness questionnaire which comprised of 4 items where a response of ‘Yes’ was scored as 1 and ‘No’ was scored as 0. Positive response (Yes) was indicative of subjective dryness. Utilizing WHO 2013 caries criteria,10 clinical evaluation of oral caries was conducted.\n\nThe criteria for diagnosing a tooth status and the coding are as follows:\n\n“0 = Sound\n\n1 = Caries\n\n2 = Filled with caries\n\n3 = Filled, no caries\n\n4 = Missing due to caries\n\n5 = Missing for any other reason\n\n6 = Fissure sealant\n\n7 = Fixed dental prosthesis/crown abutment, veneer, implant\n\n8 = Unerupted\n\n9 = Not recorded”\n\nClinical examination of dental caries was followed by saliva collection of each patient.\n\nTo avoid confounding brought on by diurnal fluctuation, saliva was taken from each subject at the same time of day (between 9 and 11 AM). Viscosity was assessed visually in the oral region by observing the consistency of unstimulated saliva. Normal viscosity was indicated by watery, transparent spit. Saliva that was sticky, foamy, and effervescent was a sign of increased viscosity.\n\nSalivary parameters were assessed using GC Saliva-Check BUFFER kit (GC India Dental Pvt. Ltd.), comprised of graduated collecting cylindrical tube with pipettes, pH strips, buffer strips, colour indicator chart and paraffin wax.11 Saliva was stimulated with paraffin wax. The participants in the research were instructed to chew on a portion of paraffin wax for 5 minutes while spitting into a gathering cup every 30 seconds. Patients were handed graded collecting cylindrical tubes and instructed to sit up straight for five minutes. They were told to spit into the conduit for five minutes without ingesting (drooling method). The salivary composition, which included USFR, SFR, pH, and buffering capacity, was estimated from the collected saliva. Normal range of USFR is 0.2-0.3 ml/ min and below 0.2ml/ min was considered as reduced salivary flow. Normal range of SFR is 1-3 ml/min and below 1ml/min was considered as reduced salivary flow.\n\nThe pH was measured using pH strips with unstimulated saliva. The participants in the research were told to expectorate any accumulated saliva into the gathering cup. For 10 seconds, the pH strip was inserted into the saliva. The strip’s hue was contrasted with the colour indicator chart, where green represented healthy saliva. Yellow and red colours indicated moderately and highly acidic saliva respectively. Buffering capacity was measured with stimulated saliva using buffer strips.\n\nStimulated saliva was drawn from the collection cup using a pipette and one drop was dispensed to each of the three test pads. The colour of the strip was compared with the colour indicator chart where green colour denoted normal/high buffering capacity. Yellow and red colours indicated low and very low buffering capacity respectively.\n\nThe gathered information was put into a Microsoft Excel spreadsheet. The Statistical Package for Social Sciences was used to analyse the data (IBM SPSS Statistics V22.0). Statistics were analysed using both descriptive and inferential methods. Subgroup analysis was performed and analysis was done between autoimmune hyperthyroidism and autoimmune hypothyroidism. Pearson’s association, the unpaired t-test, the chi square test and Fisher exact test, as well as linear regression, were used. Dental caries was the dependent variable in a linear regression analysis with unstimulated saliva, stimulated saliva, salivary viscosity, salivary pH, and salivary buffering capacity as the independent factors. By using an online calculator,9 Kuppuswamy’s salary categories were revised with the Consumer Price Index for Industrial Workers (CPI-IW) at 291 for June 2018. A 5% level of significance (p < 0.05) was deemed acceptable.\n\n\nResults\n\nThis study included 100 AITD subjects and 100 healthy subjects (controls). The mean age for AITD group and control group were 32.20 ± 4.21years and 33.93 ± 5.55 years respectively. There was a higher proportion of female participants than males. The majority of the study subjects belonged to lower middle class (85.8%). Between the research groups, there was no statistically significant variation in terms of age (p = 0.06), gender (p = 0.30), or socioeconomic position (p = 0.29) (Table 1).\n\nThe majority of research subjects (AITD: 75%, control: 68%) had never been to the dentist. The majority of those who had attended a dentist had done so within the previous year (AITD: 72%, control: 53.1%). Tooth extraction (AITD: 40%, control: 46.9%) was the most frequently reported dental procedure, and pain was the primary factor driving dental visits (AITD: 60%, control: 62.5%). Between the research groups, there was no statistically significant variation in the duration since last dental visit (p = 0.05), the causes for the dental appointment (p = 0.82), or the type of treatment received (p = 0.76).\n\nThe majority of the AITD subjects (81%) were under anti-thyroid drugs for the past 1 year. Mean TSH values among AITD hyper and hypo groups were 0.20 ± 0.07 and 6.43 ± 1.30 respectively (Table 2). Comparing the AITD group to the control group, a substantially greater percentage of respondents reported subjective dryness (Table 3). Regarding subjective dryness, there was no statistically significant difference between the AITD hyper and hypo groups (Table 4).\n\nWhen compared to the control group, the amount of stimulated and unstimulated saliva was considerably lower in the AITD group. In comparison to the control group, a considerably greater percentage of research participants in the AITD group had increased salivary viscosity. When compared to the control group, salivary pH and buffering capacity were considerably lower in the AITD group (Table 5). Regarding salivary measures, there was no statistically significant variation between the AITD hyper and hypo groups (Table 6).\n\nAnti-thyroid medications did not significantly affect either unstimulated (p = 0.82) or stimulated salivary flow (p = 0.88), viscosity (p = 0.19), pH (p = 0.32), or buffering capacity (p = 0.36), respectively).\n\nWhen compared to the control group (56%), the AITD group (72%) experienced considerably more dental cavities. Mean number of DMFT, decayed teeth (DT) and missing (MT) teeth were significantly higher in AITD group (DMFT: 3.82 ± 1.36, DT: 3.18 ± 1.06, MT: 0.45 ± 0.83) than the control group (DMFT: 1.65 ± 0.86, DT: 1.25 ± 0.53, MT: 0.19 ± 0.59) (p < 0.001). There was no significant difference between the mean numbers of filled (FT) teeth among the AITD group (0.19 ± 0.63) and the control group (0.21 ± 0.47) (p = 0.15) (Table 7). There was no statistically significant difference among the AITD hyper and hypo groups with regard to dental caries experience (Table 8).\n\nA significant negative correlation was observed between subjective mouth dryness and “USFR” (r = -0.586, p < 0.001) and DMFT and “USFR” (r = -0.368, p < 0.001). “SFR” had a significant negative correlation with subjective mouth dryness (r = -.524, p < 0.001) and DMFT (r = -0.373, p < 0.001) respectively (Table 9).\n\n* Significant (p value < 0.05).\n\nIn the linear regression model, age (β = 0.115, R2 = 0.016, p = 0.45), gender (β = 0.089, R2 = 0.019, p = 0.44), socioeconomic status (β = 0.021, R2 = 0.001, p = 0.86), thyroid stimulating hormone (β = -0.091, R2 = 0.006, p = 0.43), salivary viscosity (β = 0.125, R2 = 0.02, p = 0.74), pH (β = -0.919, R2 = 0.01, p = 0.12) and buffering capacity (β = 0.778, R2 = 0.03, p = 0.26) were not associated with dental caries. Unstimulated saliva (β = -0.523, R2 = 0.43, p = 0.006) and stimulated saliva (β = -0.476, R2 = 0.32, p = 0.003) showed a significant association with dental caries (Table 10).\n\n\nDiscussion\n\nAutoimmune thyroiditis is a chronic disease in which the body interprets the thyroid glands and its hormones T3, T4 and TSH as threats.12 Sex hormones play a big role in triggering or protecting from autoimmunity. Estrogen has the ability to enhance the inflammatory process of the immune system and could contribute to AITD.12,13 The mean age of the AITD group was 32.20 ± 4.21 years which is similar to a previous study (30.06 years).5 The majority of participants were female which is in line with two previous studies.5,14\n\nDue to the chronic nature of autoimmune illness, there will be significant financial expenses as well as a negative effect on the patient’s health and quality of life. Dental caries are more likely to occur when socioeconomic factors, lower levels of schooling, and lower revenue are combined.15 Most of the research participants were from the lower middle class. Age, gender, and socioeconomic position among the research groups did not vary numerically significantly, indicating homogeneity.\n\nDental visits are of utmost importance to high-risk groups like autoimmune thyroid disease subjects as they are more prone to a variety of dental problems. The majority of the research participants had never been to a dentist. Most of the trips were motivated by symptoms (pain), which shows that the respondents did not fully understand the value of a preventive dental appointment.\n\nAutoimmune thyroid disease has a detrimental effect on salivary glands and cause reduction in salivary secretion.12,16 Basal metabolic rate is impacted by thyroid malfunction, and the secretary unit of the salivary duct is subsequently impacted.5 Salivary secretion is reduced in AITD hypothyroidism. This is believed to be connected to the hypothyroidism-related decreased metabolism. Although the cause is unclear, AITD hyperthyroidism can reduce saliva production when it is untreated or only partly managed.17\n\nSalivary mucins have an important role in maintaining rheological properties of saliva. AITD impairs secretary unit of salivary gland and cause decreased quality of salivary mucins which in turn affects viscosity, pH and buffering capacity.18\n\nFarsi’s criteria have been used to evaluate subjective dryness among patients with thyroid disorders. A higher proportion of AITD subjects reported subjective dryness than in the control group, suggesting the impact of AITD on salivary flow. Unstimulated and stimulated saliva were significantly reduced in the AITD group which is similar to two previous studies,5,14 suggesting consistent association between salivary flow and AITD. A higher proportion of study subjects in the AITD group experienced increased salivary viscosity and reduced salivary pH and buffering capacity, which was also similar to a previous study.5 Hence, salivary parameters are significantly affected with patients with AITD.\n\nA person with systemic hypothyroidism may have slower-healing cells and tissues, making them more vulnerable to illness. As a result, they are more likely to develop mouth and tooth conditions like dental caries, frequent mandible spasms, and bleeding lips. People who have autoimmune hyperthyroidism are more susceptible to dental caries, teeth sensitivity and pain in the jaw.13 Autoimmune thyroid disease increases the risk of dental caries which has been attributed to the reduced salivary flow caused by the condition.19 Dental caries experience was significantly higher in AITD group.\n\nIndicating the efficacy of using Farsi’s criteria to assess oral dryness, a moderately significant negative association was discovered between “unstimulated salivary flow,” “stimulated salivary flow rate,” and “subjective oral dryness.” This indicates a connection between salivary flow and caries, and a marginally significant negative association was discovered between “unstimulated salivary flow,” “stimulated salivary flow rate,” and “dental caries.” Therefore, perceived dryness may be a sign of cavities development and salivary flow rate.\n\nDental caries was used as the result variable in a study using linear regression. In contrast to demographic factors, TSH, salivary viscosity, pH, and buffering capacity, which were not linked with dental caries, the current research discovered a highly significant correlation between salivary flow and dental caries.\n\nThe current research has some strengths and limitations. We believe that this research is the first of its kind to link salivary parameters and tooth caries in AITD. Standard kits and criteria were used to evaluate salivary parameters reflecting high internal validity.\n\nAlthough it can be seen that there are risk factors, a cross-sectional research design does not allow for the evaluation of causation between study variables. Undiagnosed systemic disease could be present and could have affected the salivary metrics.\n\nProspective studies are recommended to understand changes in salivary parameters and the impact of drugs over a period of time among hypo and hyper AITD patients. There must be proper maintenance of oral hygiene and diet modifications.\n\nPeriodic dental management should be conducted by well trained dentists. Even if there are no comorbid conditions, dental therapy adjustments may be required for individuals who are receiving medical supervision and follow-up for an autoimmune thyroid disease.\n\nThyroid dysfunction can affect every system in the body, including the mouth. An overabundance or underabundance of these hormones has a negative impact on the oral cavity. The endocrinologist must be aware with the oral symptoms of thyroid dysfunctions before treating a patient with a thyroid disease. Prior to receiving dental care from a dentist, patients who have thyroid dysfunction and those who are on medication for it need to properly manage their risks. Thus, in order to preserve the patient’s thyroid and oral health, contact between the dentist and endocrinologist must be two-way.\n\n\nConclusion\n\nThe current study may indicate an underlying association between thyroid and salivary gland dysfunction. Dental caries is a multi-factorial condition where diet and oral hygiene habits play key roles. Hence, future studies should take these factors into consideration to determine whether thyroid disorder alone can cause salivary gland dysfunction resulting in oral dryness and high dental caries experience.", "appendix": "Data availability\n\nfigshare: Association between dental caries experience and salivary profile among autoimmune thyroid disease subjects - a cross-sectional comparative study.xlsx, https://doi.org/10.6084/m9.figshare.23300891.v1. 20\n\nThis project contains the following underlying data:\n\n- Term paper data entry.xlsx (underlying raw data file).\n\nfigshare: Blank copy (proforma).docx, https://doi.org/10.6084/m9.figshare.23585322.v1. 21\n\nThis project contains the blank questionnaire and data collection form.\n\nfigshare: Data key.xlsx, https://doi.org/10.6084/m9.figshare.23585319.v1. 22\n\nThis project contains the data key for the underlying data file.\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\nOrtarzewska M, Nijakowski K, Kolasińska J, et al.: Salivary Alterations in Autoimmune Thyroid Diseases: A Systematic Review. Int. J. Environ. Res. Public Health. 2023 Mar 9; 20(6): 4849. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFallahi P, Ferrari SM, Antonelli A: Autoimmune Thyroiditis.Gu D, Dupre ME, editors. Encyclopedia of Gerontology and Population Aging. Cham: Springer; 2021. Publisher Full Text\n\nSwain M, Swain T, Mohanty BK: Autoimmune thyroid disorders—An update. Indian J. Clin. Biochem. 2005; 20(1): 9–17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMeshaikhy RBAL, Al Rawi NA: Assessment of Dental Caries Experience Among Patients with Thyroid Disorders Attending Different Hospitals in Baghdad City/Iraq. J. Res. Med. Dent. Sci. 2020; 8(5): 37–43.\n\nBixler D, Muhler JC: The relation of thyroid gland activity to the incidence of dental caries in the rat: II. A comparison of caries incidence under paired-feeding technics. J. Dent. Res. 1957; 36(6): 880–882. PubMed Abstract \| Publisher Full Text\n\nNaik MM, Vassandacoumara V: Qualitative and quantitative salivary changes and subjective oral dryness among patients with thyroid dysfunction. Indian J. Dent. Res. 2018; 29(1): 16–21. PubMed Abstract \| Publisher Full Text\n\nList of hospitals in Bangalore: (Accessed on 06/05/2018). Reference Source\n\nSyed YA, Reddy BS, Ramamurthy TK, et al.: Estimation of salivary parameters among autoimmune thyroiditis patients. J. Clin. Diagn. Res. 2017; 11(7): ZC01–ZC04. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSharma R: Online interactive calculator for real-time update of Kuppuswamy’s socioeconomic status scale. (Accessed on 06/08/2018). Reference Source\n\nWorld Health Organization: Oral Health Surveys-Basic methods. 5th ed.Geneva: WHO; 2013.\n\nSaliva testing-GC Australasia: (Accessed on 06/05/2018). Reference Source\n\nWhy do autoimmune diseases affect more females than males? (Accessed on 09/12/2018). Reference Source\n\nBliddal S, Nielsen CH, Feldt-Rasmussen U: Recent advances in understanding autoimmune thyroid disease: the tallest tree in the forest of polyautoimmunity. F1000Res. 2017; 6(1): 4–17. Publisher Full Text\n\nAgha-Hosseini F, Shirzad N, Moosavi MS: Evaluation of xerostomia and salivary flow rate in Hashimoto’s Thyroiditis. Med. Oral Patol. Oral Cir. Bucal. 2016; 21(1): e1–e5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTooth decay might be a symptom of thyroid disease. (Accessed on 12/12/2018). Reference Source\n\nDayan CM, Daniels GH: Chronic autoimmune thyroiditis. N. Engl. J. Med. 1996; 335(2): 99–107. Publisher Full Text\n\nCastro I, Sepulveda D, Cortes J, et al.: Oral dryness in Sjögren’s syndrome patients. Not just a question of water. Autoimmun. Rev. 2013; 12(5): 567–574. PubMed Abstract \| Publisher Full Text\n\nVijay A, Inui T, Dodds M, et al.: Factors that influence the extensional rheological property of saliva. PLoS One. 2015; 10(8): e0135792. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAutoimmune diseases’ effect on oral health: (Accessed on 09/12/2018). Reference Source\n\nAparna KS: Association between dental caries experience and salivary profile among autoimmune thyroid disease subjects - a cross-sectional comparative study.xlsx. [Dataset]. figshare. 2023. Publisher Full Text\n\nAparna KS: BLANK COPY (PROFORMA).docx. Dataset. figshare. 2023. Publisher Full Text\n\nAparna KS: Data key.xlsx. Dataset. figshare. 2023. Publisher Full Text" }	[ { "id": "191038", "date": "21 Aug 2023", "name": "Ridhima Gaunkar", "expertise": [ "Reviewer Expertise Epidemiology", "Oral health promotion and disease prevention", "Tobacco control", "Research methodology and Statistics." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe introduction provides a sound outline of the research context stressing on the immune dysregulation in AITD and its effect on salivary characteristics and dental caries. The research question and objectives are clearly stated and open the way for subsequent sections of the article.\nThe Methodology section is exhaustive and logically organized, providing a transparent understanding of the design of the study, methods of data acquisition and statistical analysis. The attention to calibration and validation of tools, ethical issues, explicit description of sample size estimation clearly enhances internal validity of the study.\nThe results section is logically structured and provides detailed data analysis of variables related to demographics, dental caries, salivary parameters, thyroid function, correlations, and linear regressions.\nThe discussion section adequately summarizes the study findings, provides relevant pointers from previous studies, and graciously acknowledges limitations. Its strength lies in suggesting prospective studies in future and a note on how dentists and endocrinologists can collaborate to address oral health problems in thyroid dysfunction patients.\nHowever, in the text description regarding anti-thyroid drugs (table 2), it would be better if the results are presented as 'less than one year' and 'one year and greater' instead of \"The majority of the AITD subjects (81%) were under anti-thyroid drugs for the past 1 year.\" for better clarity and understanding.\nIn table 7, the p value for DT (AITD group vs Control group should also be made bold) as it is statistically significant.\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": "223549", "date": "14 Dec 2023", "name": "Smitha B Kulkarni", "expertise": [ "Reviewer Expertise Xerostomia related oral health problems", "different mouthwashes for the treatment of gingivitis and prevention of dental caries" ], "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\nTitle: Title is apt. Age group of the study subjects could have been mentioned.\nThe introduction gives a detailed outline of the need for the study and the research questions along with objectives are clearly stated.\nMethodology: Inclusion and exclusion criteria are clearly stated. Sample size determination is clear.\nMethodology is explained in detail and gives a very good understanding of the study. Calibration and validation of the tools are explicitly mentioned Most of the confounding factors are eliminated.\nStatistical analysis is explained clearly.\nResults are well structured with good detailed explanation with tables related to all the parameters.\nDiscussion is elaborate and conclusions are supported by the results.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "223547", "date": "15 Dec 2023", "name": "Amit Vasant Mahuli", "expertise": [ "Reviewer Expertise Dental Public Health", "Research", "public health", "Oral Cancer", "Periodontal 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\nAbstract: The abstract is well written and gives the gist of the article; however, the conclusion can be more specific with the results obtained. Introduction: It explains AITD and its relation to salivary secretions. It establishes the role of salivary secretions changes and their effects on oral health, thus establish the need for study Methodology: It explicitly mentions sample size and sampling, inclusion and exclusion criteria, cases and controls, data collection, and a statistical plan. Results: It explains the differences between the AITD group and the control group and further explains the hyperthyroid and hypothyroid conditions. Linear regression analysis with dental caries as a dependent variable shows a significant relationship between unstimulated and stimulated saliva. The author might have also considered the duration of diagnosis and duration of anti-thyroid drug usage, as they will influence the salivary secretion and process of dental caries. Discussion: The discussion is very well articulated and mentions study limitations and recommendations. Conclusion: The conclusion is more general in nature. The authors can be specific with the study results obtained, even though some results might not be statistically significant but indicate a difference.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-833
https://f1000research.com/articles/12-238/v1	03 Mar 23	{ "type": "Research Article", "title": "Genetic diversity and population structure of Capitulum mitella (Linnaeus, 1767) in Fujian (China) revealed by mtDNA COI sequences", "authors": [ "Rouxin Sun", "Zhilan Zhang", "Qiong Wu", "Peng Xiang", "Yanguo Wang", "Bingpeng Xing", "Rouxin Sun", "Zhilan Zhang", "Qiong Wu", "Peng Xiang", "Yanguo Wang" ], "abstract": "Background: Capitulum mitella is a widely distributed and ecologically important stalked barnacle that settles extensively on rocky shores. This species contributes to the structural complexity of intertidal habitats and plays a critical role in the marine ecosystem. This study aimed to reveal the genetic diversity and population structure of C. mitella by analyzing the mitochondrial cytochrome oxidase I (COI) gene. Methods: A 683bp fragment of the COI gene was sequenced from 390 individuals sampled from six localities in Fujian, China. Results: A total of 84 distinct haplotypes were identified through the analysis of 82 polymorphic sites, resulting in an average haplotype diversity (h) of 0.660 and nucleotide diversity (π) of 0.00182. Analysis of molecular variance (AMOVA) and pairwise FST statistics showed no significant population structure. Neutrality tests and mismatch distributions provided evidence of recent population expansion for the species. Conclusions: We suggest that the species' high dispersal ability, and ocean currents coupled with limited physical barriers in the region, contribute to its current phylogeographic structure. These findings enhance our comprehension of the genetic diversity and population structure of C. mitella, providing valuable insights for future conservation efforts.", "keywords": [ "Capitulum mitella", "mitochondrial DNA", "genetic diversity", "population structure" ], "content": "Introduction\n\nBarnacles are a key group of crustaceans that occupy the intertidal zone and have a vital effect in shaping the ecology of intertidal communities (Lim and Hwang, 2006). Capitulum mitella (Linnaeus, 1767), the single species within the genus Capitulum Gray (Crustacea, Maxillopoda, Cirripedia, Thoracica), is an ecolgically significant stalked barnacle that aggregates and settles extensively on rocky shores (Jones, 1994; Lee et al., 2000). C. mitella is a dominant organism in intertidal coastal ecosystems with a widespread distribution throughout warmer regions of the Indo-Pacific, from Madagascar to southern Japan. It is also considered a commercially valuable species due to its high protein content, low-fat levels, and rich mineral content. It has strong market demand, particularly in the Fujian province, where it is widely consumed as a seafood product. However, C. mitella populations have declined in recent years due to overfishing, habitat destruction, and slow growth. To ensure the effective management and protection of this economically valuable species, a comprehensive understanding of its population genetic structure and genetic diversity is crucial (Ortega-Villaizán Romo et al., 2006). Unfortunately, the population genetic structure of C. mitella in the Fujian province coast has yet to be extensively studied. This knowledge gap underscores the urgency for further investigation to grasp the genetic diversity and population structure of this key species and secure its sustainable utilization and conservation.\n\nMitochondrial DNA (mtDNA) is widely used as an ideal marker for investigating genetic diversity and population structure due to its rapid evolutionary rate, non-recombining nature, and simple amplification procedure (Ren et al., 2017; Xu et al., 2019). The COI gene within mitochondrial DNA (mtDNA) is a commonly utilized molecular marker for resolving phylogeographic structures in marine invertebrates (Ajao et al., 2021; Xu et al., 2019; Yuan et al., 2016). This study aimed to explore the genetic diversity and population structure of C. mitella populations along the coast of Fujian province utilizing the COI gene. The results would be important for the conservation and sustainable management of this species.\n\n\nMethods\n\nEthical review and approval were not required for this study because this research is about Capitulum mitella, a common invertebrate and a seafood species that are not protected. After collection, we immediately placed them in 95% ethanol for preservation and all efforts were made to ameliorate any suffering of the animals.\n\nA total of 390 individual C. mitella were collected from six locations in Fujian Province, China, during a survey conducted between July 2020 and September 2021. The collection site information is depicted in Figure 1. The specimens were stored in 95% ethanol at −20°C and muscle tissue was then extracted for DNA isolation.\n\nND=Ningde, FZ=Fuzhou, PT=Putian, QZ=Quanzhou, XM=Xiamen, ZZ=Zhangzhou.\n\nThe amplification of the mitochondrial COI gene was carried out using the Lco1490/Hco2198 primers (Folmer et al., 1994) in a 25 μL reaction volume. The reaction consisted of 12 μL Taq plus Master Mix II (Dye Plus), 1 μL each of the 10 μM primer concentration, 1 μL of DNA extract, and 11 μL nuclease-free water. The PCR thermal cycling profile was as follows: 94°C for 1 min, 15 cycles of denaturation at 94°C for 45 sec, annealing at 43°C (+0.5°C per cycle) temperature for 35 sec, extension at 72°C for 45 sec, followed by 20 cycles annealing at 50°C, with a final extension at 72°C for 10 mins. The PCR products were screened for quality control purposes on a 1.0% agarose gel. The sequencing in both directions was carried out by Sangon Biotech (Shanghai).\n\nMEGA 7.0 was used to edit and aligned the sequences, and calculate their base content. The identification of haplotypes was performed using the software DnaSP version 5.0 (Rozas et al., 2003), and the results were submitted to the GenBank database (accession numbers: ON495446 - ON495585). To investigate the relationships among haplotypes, we utilized NETWORK software version 4.613 (Bandelt et al., 1999) for visualization, and constructed a phylogenetic tree using the neighbor-joining (NJ) method with 1000 bootstrap replicates to assess branch reliability. We then calculated molecular diversity parameters using DNASP version 5.10.01 (Librado and Rozas, 2009) and Arlequin version 3.5 (Excoffier and Lischer, 2010), including haplotype diversity (h), nucleotide diversity (π) for each population, and analysis of molecular variance (AMOVA). To study demographic history, we evaluated the mismatch distribution and neutrality statistics, such as Tajima's D (Tajima, 1989) and Fu's FS test (Fu, 1997). In the event of a population expansion, we estimated the time of expansion (t) using τ=2μt (Rogers and Harpending, 1992), where we assumed a mutation rate of 3.1% per million years and a generation time of 1 year (Campo et al., 2010).\n\n\nResults\n\nIn this study, a 683 base pair (bp) segment of the COI gene was obtained from 390 individuals sampled from six populations. The average composition of the four nucleotides (A, T, C, and G) was found to be 18.19%, 42.93%, 14.65%, and 24.22%, respectively. It was determined that none of the sequences contained premature stop codons, insertions, or deletions. A nucleotide pair frequency analysis of the entire dataset revealed the presence of 82 variable sites (12.00%) among 683 sites, including 38 parsimony informative sites and 44 singleton sites.\n\nA total of 84 haplotypes were identified among 390 individuals, with 59 of them being private and 25 being shared (Table 1, Figure 2). The most dominant haplotype H2 was identified in all six populations, accounting for 57.44% (224/390) of all C. mitella specimens. Two haplotypes (H5 and H9) were shared by populations from five localities, while 59 haplotypes (accounting for 70.24%) were private. The ND population exhibited the highest number of unique haplotypes (32), followed by PT (27), FZ (20), QZ (19), ZZ (17), and XM (12), according to Table 2. The average haplotype diversity (h) was calculated to be 0.660, with the XM population showing the lowest value (0.475) and the ND population showing the highest value (0.789). The average nucleotide diversity (π) was found to be 0.0018, with a range of 0.0016 in the XM population to 0.0025 in the ND population (Table 2).\n\nIn order to analyze the genetic structure of C. mitella populations, molecular variation analysis (AMOVA) and pairwise FST values were employed. Results from the AMOVA analysis indicated that 99.77% of the genetic variation was found within populations, however, 0.23% were corresponded to among-population variation (Table 3). The ΦST values were not significantly different from zero in the six populations (ΦST=0.00225), indicating a lack of significant genetic variation among these populations. The pairwise population FST estimates obtained through an exact test were generally low, ranging from 0.00574 to 0.01144 among the six populations (Table 4). A neighbor-joining (NJ) tree constructed using 84 haplotypes demonstrated a shallow genetic structure (illustrated in Figure 3).\n\nThe neutrality tests, including Tajima's D and Fu's FS showed significantly negative results for all populations of C. mitella, indicating a recent population expansion or evidence of purifying selection (Table 5). The unimodal pattern observed in the mismatch distribution analysis of COI haplotypes (Figure 4) supports the hypothesis of a sudden population expansion. Furthermore, the populations displayed no significant values for the SSD and raggedness index analysis, ranging from 0.00075 to 0.09248 and 0.045 to 0.135, respectively (Table 5). These findings provide evidence of a good fit between the observed and expected distributions. Using the molecular clock estimates of other barnacle species, the population expansion of C. mitella is estimated to have taken place approximately 15,000 years ago.\n\n* Indicate that values are significant in the same group (P<0.05).\n\n\nDiscussion\n\nThe investigation of genetic diversity is the foundation for understanding the evolution of life and species diversity. By examining genetic diversity, we gain insights into the genetic composition of a population, its evolutionary history, and the mechanisms behind variation and evolution (Wang et al., 2019; Zheng et al., 2019). A major method for studying genetic diversity is molecular genetics techniques, such as sequencing the DNA of individuals or populations. In this research, the mitochondrial COI gene was used to examine the genetic diversity and population structure of C. mitella in the Fujian province. Results showed an average haplotype diversity (h) of 0.660 and a nucleotide diversity (π) of 0.00182, with 84 haplotypes identified and a star-like haplotype network (Figure 2). Out of the haplotypes, 59 were detected only at single localities, while the other 25 were present in two or more locations (Table 2). The results indicate that the C. mitella in Fujian province has a medium to high level of genetic diversity, with a low nucleotide diversity. This is comparable to the findings in other invertebrates, such as Portunus trituberculatus (h=0.582, π=0.00158) (Liu et al., 2009), but higher than those observed in China (h=0.490, π=0.00158), and lower than the Korean population (h=0.909, π=0.00550) (Yoon et al., 2013). The results of this study suggest that the C. mitella in Fujian province experienced a rapid population expansion from an ancestral population with a small effective size. This is indicated by the presence of rare haplotypes and low nucleotide diversity. This phenomenon could be attributed to a sudden increase in population size, which resulted in the preservation of rare haplotypes that would otherwise have been lost due to genetic drift (Zane et al., 2006). The small effective population size also suggests that this process of expansion occurred relatively recently, as a larger population size would have resulted in the elimination of these rare haplotypes over time (Nehemia et al., 2019).\n\nThis study of the genetic diversity of C. mitella populations in Fujian province found no evidence of a phylogeographic structure, as supported by the pairwise FST statistics and AMOVA analyses.\n\nThe results of the neighbor-joining tree analysis indicate that the haplotype relationships of C. mitella in Fujian province are shallow and there is no clear geographic association. This may be due to high gene flow among populations. The findings of this study suggest that the high dispersal capability of C. mitella's planktonic larvae is a key factor in promoting gene flow across vast geographic areas among invertebrate populations, thus maintaining or increasing genetic diversity. The duration of the larval stage, which can last up to 14 days (Yuan et al., 2016), enables C. mitella to disperse over long distances. The distribution of C. mitella populations is also influenced by a range of physical oceanographic factors, such as the presence of physical barriers, ocean currents, and wind patterns (Schilling et al., 2020).\n\nThe results of Tajima's D and Fu's Fs neutrality tests in all localities of C. mitella showed negative and significant values (Table 5), indicating a recent population expansion. This conclusion is further supported by the unimodal mismatch distribution, high haplotype diversity, and low nucleotide diversity. The estimated date of the population expansion is estimated to be around 15,000 years ago, during the Pleistocene. The Pleistocene glaciations have been shown to significantly impact the population structure of marine species, with a reduction in population size during glacial periods and rapid expansion during interglacial periods (Wilson and Eigenmann Veraguth, 2010). This pattern of demographic fluctuations has directly influenced the distribution and population size of the C. mitella species.\n\nIn summary, the present study aimed to investigate the genetic diversity of C. mitella populations along the Fujian coast using mitochondrial COI gene analysis. Results revealed medium to high levels of haplotype diversity and low nucleotide diversity, with 84 haplotypes identified and no significant genetic structure among populations. These findings suggest a high degree of gene flow and a lack of geographic associations. The demographic history of the species, including the influence of Pleistocene glaciations, may have played a role in shaping its current distribution and population size. The findings of this study emphasize the significance of genetic studies to a comprehensive understanding of the population genetics of C. mitella, particularly to inform its conservation and management. Further research using more populations and more sensitive molecular markers is needed to gain a more complete picture.", "appendix": "Data availability\n\nNCBI: Capitulum mitella voucher AJ1 cytochrome c oxidase subunit I (COX1) gene, partial cds; mitochondrial. Accession number: ON495446; https://identifiers.org/ncbiprotein:ON495446 (Xing et al., 2022a).\n\nNCBI: Capitulum mitella voucher SS15 cytochrome c oxidase subunit I (COX1) gene, partial cds; mitochondrial. Accession number: ON495585.1; https://identifiers.org/ncbiprotein:ON495585.1 (Xing et al., 2022b).\n\n\nReferences\n\nAjao AM, Nneji LM, Adeola AC, et al.: Genetic diversity and population structure of the native Western African honeybee (Apis mellifera adansonii Latreille, 1804) in Nigeria based on mitochondrial COI sequences. Zool. Anz. 2021; 293: 17–25. Publisher Full Text\n\nBandelt H-J, Forster P, Röhl A: Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 1999; 16: 37–48. PubMed Abstract \| Publisher Full Text\n\nCampo D, Molares J, Garcia L, et al.: Phylogeography of the European stalked barnacle (Pollicipes pollicipes): identification of glacial refugia. Mar. Biol. 2010; 157: 147–156. Publisher Full Text\n\nExcoffier L, Lischer HE: Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 2010; 10: 564–567. PubMed Abstract \| Publisher Full Text\n\nFolmer O, Black M, Hoeh W, et al.: DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 1994; 3: 294–299. PubMed Abstract\n\nFu Y-X: Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 1997; 147: 915–925. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJones D: Barnacles of the Cocos (Keeling) Islands. Atoll Res. Bull. 1994; 413: 1–7. Publisher Full Text\n\nLee C, Shim JM, Kim CH: Larval development of Capitulum mitella (Cirripedia: Pedunculata) reared in the laboratory. J. Mar. Biol. Assoc. U. K. 2000; 80: 457–464. Publisher Full Text\n\nLibrado P, Rozas J: DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009; 25: 1451–1452. PubMed Abstract \| Publisher Full Text\n\nLim JT, Hwang UW: The complete mitochondrial genome of Pollicipes mitella (Crustacea, Maxillopoda, Cirripedia): non-monophylies of maxillopoda and crustacea. Mol. Cells. 2006 Dec 31; 22(3): 314–322. PubMed Abstract\n\nLiu Y, Liu R, Ye L, et al.: Genetic differentiation between populations of swimming crab Portunus trituberculatus along the coastal waters of the East China Sea. Hydrobiologia. 2009; 618: 125–137. Publisher Full Text\n\nNehemia A, Ngendu Y, Kochzius M: Genetic population structure of the mangrove snails Littoraria subvittata and L. pallescens in the Western Indian Ocean. J. Exp. Mar. Biol. Ecol. 2019; 514-515: 27–33. Publisher Full Text\n\nOrtega-Villaizán Romo MDM, Suzuki S, Nakajima M, et al.: Genetic evaluation of interindividual relatedness for broodstock management of the rare species barfin flounder Verasper moseri using microsatellite DNA markers. Fish. Sci. 2006; 72: 33–39. Publisher Full Text\n\nRen G, Ma H, Ma C, et al.: Genetic diversity and population structure of Portunus sanguinolentus (Herbst, 1783) revealed by mtDNA COI sequences. Mitochondrial DNA Part A. 2017; 28: 740–746. PubMed Abstract \| Publisher Full Text\n\nRogers AR, Harpending H: Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 1992; 9: 552–569. PubMed Abstract\n\nRozas J, Sánchez-DelBarrio JC, Messeguer X, et al.: DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 2003; 19: 2496–2497. PubMed Abstract \| Publisher Full Text\n\nSchilling HT, Everett JD, Smith JA, et al.: Multiple spawning events promote increased larval dispersal of a predatory fish in a western boundary current. Fish. Oceanogr. 2020; 29: 309–323. Publisher Full Text\n\nTajima F: Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989; 123: 585–595. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang S-H, Zhang C, Shang M, et al.: Genetic diversity and population structure of native mitten crab (Eriocheir sensu stricto) by microsatellite markers and mitochondrial COI gene sequence. Gene. 2019; 693: 101–113. PubMed Abstract \| Publisher Full Text\n\nWilson AB, Eigenmann Veraguth I: The impact of Pleistocene glaciation across the range of a widespread European coastal species. Mol. Ecol. 2010; 19: 4535–4553. PubMed Abstract \| Publisher Full Text\n\nXing, et al.: Capitulum mitella voucher AJ1 cytochrome c oxidase subunit I (COX1) gene, partial cds; mitochondrial. [Data set]. NCBI GenBank. 2022a. Accession number: ON495446. Reference Source\n\nXing, et al.: Capitulum mitella voucher SS15 cytochrome c oxidase subunit I (COX1) gene, partial cds; mitochondrial. [Data set]. NCBI GenBank. 2022b. Accession number: ON495585.1. Reference Source\n\nXu L, Wang L, Ning J, et al.: Diversity of marine planktonic ostracods in South China Sea: a DNA taxonomy approach. Mitochondrial DNA Part A. 2019; 30: 118–125. Publisher Full Text\n\nYoon M, Jung J-Y, Kim DS: Genetic diversity and gene flow patterns in Pollicipes mitella in Korea inferred from mitochondrial DNA sequence analysis. Fish Aquat. Sci. 2013; 16: 243–251. Publisher Full Text\n\nYuan T-P, Huang Y-P, Miao S-Y, et al.: Genetic diversity and population structure of Capitulum mitella (Cirripedia: Pedunculata) in China inferred from mitochondrial DNA sequences. Biochem. Syst. Ecol. 2016; 67: 22–28. Publisher Full Text\n\nZane L, Marcato S, Bargelloni L, et al.: Demographic history and population structure of the Antarctic silverfish Pleuragramma antarcticum. Mol. Ecol. 2006; 15: 4499–4511. PubMed Abstract \| Publisher Full Text\n\nZheng J-H, Nie H-T, Yang F, et al.: Genetic variation and population structure of different geographical populations of Meretrix petechialis based on mitochondrial gene COI. J. Genet. 2019; 98: 1–9. Publisher Full Text" }	[ { "id": "165504", "date": "17 Apr 2023", "name": "Jun Sun", "expertise": [ "Reviewer Expertise Molecular biological oceanography" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present an interesting study on Genetic diversity and population structure of Capitulum mitella (Linnaeus, 1767) in Fujian (China) by mtDNA COI sequences. The bright side of the manuscript is that to provide the current genetic structure of the species in Fujian (China) using mtDNA COI sequences. However, some points are missing (mentioned below) in the manuscript. Therefore, I would like to make some suggestions to improve the quality of the paper as below:\n“ C. mitella is a dominant organism in intertidal coastal ecosystems with a widespread distribution throughout warmer regions of the Indo-Pacific, from Madagascar to southern Japan.” Please rephase the sentence. Ecosystem services of the species can be mentioned. More context is needed, alone this is subjective.\n\n“Mitochondrial DNA (mtDNA) is widely used as an ideal marker for investigating genetic diversity and population structure due to its rapid evolutionary rate, non-recombining nature, and simple amplification procedure (Ren et al., 2017; Xu et al., 2019).” The authors should explain the importance of using different genetic markers, including COI gene, to better understand the current population structure.\n\nPlease could you include the populations to be studied in the main text? They are only detailed in the caption of figure. Please include the full name in addition to the abbreviation. Some information describing the study area would be great.\n\nIn the section \"DNA extraction and PCR amplification\", how the DNA was extracted is missing. Please indicate the methodology used. Also indicate the commercial name of the reagents used.\n\nIn the sentence, 'MEGA 7.0 was used to edit and align the sequences,' the word 'aligned' should be changed to 'align'.\n\nPlease specify what you mean by SSD before the acronym (sum of squared deviation) and include the acronym after raggedness index analysis (Rg).\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": "9888", "date": "13 Jul 2023", "name": "bingpeng xing", "role": "Author Response", "response": "1.“ C. mitella is a dominant organism in intertidal coastal ecosystems with a widespread distribution throughout warmer regions of the Indo-Pacific, from Madagascar to southern Japan.” Please rephase the sentence. Ecosystem services of the species can be mentioned. More context is needed, alone this is subjective. Thank you. We have already rewritten that section. 2.“Mitochondrial DNA (mtDNA) is widely used as an ideal marker for investigating genetic diversity and population structure due to its rapid evolutionary rate, non-recombining nature, and simple amplification procedure (Ren et al., 2017; Xu et al., 2019).” The authors should explain the importance of using different genetic markers, including COI gene, to better understand the current population structure. Thank you for your suggestion. We appreciate the importance of incorporating different genetic markers, including the COI gene, to enhance our understanding of the current population structure. We have already rewritten that section and made some additions. 3. Please could you include the populations to be studied in the main text? They are only detailed in the caption of figure. Please include the full name in addition to the abbreviation. Some information describing the study area would be great. Thank you for your suggestion. We have made the necessary revisions. 4. In the section \"DNA extraction and PCR amplification\", how the DNA was extracted is missing. Please indicate the methodology used. Also indicate the commercial name of the reagents used. Thank you. We have already added that section as per your request. 5. In the sentence, 'MEGA 7.0 was used to edit and align the sequences,' the word 'aligned' should be changed to 'align'. Thank you. The word 'aligned' has been changed to 'align'. 6. Please specify what you mean by SSD before the acronym (sum of squared deviation) and include the acronym after raggedness index analysis (Rg). Thank you. We have made the necessary revisions as this suggestion." } ] }, { "id": "172535", "date": "30 May 2023", "name": "Alex Nahnson Nehemia", "expertise": [ "Reviewer Expertise Aquatic resource 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\nThis manuscript is great. It involves mitochondrial COI sequencing as well as some well-accepted basic analysis and interpretations.\nHowever, the manuscript is suitable for publication following some minor revisions\nAlthough the authors stated in the introduction that Capitulum mitella species is a stalked barnacle that aggregates and settles extensively on rocky shores, the authors should clearly at least describe the developmental mode of the study species because it is well-known that developmental type (for example, planktotrophic species, direct-developing species without a pelagic larval phase) plays a significant role in determining population genetic structure of marine invertebrates.\n\nI advise utilizing MEGA software that is more recent, such as MEGA 11, rather than the old version MEGA 7.\n\nAlthough the authors performed a pairwise FST test, I advise doing additional statistical tests to support the findings of population genetic structure. As a result, I advise using hierarchical AMOVA. To investigate every clustering possibility, SAMOVA would be the best choice. In order to determine whether isolation by distance (IBD) may be influencing the genetic structure of the population in this species, the author may also need to undertake testing for IBD.\n\nI recommend performing post hoc analysis, such as sequential Bonferroni correction for pairwise analysis, because it is advised to perform a multiple-comparison correction when several dependent or independent statistical tests are being performed simultaneously. The authors indicated how molecular variation analysis (AMOVA) was performed in the methodology part, but did not describe how pairwise population FST estimates were carried out; instead, the description is shown in the section of results.\n\nIn order to compare the results of the genetic diversity and demographic history with the effective population size of Capitulum mitella, the authors can estimate this population size using software like n-MIGRATES.\n\nAdditionally, authors must confirm whether they used pairwise population FST (use conversional F-statistics) or ΦST (calculate distance matrix) for subpopulation comparisons.\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": "9889", "date": "13 Jul 2023", "name": "bingpeng xing", "role": "Author Response", "response": "1. Although the authors stated in the introduction that the Capitulum mitella species is a stalked barnacle that aggregates and settles extensively on rocky shores, the authors should clearly at least describe the developmental mode of the study species because it is well-known that developmental type (for example, planktotrophic species, direct-developing species without a pelagic larval phase) plays a significant role in determining population genetic structure of marine invertebrates. Thank you very much for your valuable suggestion. We have supplemented the content accordingly. C. mitella is a dominant organism in intertidal coastal ecosystems with a widespread distribution throughout warmer regions of the Indo-Pacific, from Korea through India to the West Pacific Ocean. It like other barnacles, has a biphasic life history: sessile adults and planktonic larvae. They have six naupliar stages and one cyprid stage, when it fixes itself in place, undergoes metamorphosis, and becomes a sessile juvenile(Lee et al., 2000). It is commonly found attached to rocks in the lower part of the intertidal zone, particularly in areas with strong currents. It tends to occur in dense populations, often crowded together in cracks and grooves on otherwise smooth rocky surfaces. Its attachment to rocks provides shelter and refuge for various organisms, influencing their distribution and interactions. Additionally, the population density of C. mitella in cracks and grooves can shape the physical structure of the intertidal zone. C. mitella also plays a vital role in intertidal ecosystems by filtering food particles from the water. This feeding behavior contributes significantly to nutrient cycling and energy flow within the ecosystem. By consuming organic detritus, algae, and small invertebrates, C. mitella helps maintain the overall productivity and balance of the intertidal community. 2. I advise utilizing MEGA software that is more recent, such as MEGA 11, rather than the old version MEGA 7. Thank you very much for your suggestion， we have made the changes as per your request. 3. Although the authors performed a pairwise FST test, I advise doing additional statistical tests to support the findings of population genetic structure. As a result, I advise using hierarchical AMOVA. To investigate every clustering possibility, SAMOVA would be the best choice. In order to determine whether isolation by distance (IBD) may be influencing the genetic structure of the population in this species, the author may also need to undertake testing for IBD. Thank you very much for your feedback. This suggestion is excellent and addresses the question of whether isolation by distance (IBD) is influencing the genetic structure of the population. In our study, we focused only on resources within a single province, where the geographic distances were relatively small, and no genetic differentiation was observed among populations. Therefore, we did not employ this method. However, moving forward, we will adopt your recommended approach to investigate the distribution, dispersal, genetic structure, and variations of this species along the Chinese coast. By doing so, we hope to obtain more comprehensive and in-depth results. 4. I recommend performing post hoc analysis, such as sequential Bonferroni correction for pairwise analysis, because it is advised to perform a multiple-comparison correction when several dependent or independent statistical tests are being performed simultaneously. The authors indicated how molecular variation analysis (AMOVA) was performed in the methodology part, but did not describe how pairwise population FST estimates were carried out; instead, the description is shown in the section of results. Thank you for your suggestion. We have already supplemented that section. 5. In order to compare the results of the genetic diversity and demographic history with the effective population size of Capitulum mitella, the authors can estimate this population size using software like n-MIGRATES. Thank you for your suggestion. We highly appreciate your proposed approach, and similar to the third point, we will adopt this method to study the distribution, dispersal, genetic structure, and variations of this species along the Chinese coast, to achieve more comprehensive and in-depth results through this approach. 6. Additionally, authors must confirm whether they used pairwise population FST (use conversational F-statistics) or ΦST (calculate distance matrix) for subpopulation comparisons. Thank you for your suggestion. We have already confirmed and supplemented this section. Thank you once again for your valuable suggestions." } ] } ]	1	https://f1000research.com/articles/12-238
https://f1000research.com/articles/12-93/v1	24 Jan 23	{ "type": "Research Article", "title": "Computer-aided drug design approaches applied to screen natural product’s structural analogs targeting arginase in Leishmania spp", "authors": [ "Haruna Luz Barazorda-Ccahuana", "Luis Daniel Goyzueta-Mamani", "Mayron Antonio Candia Puma", "Camila Simões de Freitas", "Grasiele de Sousa Vieria Tavares", "Daniela Pagliara Lage", "Eduardo Antonio Ferraz Coelho", "Miguel Angel Chávez-Fumagalli", "Haruna Luz Barazorda-Ccahuana", "Luis Daniel Goyzueta-Mamani", "Mayron Antonio Candia Puma", "Camila Simões de Freitas", "Grasiele de Sousa Vieria Tavares", "Daniela Pagliara Lage", "Eduardo Antonio Ferraz Coelho" ], "abstract": "Introduction: Leishmaniasis is a disease with high mortality rates and approximately 1.5 million new cases each year. Despite the new approaches and advances to fight the disease, there are no effective therapies. Methods: Hence, this study aims to screen for natural products' structural analogs as new drug candidates against leishmaniasis. We applied Computer-aided drug design (CADD) approaches, such as virtual screening, molecular docking, molecular dynamics simulation, molecular mechanics–generalized Born surface area (MM–GBSA) binding free estimation, and free energy perturbation (FEP) aiming to select structural analogs from natural products that have shown anti-leishmanial and anti-arginase activities and that could bind selectively against the Leishmania arginase enzyme. Results: The compounds 2H-1-benzopyran, 3,4-dihydro-2-(2-methylphenyl)-(9CI), echioidinin, and malvidin showed good results against arginase targets from three parasite species and negative results for potential toxicities. The echioidinin and malvidin ligands generated interactions in the active center at pH 2.0 conditions and hydrogen bonds enhancing enzyme–ligand coupling. Conclusions: This work suggests the potential anti-leishmanial activity of the compounds and thus can be further in vitro and in vivo experimentally validated.", "keywords": [ "leishmaniasis", "Leishmania arginase", "computer-aided drug design", "molecular dynamics simulation", "antiprotozoal agents", "drug discovery" ], "content": "Introduction\n\nLeishmaniasis is an ancient disease that has been described in archaic ceramics, statues, and writings, and in molecular findings from mummified human bodies and archaeological material.1 The disease causes high morbidity and mortality worldwide, where about one billion people are at risk of infection across 98 countries, with over 1.5 million new cases and 20,000-40,000 deaths reported each year.2,3 The increase in leishmaniasis incidence and prevalence is mainly attributed to several risk factors that are man-propelled,4 whereas, in many regions, the transmission pattern shows expansion, with new territories affected by the disease.5,6 Also, leishmaniasis has gained greater importance in HIV-infected patients as an opportunistic infection in areas where both pathogens are endemic.7 Leishmaniasis is caused by the protozoan parasites of the genus Leishmania (Kinetoplastida: Trypanosomatidae), which has a digenetic life cycle that alternates between the midgut of sandflies and the phagolysosomes of mammalian macrophages.8 When exposed to extreme environmental changes, such as low pH, the parasites respond to the acidification of their environment by changing the pattern of expression of several proteins.9,10 About 21 parasite species can infect mammals and many of them cause human disease11 and the clinical manifestations depend on both the parasite species and the hosts’ immune response,12 varying from a chronic, slow-to-heal disease known as tegumentary leishmaniasis (TL), to a potentially fatal form of the disease, namely, visceral leishmaniasis (VL), in which parasites disseminate to internal organs, such as the liver, spleen, and bone marrow.13\n\nDespite significant progress, the development of a human vaccine remains hampered by significant gaps in the development pipeline14; and the treatment against disease has used drugs that cause side effects in the patients, such as myalgia, arthralgia, anorexia, fever, and urticaria, as well as toxicity in the liver, kidneys, and spleen.15 Therefore, the necessity for cost-effective treatment which promotes the cure completely, with few side effects, low relapse rates, high effectiveness, and a reduction of toxicity remains.16 The number of drugs derived from natural products (NPs) present in the total amount of drug launchings in the market over four decades represents a significant source of new pharmacological entities,17 while a series of secondary plant-purified products has already been described with leishmanicidal potential.18–21 Likewise, computer-aided drug design (CADD) can be defined as computational approaches that are used to discover, develop, and analyze drug and active molecules with similar biochemical properties,22 and this has become crucial for screening of potential metabolite databases from natural sources that can be repurposed against diseases for faster, safer, and cheaper drug development.23,24 The strategy of target-based drug discovery is used extensively by the pharmaceutical industry and has been applied to leishmaniasis.25,26 However, in silico methods to identify new potential drugs to be applied against leishmaniasis present limitations, such as the dependency on the quality, accuracy, and completeness of the information present in databases.27 The arginase (ARG) enzyme has recently obtained considerable attention since new studies have highlighted it as a potential therapeutic target in leishmaniasis.28 ARG is the first enzyme of the polyamine pathway and catalyzes the conversion of L-arginine to L-ornithine and urea, down-regulating the polyamine pathway, affecting the parasite growth and infectivity.29 The inhibition results in a lack of protection against reactive oxygen species (ROS), which damages Leishmania’s genetic material and ultimately leads it to die by apoptosis.30 As a result, various NPs have demonstrated anti-arginase action,31,32 and the majority of these NPs have also demonstrated a strong affinity against human ARG.33 In the current study, we used CADD techniques, such as virtual screening, molecular docking, and molecular dynamics simulations, to identify structural analogs of NPs that have demonstrated anti-leishmanial and anti-ARG activities and that may bind specifically to the Leishmania ARG. Our goal was to identify a promising compound candidate that could be used in the treatment of leishmaniasis.\n\n\nMethods\n\nThe search for natural products with anti-leishmanial and anti-ARG activities was performed at the Nuclei of Bioassays, Ecophysiology, and Biosynthesis of Natural Products Database (NuBBEDB) online web server (version 2017) (http://nubbe.iq.unesp.br/portal/nubbe-search.html, accessed on 23 January 2022), which contains the information of more than 2,000 natural products and derivatives34; while the “anti-leishmanial property” was selected in the biological properties segment of the web server. The bibliographic data extraction, regarding the compounds found in NuBBEDB, was performed from the National Center for Biotechnology Information (NCBI) databases (https://www.ncbi.nlm.nih.gov/pubmed/, accessed on 07 February 2022); and the simplified molecular-input line-entry system (SMILES) was searched and retrieved from PubChem server (https://pubchem.ncbi.nlm.nih.gov/, accessed on 10 February 2022).35 Likewise, the physicochemical properties: total molecular weight (MW), octanol/water partition coefficient (iLOGP), number of H-bond acceptors (HBAs), number of H-bond donors (HBDs), and the topological polar surface area (TPSA), for each compound were calculated within the Osiris DataWarrior v5.2.01 software36; and, the rotatable bonds (RB); number of heavy atoms (NHA); and synthetic accessibility (SynAcce) were calculated within SwissADME server (http://www.swissadme.ch/index.php, accessed on 15 February 2022).37\n\nThe SMILES from the compounds were used for high throughput screening to investigate structural analogs by the SwissSimilarity server (http://www.swisssimilarity.ch/index.php, accessed on 01 March 2022)38; whereas the commercial class of compounds was selected and the Zinc-drug like compound library, which comprises 9’205’113 molecules, with the combined screening method, was chosen for the high throughput screening to achieve the best structural analogs. The zinc-drug like compound library selection allowed the screening of compounds in the subsequent commercially available chemical libraries: Enamine, ChemBridge, Maybridge, Asinex, AsisChem, Otava, SPECS, TimTec, Vitas, Life Chemicals, ChemDiv, and Innovapharm.39 Threshold values for positivity were selected by default parameters. Also, the FASTA sequences of the ARG sequences from L. infantum (A4IB49), L. mexicana (Q6TUJ5), L. brasiliensis (A4HMH0), and Homo sapiens (P05089) were retrieved from UniProt database (http://www.uniprot.org/, accessed on 03 March 2022) (RRID:SCR_002380), and subjected to automated modeling in SWISS-MODEL40 (RRID:SCR_018123).\n\nFurthermore, the compounds were imported into Open Babel (RRID:SCR_014920) within the Python Prescription Virtual Screening Tool41 and subjected to energy minimization. PyRx (RRID:SCR_018548) performs structure-based virtual screening applying molecular docking simulations using the AutoDock Vina tool42 (RRID:SC_011958), whereas the drug targets were uploaded as macromolecules. For the analysis, the search space encompassed the whole of the modeled 3D models, and the molecular docking simulation was then run at an exhaustiveness of 8 and set to only output the lowest energy pose. The Osiris Data Warrior software was employed to calculate the potential tumorigenic, mutagenic, and reproductive effects, and irritant action of selected compounds predicted by comparison with a precompiled fragment library derived from the Registry of Toxic Effects of Chemical Substances (RTECS) database.36\n\nLigands preparation was based on the results from the virtual screening analysis; while the geometry optimization of these compounds was made in the Avogadro v. 1.2.0 program43 (RRID:SCR_015983) and the ACPYPE (AnteChamber PYthon Parser interfacE)44 server was employed to generate the topologies and parameters for molecular dynamics (MD) simulation. We determined the 3D structural conformation of L. infantum ARG by homology modeling with L. mexicana ARG (PDB ID: 4ITY) as a template in the SWISS-MODEL online server40 and afterwards we determined the protonation/deprotonation states at pH 2.0 and pH 7.0 in the PDB2PQR.45 Since ARG is a trimeric metalloprotein with three active sites binding to two manganese atoms (Mn+2), we fixed the Mn+2 coordination with active site residues and a hydroxyl molecule (OH−1), considering the following coordination: first Mn+2 with His114 (ND1), ASP137 (OD2), ASP141 (OD2), ASP243 (OD2) and the second Mn+2 with ASP137 (OD1), HIS139 (ND1), ASP243 (OD1) and ASP245 (OD2). The MD simulation was reproduced in GROMACS v. 202046 (RRID:SCR_014565), considering the AMBER9947 force field. The systems were solvated with the TIP3P water model, and Na+1 or Cl−1 ions were added for neutralization. The box size was 12×12×12 nm. Thus, the energy minimization was performed with the steep-descent algorithm with 20000 steps of calculation. The MD simulation was done in two steps; the first step was in the canonical ensemble (NVT) considering distance restraint of Mn+2 to the active site by 5 ns. The second step was the MD production in the isothermal-isobaric ensemble (NPT) with a time of 100 ns. The V-rescale48 thermostat was used to regulate the temperature at 309.65 K and the Parrinello-Rahman barostat at a reference pressure of 1 bar. Molecular docking was done with the DockThor online server49; in the last frame, the molecular docking at two pH conditions was used as a receptor. A grid was considered in the active site of ARG (ChainA). The complex models with the best scores were chosen, and these were subsequently simulated in the isothermal-isobaric ensemble NPT for 10 ns. Gibbs free energy was calculated by the molecular mechanics-generalized Born surface area (MM-GBSA)50 method in gmx_MMPBSA tool based on AMBER’s MMPBSA.py, and AmberTools2051 (RRID:SCR_014565) package was used. Additionally, to compare the binding free energy studies, we include the free energy perturbation (FEP) analysis where the Bennett acceptance ratio (BAR) calculates the free energy differences.52 This analysis is achieved with the free energy implementation by the GROMACS tool.\n\nResults were entered into Microsoft Excel (version 10.0, Microsoft Corporation, Redmond, WA, USA) spreadsheets and analyzed by GraphPad Prism version 9.4.0 for Windows, GraphPad Software, San Diego, California USA, (http://www.graphpad.com) (RRID:SCR_002798). To evaluate the correlation between the binding affinities of the compounds against the protein targets, they were placed in a linear regression plot and analyzed by Pearson’s correlation coefficient; differences were considered significant when p<0.05. Further, the selectivity score of binding affinities was calculated as described53; where a selectivity value >1 indicates a priority of the compounds to bind to the parasite ARG over the human target. Heatmaps were constructed in the R programming environment (version 4.0.3) using the “heatmap 2” function in the package “gplots”.54\n\n\nResults\n\nIn this work, a search was performed in the NuBBEDB for NPs that had been described with anti-leishmanial and anti-ARG activities. The search in the database resulted in 33 NPs described with anti-leishmanial activity, whereas six of them had also been described as inhibitors of ARG activity. Startlingly, all the NPs selected were described in the same article, in which the compounds were isolated from Byrsonima coccolobifolia species and tested for in vitro anti-ARG activity.55 Since no anti-leishmanial activity was reported in the article, a cross-reference search for each compound was performed in the PubMed database to validate the properties. Thereafter, the SMILES from quercetin (NuBBE_122), isoquercetin (NuBBE_123), quercitrin (NuBBE_161), (+)-syringaresinol (NuBBE_214), catechin (NuBBE_287) and (-)-epicatechin (NuBBE_866) were obtained from PubChem and submitted to physicochemical properties analysis related to an absorption, distribution, metabolism, and excretion (ADME) profile; Lipinski’s rule of five (MW, iLOGP, HBAs and HBDs),56 the quantitative estimate of drug-likeness (TPSA, RB, NHA and the number of alerts for undesirable substructures)57 and the synthetic accessibility,58 of the NPs are shown in Table 1.\n\nTo find structural analogs to the six NPs selected, a search of the SwissSimilarity server employing the commercial zinc-drug like compound library was performed, resulting in 400 analogs for each NP; however, the search comprised a high degree of redundancy between the analogs and a step in which duplicated compounds were excluded was executed, resulting in a total of 1499 unique compounds selected for virtual screening (Figure 1). The virtual screening results against Leishmania infantum and human ARG are plotted in Figure 1A, where a positive linear relationship between the binding affinities of the compounds toward both targets is shown [Pearson r:0.931; r2:0.868]. Later, aiming to select compounds that showed higher affinity toward L. infantum ARG, the selectivity was calculated, and compounds with scores >1 were screened, resulting in 25 compounds selected (Figure 1A). Since in vitro evidence of inter-species differences in the susceptibility of parasites to anti-leishmanial drugs has been reported,59 putative drug candidates must be active against several species of the parasite60; in this way, the selectivity of the compounds against L. mexicana and L. braziliensis ARG were also calculated and plotted in a heatmap; each compound’s results showed differences in their affinities profile (Figure 1B). Also, to select potential nontoxic candidates, the tumorigenic, mutagenic and reproductive effects, as well as irritant action were assessed for the 25 compounds (Figure 1C). Thus, the compounds 2H-1-benzopyran, 3,4-dihydro-2-(2-methylphenyl)- (9CI) (ZINC39120134) (Figure 1D), echioidinin (ZINC14807307) (Figure 1E), and malvidin (ZINC897714) (Figure 1F) were selected for further analysis, since they showed favorable binding affinities against the three parasite species targets and negative results for potential toxicities.\n\nBinding affinities toward L. infatum and H. sapiens ARG targets were analyzed by linear regression and Pearson’s correlation coefficient. Solid orange line: linear regression; dotted orange lines: 95% confidence intervals. The solid green square was calculated using the maximum binding affinities of the 6 NPs (A). Normalized binding affinities heatmap of 25 selected compounds on L. infantum, L. mexicana, and L. braziliensis against their human homolog (B). Binary heatmap showing positive (red) or negative (blue) predicted toxicities (C). Chemical structure of ZINC39120134 (D), ZINC14807307 (E), and ZINC897714 (F).\n\nL. infantum ARG is an enzyme with trimeric conformation (ChainA, ChainB, and ChainC) and its structure showed stable behavior during a 100 ns of MDS performed at pH 2.0 and pH 7.0 (Figure 2). Here we included the metal ions (Mn+2) and one hydroxyl molecule (OH−1) for each active site, and it was observed that some regions lose their structural conformation at pH 2.0 conditions (green color). In addition, compared to ARG at pH 7.0, ARG at pH 2.0 exhibits large structural alterations and high variations per residue (see Figure 3A and 3B). In Figure 3C, the radius of gyration shows lower compaction of whole protein during the MDS at pH 7.0 than at pH 2.0. The report of the trajectory of each complex system (enzyme-ligand) and the protein without ligand is shown in Figure 4. Since the root-mean-squared deviation (RMSD) is a noteworthy analysis to verify the similarity between a protein-bound and not bound ligand.61 The RMSD values in nm are presented that were taken from the ChainA of each protein in different pH conditions, whereas the enzyme-ligand systems presented greater conformational changes in the substrate-binding site (Figure 4A). Likewise, radius of gyration (RG) analysis verifies the compactness of protein structures, where the lowest RG demonstrates the tightest packing and high conformational stability.62 The results showed that, at pH 2.0, low compactness and a large broadening of the macromolecules are reported (Figure 4B). Figure 4C shows the root-mean-squared fluctuation (RMSF) per residue of the backbone, where high fluctuations were shown from residue 50 to 100 in both systems. From the enzyme-ligand simulation results, we take each simulation’s last frames (Figure 5). The ligand ZINC897714 generates exciting interactions in the active center at the pH conditions evaluated and, at pH 7.0, hydrogen bonds are observed, which benefits enzyme-ligand coupling.\n\nColors blue and green represent the cartoon representation of pH 2.0 and pH 7.0. The red box shows the active site of ARG.\n\n(A) RMSD is shown the conformational changes reported at pH 2.0. (B) SASA shows a greater solvent access surface area to ARG at pH 2.0 than at pH 7.0. (C) RG shows the same behavior as RMSD.\n\nMore significant conformational changes of ARG enzyme are shown at pH 2.0. (A) RMSD plot of ChainA concerning the whole protein. (B) RG analysis. (C) RMSF per residue of backbone.\n\n(A) Last frame at pH 2.0. and (B) Last frame at pH 7.0. Green represents the hydrophobic interaction between enzyme-ligand, color sky blue represents the hydrogen bond interaction.\n\nThe binding free energy analysis of pH 2.0 and pH 7.0 from the frames of each simulation is shown in Table 2. The propitious energetic contribution with a binding free energy of -15.665 kcal/mol (ZINC14807307/pH7) maximum and -0.149 kcal/mol (ZINC39120134/pH2) minimum were obtained. The estimated phase-gas binding free energy (ΔGgas) provided the highest energy contributions for ZINC14807307 in both pHs and ZINC39120134 at pH 7.0. Contrary, the van der Waals energies (ΔEvdW) provided the highest energy contributions at pH 2.0 in ZINC39120134.\n\nIt is well understood that hydrophobic interactions favorably contribute to binding. In the systems with ZINC897714, the electrostatic energies (ΔEele) contributed negatively to the binding enzyme-ligand, which is attributed to the total net positive charge of the ligand and the pocket residues (induced by the protonation states at pH 2.0 and pH 7.0). Despite this, the solvation energies (ΔGsolv) offset the positive electrostatic interactions, thus favorably contributing to the binding of ZINC897714 to ARG in both pHs (ZINC897714/pH2 = -539.120 kcal/mol and ZINC897714/pH7 = -17.590 kcal/mol). These results show that the protonation states at a given pH can positively or negatively favor the enzyme-ligand binding, where it is expected that at a pH above 7.0 the enzyme-ligand binding can be increased. Therefore, these electrostatic interactions make a substantial contribution.\n\nIn an attempt to improve the enzyme-ligand binding energy analysis, the FEP approach was used, which estimates the difference in free energy between two states (A state and B state) by slowly change from one state to another. A state corresponds to the initial state of free energy and B state corresponds to the final state. This study sampled 20 microstates with a time of 20 ns for each microstate; the results are presented in Table 3. Herein, it is observed that, at both pHs, the best compounds occurred in the following order: ZINC14807307 > ZINC897714 > ZINC39120134. On the other hand, the compounds ZINC14807307 and ZINC897714 are shown to be stable at pH 2.0 conditions.\n\n\nDiscussion\n\nThe World Health Organization (WHO) considers leishmaniasis to be one of the major neglected global diseases and responsible for millions of disability-adjusted life years (DALYs), representing one of the top burdens among the neglected tropical diseases.63 Worldwide, 13 countries have a high burden of VL (Bangladesh, China, Ethiopia, Georgia, India, Kenya, Nepal, Paraguay, Somalia, South Sudan, Spain, Sudan, and Uganda), and 11 have a high burden of TL (Afghanistan, Algeria, Colombia, Iran, Morocco, Pakistan, Peru, Saudi Arabia, Syrian Arab Republic, Tunisia, and Turkey), while Brazil has a high burden of both clinical forms.64 Thus, TL treatment choice is based on the clinical presentation and infecting species, while any person with VL signs and symptoms and a verified diagnosis warrants chemotherapy.65 The range of currently available drugs for treating leishmaniasis is relatively small and it includes repurposed molecules, such as amphotericin B, miltefosine, and paromomycin; while few new drug candidates reached clinical trials in the last decades.66,67 For these reasons, the investigation of new therapies has been very active recently, and a wide range of compounds have been identified as potential hits and leads.68 The unique and vast chemical diversity of NPs places them as a major component of the biologically relevant chemical space,69 while NP classes like alkaloids, coumarins, flavonoids, lignans, neolignans, quinones, and terpenoids have demonstrated anti-leishmanial activity.70 Several of these that target Leishmania ARG have been investigated for their potential as new drug candidates, although quercetin,71–73 catechin, (-)-epicatechin, (+)-syringaresinol, isoquercetin, quercitrin, resveratrol, and cinnamic acid derivatives had shown in vitro efficacy.31,33,74 Additionally, certain NPs had demonstrated favorable in vivo effectivity, including epigallocatechin gallate,75 gallic acid,76 rosmarinic acid,77 and quercetin.78,79 The equilibrium between biological activity and pharmacological qualities is one of several aspects, nevertheless, that restricts the translation of NPs into commercial drugs.80,81 In silico based drug repositioning potential for discovering new applications for existing drugs and for developing new drugs in pharmaceutical research and the industry has gained importance82,83; whereas, in the chemical structure and molecule information approach, the structural similarity is incorporated with molecular activity and other biological information to identify new associations.84\n\nThe present work aimed to apply CADD approaches to select analogs to NPs with known anti-leishmanial and anti-ARG activities; although results of the quercetin analogs, the anthocyanin malvidin (ZINC897714; PubChem CID: 159287), and the flavone echioidinin (ZINC14807307; PubChem CID: 15559079) showed favorable binding affinity to L. infantum, L. mexicana, and L. braziliensis ARG and no predicted toxicity. Besides that, in the ARG super-family, the active site is conserved in all organisms, which includes the coordination of divalent metal Mn2+,85 and differences between the parasite and its human homolog have been described,86,87 highlighting the possibility to target selectively the parasite enzyme. However, recently, cinnamides88 and 1-phenyl-1H-pyrazolo[3,4-d] pyrimidine synthetic derivatives89 have been described as potential selective inhibitors of parasite ARG and have shown in vitro anti-leishmanial activity. A major bottleneck of drug discovery for leishmaniasis was aimed at the in silico workflow proposed, which is that compounds must show activity in the acidic environment of the phagolysosome90; thus, the analyzed compounds in this work showed stable enzyme-ligand interaction and favorable binding free energy at pH 2.0 in MDS analysis. However, when taking into consideration the target product profile (TPP), proposed by the Drugs for Neglected Diseases initiative (DNDi), which includes regard for the oral route of administration for new candidates,91 both ADME profiles showed the potential for oral route administration and high bioavailability, but only malvidin results have been ratified by experimental studies published elsewhere.92–94 Furthermore, malvidin has shown the potential to be an antioxidant, anti-hypertensive, anti-inflammatory, anti-obesity, anti-osteoarthritis, anti-proliferative, and anticancer drug candidate,95–99 whereas to the best of our knowledge no research has been published studying the potential pharmacological activity of echioidinin. Anthocyanins are commonly found in many plants, while the most common types are cyanidin, delphinidin, pelargonidin, peonidin, petunidin, and malvidin, which are distributed in fruits and vegetables in 50%, 12%, 12%, 12%, 7%, and 7% proportions, respectively.100 These molecules are more stable at a lower pH solution, and in such conditions the flavylium cation formed enables the anthocyanin to be highly soluble in water.101 The physicochemical properties offered by anthocyanins should be considered of interest for anti-leishmanial drug discovery since the parasite is adapted to live in parasitophorous vacuoles of infected macrophages in mammalian hosts, where it survives, proliferates, and is responsible for the development of the active disease.102 Recently, the anthocyanidin profile of Arrabidaea chica has been examined and its anti-leishmanial activity analyzed,103 and carajurin (PubChem CID: 44257040) showed the highest activity against the intracellular parasites, altering all parameters of in vitro infection.104 Additionally, it has been shown that carajurin leads to a decrease in the mitochondrial membrane potential, an increase in ROS production, and cell death by late apoptosis in L. amazonensis.105 Furthermore, flavones showing anti-leishmanial potential have been described in the literature,106 whereas apigenin (PubChem CID: 5280443) and luteolin (PubChem CID: 5280445) have shown the potential of inhibiting the growth of L. amazonensis.107\n\nLimitations of the present study should be also mentioned, such as the protein dynamics and complex stabilities with MDS lasting within nanoseconds scales (0-100 ns), while most structural dynamics and biological activities of proteins occur within timescales of microseconds and milliseconds.108 Even so, complex dynamics and interactions between enzymes and ligands have been reported using nanosecond timescales.109,110 Additionally, the work did not include in vitro or in vivo validation. It is important to note that anti-leishmanial in vitro assays have drawbacks, including metabolic differences between the amastigote and promastigote stages,111 variations in drug effectiveness and susceptibility among parasites isolated from patients,112 and a variety of biochemical pathways linked to drug-resistant phenotypes in the parasite,113,114 which can lead to false positive results. Additionally, numerous animal models are used in the validation tests for VL and TL drug candidates; however, due to insufficient translation to human disease, their predictive value is frequently low. Furthermore, reliable main models for VL are frequently employed, including Syrian golden hamsters and BALB/c mice,115,116 while there are no validated animal models for TL since different species experience varied clinical symptoms, and current models lack human characteristics such as pathophysiology, symptomatology, and treatment response.117\n\n\nConclusion\n\nIn the first screening, this work identified three substances with natural products structural analogs with potential effects against Leishmania ARG using in silico analysis from the available data and research of natural products found in databases. The substances were: ZINC39120134 (3,4-dihydro-2-(2-methylphenyl)-(9CI)), ZINC14807307 (echioidinin) and ZINC897714 (malvidin), where the most suitable compounds were ZINC14807307 and ZINC897714, showing favorable binding affinity to L. infantum, L. mexicana, and L. braziliensis ARG, no potential toxicity and stability at pH 2.0; important factors due to the acidic environment of the phagolysosomes of mammalian hosts. Taking into consideration that the oral bioavailability of malvidin has experimental data published and that its pharmacological potential has been widely studied, the results presented in this work warrant further in vitro and in vivo studies using malvidin to confirm its potential as a drug candidate against leishmaniasis.", "appendix": "Data availability\n\nFigshare. Supplementary material. https://doi.org/10.6084/m9.figshare.21867822.v1. 118\n\nThis project contains the following underlying data:\n\n• Table S1. (Compounds obtained by chemical similarity against the natural products analyzed)\n\n• Table S2. (Virtual screening results of the compounds selected against L. infatum and H. sapiensarginase enzymes)\n\n• Table S3. (Virtual screening results of the compounds selected against L. braziliensis and L. mexicana arginase enzymes)\n\n• Table S4. (Toxicity prediction of the selected compounds)\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\nTuon FF, Neto VA, Amato VS: Leishmania: origin, evolution and future since the precambrian. FEMS Immunol. Med. Microbiol. 2008; 54(2): 158–166. PubMed Abstract \| Publisher Full Text\n\nAlvar J, Vélez ID, Bern C, et al.: Leishmaniasis worldwide and global estimates of its incidence. PLoS One. 2012; 7(5): e35671. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHotez PJ: The rise of leishmaniasis in the twenty-first century. Trans. R. Soc. 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PubMed Abstract \| Publisher Full Text\n\nD’Antonio EL, Ullman B, Roberts SC, et al.: Crystal structure of arginase from leishmania mexicana and implications for the inhibition of polyamine biosynthesis in parasitic infections. Arch. Biochem. Biophys. 2013; 535(2): 163–176. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRoberto E, da Silva J , Alfredo dos Santos Simone Come A, et al.: Cinnamides target leishmania amazonensis arginase selectively. Molecules. 2020; 25(22): 5271. Publisher Full Text\n\nFeitosa LM, da Silva ER , Hoelz LVB, et al.: New pyrazolopyrimidine derivatives as leishmania amazonensis arginase inhibitors. Bioorg. Med. Chem. 2019; 27(14): 3061–3069. PubMed Abstract \| Publisher Full Text\n\nAlcântara LM, Ferreira TCS, Gadelha FR, et al.: Challenges in drug discovery targeting tritryp diseases with an emphasis on leishmaniasis. Int. J. Parasitol. Drugs Drug Resist. 2018; 8(3): 430–439. 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PubMed Abstract \| Publisher Full Text\n\nMa Y, Li Y, Zhang H, et al.: Malvidin induces hepatic stellate cell apoptosis via the endoplasmic reticulum stress pathway and mitochondrial pathway. Food Sci. Nutr. 2020; 8(9): 5095–5106. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSaulite L, Jekabsons K, Klavins M, et al.: Effects of malvidin, cyanidin and delphinidin on human adipose mesenchymal stem cell differentiation into adipocytes, chondrocytes and osteocytes. Phytomedicine. 2019; 53: 86–95. PubMed Abstract \| Publisher Full Text\n\nHuang W-Y, Liu Y-M, Wang J, et al.: Anti-inflammatory effect of the blueberry anthocyanins malvidin-3-glucoside and malvidin-3-galactoside in endothelial cells. Molecules. 2014; 19(8): 12827–12841. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaba AB, Nivetha R, Chattopadhyay I, et al.: Blueberry and malvidin inhibit cell cycle progression and induce mitochondrial-mediated apoptosis by abrogating the jak/stat-3 signalling pathway. Food Chem. Toxicol. 2017; 109: 534–543. PubMed Abstract \| Publisher Full Text\n\nMazewski C, Liang K, de Mejia EG: Comparison of the effect of chemical composition of anthocyanin-rich plant extracts on colon cancer cell proliferation and their potential mechanism of action using in vitro, in silico, and biochemical assays. Food Chem. 2018; 242: 378–388. PubMed Abstract \| Publisher Full Text\n\nCastañeda-Ovando A, Pacheco-Hernández ML, Páez-Hernández ME, et al.: Chemical studies of anthocyanins: A review. Food Chem. 2009; 113(4): 859–871. Publisher Full Text\n\nKhoo HE, Azlan A, Tang ST, et al.: Anthocyanidins and anthocyanins: Colored pigments as food, pharmaceutical ingredients, and the potential health benefits. Food Nutr. Res. 2017; 61(1): 1361779. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBurchmore RJS, Barrett MP: Life in vacuoles–nutrient acquisition by leishmania amastigotes. Int. J. Parasitol. 2001; 31(12): 1311–1320. PubMed Abstract \| Publisher Full Text\n\nMoragas-Tellis CJ, Almeida-Souza F, do Socorro dos Santos Chagas M , et al.: The influence of anthocyanidin profile on antileishmanial activity of arrabidaea chica morphotypes. Molecules. 2020; 25(15): 3547. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSilva-Silva JV, Moragas-Tellis CJ, Chagas MSS, et al.: Carajurin: A anthocyanidin from arrabidaea chica as a potential biological marker of antileishmanial activity. Biomed. Pharmacother. 2021a; 141: 111910. PubMed Abstract \| Publisher Full Text\n\nSilva-Silva JV, Moragas-Tellis CJ, Chagas MSS, et al.: Carajurin induces apoptosis in leishmania amazonensis promastigotes through reactive oxygen species production and mitochondrial dysfunction. Pharmaceuticals. 2022; 15(3): 331. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSasidharan S, Saudagar P: Flavones reversibly inhibit leishmania donovani tyrosine aminotransferase by binding to the catalytic pocket: An integrated in silico-in vitro approach. Int. J. Biol. Macromol. 2020; 164: 2987–3004. PubMed Abstract \| Publisher Full Text\n\nSilva-Silva JV, Moragas-Tellis CJ, do Socorro dos Santos Chagas M , et al.: Antileishmanial activity of flavones-rich fraction from arrabidaea chica verlot (bignoniaceae). Front. Pharmacol. 2021b; 12: 703985. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrust R, Lukacs A, Haigney A, et al.: Proteins in action: Femtosecond to millisecond structural dynamics of a photoactive flavoprotein. J. Am. Chem. Soc. 2013; 135(43): 16168–16174. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRugani JN, Quaresma PF, Gontijo CF, et al.: Intraspecies susceptibility of leishmania (viannia) braziliensis to antileishmanial drugs: antimony resistance in human isolates from atypical lesions. Biomed. Pharmacother. 2018; 108: 1170–1180. PubMed Abstract \| Publisher Full Text\n\nAndrade JM, Gonçalves LO, Liarte DB, et al.: Comparative transcriptomic analysis of antimony resistant and susceptible leishmania infantum lines. Parasit. Vectors. 2020; 13(1): 1–15. Publisher Full Text\n\nMaes L, Beyers J, Mondelaers A, et al.: In vitro ‘time-to-kill’assay to assess the cidal activity dynamics of current reference drugs against leishmania donovani and leishmania infantum. J. Antimicrob. Chemother. 2017; 72(2): 428–430. PubMed Abstract \| Publisher Full Text\n\nOliveira DM, Mariana Amália F, Costa MA, et al.: Evaluation of parasitological and immunological parameters of leishmania chagasi infection in balb/c mice using different doses and routes of inoculation of parasites. Parasitol. Res. 2012; 110(3): 1277–1285. PubMed Abstract \| Publisher Full Text\n\nGarg R, Dube A: Animal models for vaccine studies for visceral leishmaniasis. Indian J. Med. Res. 2006; 123(3): 439–454. PubMed Abstract\n\nMears ER, Modabber F, Don R, et al.: A review: the current in vivo models for the discovery and utility of new anti-leishmanial drugs targeting cutaneous leishmaniasis. PLoS Negl. Trop. Dis. 2015; 9(9): e0003889. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBarazorda-Ccahuana HL, Goyzueta-Mamani LD, Candia-Puma MA, et al.: Computer-aided drug design approaches applied to screen natural product’s structural analogs targeting arginase in Leishmania spp. Figshare. Supplementary material.2023.Reference Source" }	[ { "id": "165815", "date": "11 Apr 2023", "name": "Francisco Centeno", "expertise": [ "Reviewer Expertise Bioinformatics", "Arginase", "Protein structure" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors of this study employed various CADD techniques to screen structural analogs of natural products that could potentially serve as new therapeutic agents against leishmaniasis. The study is well-oriented and well-planned, particularly about how the screening of candidate molecules has been carried out from various compound libraries. This last point seems to be the best and most consistent aspect of the work in its current format.\nHowever, all the work on simulating the molecular dynamics of the interaction between the ligands and the arginase of L. infantum is based on the structure determined in Swiss-Model, using the structure of the arginase of L. mexicana as a template. Since the entire study relies on this structure determination being accurate, it is crucial that sufficient structural data be incorporated into this work to convincingly demonstrate that the structure determination obtained in silico is the best possible.\nIn this regard, some issues also arise that should be addressed:\nHave any refinements been made to the structure initially obtained from Swiss-Model to improve it?\n\nWhy has only the arginase from L. infantum been chosen for dynamic simulation studies, and not the arginases from L. brasiliensis and/or L. mexicana, whose structures are known? It would be interesting to compare the dynamic data obtained for L. infantum with those obtained for L. mexicana, whose structure is known.\nAnother important point that limits the work presented, in which I agree with the authors, is that the time scales obtained for the stabilities of the arginase-ligand complexes are surprisingly short. Although the authors discussed this in the discussion section, their explanation seems implausible to me. To clarify this point, I suggest comparing the stability times of the complexes with those obtained with the physiological ligand, arginine, and comparing the arginine complexes with human and L. mexicana arginases, both of which are proteins with known structures.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "9665", "date": "24 May 2023", "name": "Miguel Angel Chavez-Fumagalli", "role": "Author Response", "response": "REVIEWER 1 The authors of this study employed various CADD techniques to screen structural analogs of natural products that could potentially serve as new therapeutic agents against leishmaniasis. The study is well-oriented and well-planned, particularly about how the screening of candidate molecules has been carried out from various compound libraries. This last point seems to be the best and most consistent aspect of the work in its current format. ANSWER: Thank you for your assessment and constructive criticism. We have included all the recommendations described below to improve the manuscript. However, all the work on simulating the molecular dynamics of the interaction between the ligands and the arginase of L. infantum is based on the structure determined in Swiss-Model, using the structure of the arginase of L. mexicana as a template. Since the entire study relies on this structure determination being accurate, it is crucial that sufficient structural data be incorporated into this work to convincingly demonstrate that the structure determination obtained in silico is the best possible. ANSWER: I appreciate your observation. We made comments in the methods sections of the text to address this crucial point brought up by the reviewer. In this regard, some issues also arise that should be addressed: Have any refinements been made to the structure initially obtained from Swiss-Model to improve it? ANSWER: Thanks for your assessment. As stated in the methods section we performed an automated modeling analysis and selected the best models for each target. Why has only the arginase from L. infantum been chosen for dynamic simulation studies, and not the arginases from L. brasiliensis and/or L. mexicana, whose structures are known? It would be interesting to compare the dynamic data obtained for L. infantum with those obtained for L. mexicana, whose structure is known. ANSWER: Thank you for your keen observation. We chose the ARG from L. infatum since it is the species that causes leishmaniasis, it has the most severe form of the disease, and if VL is confirmed, therapy against it is required. While many of the natural compounds included in this study bind to highly conserved residues in Leishmania ARG, according to docking experiments conducted by numerous labs. In fact, a lot of them seem to use the same residues regardless of their structural classification [da Silva, Edson Roberto, et al. \"Cinnamic acids derived compounds with antileishmanial activity target Leishmania amazonensis arginase.\" Chemical Biology & Drug Design 93.2 (2019): 139-146.]. Additionally, we restricted our research to New World Leishmaniasis because, as far as we are aware, no other crystal structures outside L. mexicana ARG have been deposited. Another important point that limits the work presented, in which I agree with the authors, is that the time scales obtained for the stabilities of the arginase-ligand complexes are surprisingly short. Although the authors discussed this in the discussion section, their explanation seems implausible to me. To clarify this point, I suggest comparing the stability times of the complexes with those obtained with the physiological ligand, arginine, and comparing the arginine complexes with human and L. mexicana arginases, both of which are proteins with known structures. ANSWER: I appreciate your observation. We made comments in the methods and results sections of the text to address this crucial point brought up by the reviewer. We carried out the MDS at 100 ns under the same conditions as those mentioned earlier in the manuscript. Since the parasite replicates in the macrophages, stability at low pH is the requirement that a medication must meet, as stated in the article. Several of the natural products that were employed as models for the selection of the structural analogs have demonstrated intracellular action in vitro." } ] } ]	1	https://f1000research.com/articles/12-93
https://f1000research.com/articles/12-451/v1	28 Apr 23	{ "type": "Case Report", "title": "Case Report: Successful results of direct varicose vein ablation with EVLA in chronic venous insufficiency patient in Indonesia", "authors": [ "Taofan Taofan", "Junichi Utoh", "Iwan Dakota", "Suci Indriani", "Choiron Abdillah", "Achmad Hafiedz Azis Kartamihardja", "Suko Adiarto", "Renan Sukmawan", "Junichi Utoh", "Iwan Dakota", "Suci Indriani", "Choiron Abdillah", "Achmad Hafiedz Azis Kartamihardja", "Suko Adiarto", "Renan Sukmawan" ], "abstract": "Background: Varicose veins are considered a chronic venous disease. Delaying treatment might cause several late complications that contribute to a high burden on healthcare systems. It may be treated with endovenous laser ablation (EVLA) and stab avulsion as additional procedures. Varicose direct ablation has been promoted to replace stab avulsion in certain conditions. Here we report the case of a 71-year-old female who presented with chronic venous insufficiency managed by an endovascular therapeutic approach using direct varix ablation for the first time in National Cardiovascular Center – Harapan Kita, Jakarta, Indonesia. Case report: A 71-year-old female came to the outpatient clinic with a large bulging vein in her leg. Duplex ultrasound showed that the great saphenous vein (GSV) was incompetent with a varicose vein in the medial part of proximal GSV below the knee. The patient underwent EVLA with direct varicose ablation using Utoh’s technique. Duplex sonography evaluation showed the right GSV was utterly obliterated, including the varicose vein. The patient was discharged two days after the procedure without significant complaints nor pain medication. Conclusions: Direct varicose ablation was proposed as a better alternative than stab avulsion. The varicose vein can be managed with EVLA without a scalpel, incision, avulsion, or phlebectomy. In this case presentation, the endovascular therapeutical approach with Utoh’s ablation technique showed promising results, and no complication was found in the patient.", "keywords": [ "Varicose Vein", "Endovenous Laser Ablation", "Stab Avulsion", "Utoh’s Technique" ], "content": "Introduction\n\nChronic vein insufficiency (CVI) is one of the most common cardiovascular pathologies. The reported prevalence showed significant variability depending on the study population, methodology, and classification. Its prevalence is still underestimated because many people affected by this disease don’t seek help as long as the signs and symptoms don’t bother them. The available results varied from 2-56% in the male population and 1-60% in the female population. CVI is more common with increasing age.1,2\n\nVaricose veins are considered a chronic venous disease (CVD). It is characterized by enlargement and tortuousaspect of superficial veins in the subcutaneous tissue, including saphenous veins, saphenous tributaries, among others. In the United States, approximately 23% of adults between ages 40 and 80 years had varicose veins, which are generally more common in women and older adults. Delayed treatment might cause several late complications, including venous ulceration, contributing to a high burden on healthcare resources.3,4\n\nEndovenous laser ablation (EVLA) is one of the non-surgical intervention options able to obliterate the affected veins. It uses heat to damage the vein wall, leading to fibrosis and the collapse of the vein.5 It usually targets lower extremity veins, including the great saphenous vein (GSV), small saphenous vein (SSV), and saphenofemoral junction. Varicosities originating from GSV and SSV can be treated with EVLA. However, large varicose veins require additional procedures such as ambulatory phlebectomy or stab avulsion.6 Direct varicose ablation is not common in general practice. A study by Park et al., published in 2007, suggested that direct laser ablation couldn’t replace classic methods for treating branch varicosities because of the high failure rate and risk of burned skin.7\n\nRecently, a study by Utoh et al. showed that in more than 44 patients with varicose veins treated by direct laser ablation using a16 G needle to insert the fiber into the varicose lumen, 93% cases of varicose vein had been obliterated, and there were no adverse events were observed.8\n\nHere we report for the first time the successful treatment of a 71-year-old female presenting varicose vein with EVLA without any surgical incision at the National Cardiovascular Centre Harapan Kita.\n\n\nCase report\n\nA 71-year-old female came to the outpatient clinic with a history of swelling and numbness in her leg more than six months. These complaints were also accompanied by a large bulging vein. She was experiencing heaviness, tiredness, and throbbing in her lower leg. The patient had a history of EVLA with varicose vein stab avulsion on her left leg two months prior. After the first procedure, she had to take the medication in order to reduce her pain for several days.\n\nVital signs of the patient were: blood pressure 88/56 mmHg, heart rate 93 beats/min, respiratory rate 26 times/minute, and a temperature of 36.5°C. Her weight was 60 kg. Chest and abdominal physical examination were normal. Both lower limbs were warm. Peripheral edema was found in both legs, more prominent on the right side with visible varicose vein in right popliteal region. Laboratory examinations were within normal limits. Electrocardiography (ECG) showed left axis deviation. Chest X-ray revealed cardiomegaly with cardiothoracic ratio of 65%. Echocardiography showed normal left ventricular systolic function with ejection fraction of 61%, concentric left ventricular hypertrophy with grade I diastolic dysfunction. Lower extremity duplex ultrasound investigation revealed severe incompetence of the right GSV above and below the knee, deep vein, and varicose vein in the medial part of the proximal GSV below the knee. The left GSV was utterly obliterated. There was no DVT in both legs. The arterial flow was normal in both legs.\n\nThe patient was diagnosed with CVI with varicose veins. She was planned to undergo EVLA on her right leg, including direct ablation on the varicose vein.\n\nThe procedure was ablation with Utoh’s technique using radial slim-type fiber and curved-like 16G IV catheter (Figure 1). After GSV ablation, we punctured the varicose vein with the ultrasound-guided method and inserted the fiber into the lumen (Figure 2). The energy used for varicose ablation was 3 watts with 20 Joule. With a similar technique, the fiber was slowly withdrawn with the speed of 0,14 cm/s (one panel in 7 s).\n\nDuplex sonography evaluation showed right GSV was utterly obliterated, including the varicose vein. The epigastric vein was still patent, with no evidence of deep vein thrombosis. The patient was still hospitalized for one day in order to observe if there was an early complication. She felt better than the first procedure because the pain was more tolerant. No events such as skin burns or thrombophlebitis were observed (Figure 3). The patient was discharged from the hospital without any significant complaints nor any medication. One month after the treatment, there was no any recurrence or complaint that found in patient (Figure 4)\n\n\nDiscussion\n\nCVD can present a wide clinical spectrum, ranging from asymptomatic with cosmetic problems only to severe manifestations such as reticular veins, edema, hyperpigmentation, eczema, varicose veins, and ulcers.4,9 Varicose veins are a common clinical manifestation of CVD. Varicose veins are veins that are enlarged and tortuous with a diameter greater than 3 mm. It might involve saphenous veins, tributaries, or non-saphenous superficial leg veins.10\n\nThe primary risk factor was female, older age, multiparity, sedentary lifestyle, obesity, and history of venous thromboembolism. Works continually in a standing position are at high risk of developing varicose veins. Despite the multifactorial etiology of varicose veins, genetic and parental factors are understudied.9,11\n\nThe varicose vein can be diagnosed by physical examination and further classified with a CEAP classification score to document the severity of the disease. It consists of clinical features of venous disease ranging from C0 (no visible signs of venous disease) to C6 (venous ulceration). The etiology of the venous condition should be determined, such as congenital, primary, or secondary. The anatomical classification depends on the location of the incompetence, including superficial, deep, or perforator. Lastly, the pathophysiology is classified into reflux, obstruction, or a combination of these conditions.4,10\n\nClinical manifestations include leg discomfort, heaviness, and pressure sensation after prolonged standing and are relieved by leg elevation, compression stockings, walking, or any measure that lowers venous pressure. Some cases are often asymptomatic but still concerned about the cosmetic appearance.9 Our patient felt discomfort and throbbing in her leg and pressure sensation after prolonged standing. The symptoms were relieved by leg elevation. There was no pain when she used her muscle to walk, indicating the problem wasn’t artery obstruction. On the medial part of the distal femoral region, dilated and bulging superficial veins were clearly seen, especially when she was in a standing position. Because of that, she was classified into the C2 category.\n\nOur patient had already used compression stockings on both legs for several weeks. She did not feel any difference. Then, she was suggested to undergo endovenous laser ablation on her right leg and planned to have direct varicose ablation. EVLA has been introduced as an alternative to classic surgical stripping in managing venous vein insufficiency of the GSV and SSV. Although surgical intervention was the gold standard for treatment after the procedure for more than a century, the days off work were very long, ranging from 18-28 days with a recurrency rate of 40% after five years of procedure. For that reason, developing minimally invasive techniques was necessary.9,12\n\nThe purpose of endovenous ablation modalities is to obliterate the insufficient vein segment. It involves a heat generator that causes local thermal injury to induce thrombosis and fibrosis. It also requires ultrasound that may detect the location of the fiber and safely advance it into near Sapheno-Femoral Junction (SFJ).12 Tumescent anesthesia is essential for this procedure. It is a technique to give a high volume but low dose anesthesia under the skin. It contains a normal saline solution with lidocaine, sodium bicarbonate, and epinephrine. An injection pump helps this solution to infiltrate into the surrounding vein area. It reduces pain and prevents burn or nerve damage by creating a heat sink that compresses the vein so the thermal energy focuses on the target vein.9,12\n\nDiode laser is very common in EVLA procedures. It allows continuous light emission in parallel directions and is relatively cheap. The fiber is inserted through the great saphenous vein until reaching near SFJ. Using a 1470 nm diode laser, an average LEED (Linear endovenous energy density) of 50-75 joule/cm is used to the vein wall. The energy is related to the diameter of the vessel. A larger vein needs more energy to be destroyed. After infiltrating tumescent local anesthesia, the fiber is withdrawn continuously at one millimeter per second until reaching the most proximal part of the targeted vein.12,13\n\nThis procedure is indicated based on anatomical, clinical, and functional conditions. The anatomical indication of the procedure was based on Class 1A recomendation from the Guidelines of the First International Consensus Conference on Endovenous Thermal Ablation for Varicose Vein Disease, stating that endovenous thermal ablation is applicable in great saphenous vein and small saphenous vein. The functional indication is based on reflux time. A reflux time of more than 500 ms in the superficial vein is indicated for the procedure. Patients with clinical classification C2 and above are clinically indicated.14\n\nOn the other hand, the procedure is contraindicated if the patient has acute deep vein thrombosis, acute superficial phlebitis, obstruction of the deep vein, or acute infection at the puncture site. Several conditions should avoid undergoing EVLA, such as pregnancy, a significant peripheral arterial disease with a prominent decrease of ankle-brachial index, allergy to the tumescent solution, or immobilized patients caused by severe chronic disease.14\n\nOur patient came to the outpatient clinic with symptoms of chronic venous disease, including swelling, numbness, heaviness, tiredness, and throbbing in the right lower leg. She also had a varicose vein in the medial part of the right tibial proximal. From her last duplex ultrasound examination, reflux time was 1020 ms. There was no evidence of deep vein thrombosis or occlusion. Her peripheral artery was good, without visible plaque seen. After this clear indication and without any contraindication, she was admitted to the procedure room.\n\nThe initial procedure was standard EVLA for the great saphenous vein as the primary target using a 1470 R diode laser. The fiber was inserted through GSV, and the tip was placed at a maximum of 2 cm from SFJ, confirmed using ultrasound and visualization of the red beam through the skin. The distance was related to the possibility of endothermal heat induced thrombosis (EHIT) and the recurrence rate due to the recanalization process that tip distance from SFJ > 2.5 cm correlated with a low prevalence of EHIT.15 On the other hand, minimal distance from the tip to SFJ was correlated with a more successful procedure and reduced recurrence rate.16\n\nUtoh et al. introduced the technique to infiltrate a tumescent solution between SFJ and the distal tip of the fiber. The most proximal part of GSV was compressed because of the tumescent infiltration, so the fiber can be placed as near as 5-10 mm from the epigastric vein to maximize the chance of a successful procedure. At the same time, the EHIT complication still can be avoided13 based on anatomical consideration, and it is known that EVLA on the distal below the knee is at high risk of causing nerve damage in the saphenous region. The distance between the vein and the nerve is getting closer distally.17\n\nUtoh et al. showed that enough tumescent local anesthesia surrounding the vein and keeping the distance between the nerve and vein effectively reduced post-procedural neurologic symptoms. This study also introduced modifications regarding the use of energy and LEED. The energy used on GSV above the knee was 7 watts with a LEED of 50-70 J/cm. When it reached bifurcation of the posterior arcuate vein, the ablation was temporarily stopped, and the energy was reduced to 5 watts with a target LEED was 20-25 J/cm. This method is known as two-step ablation, and the outcome was extraordinarily effective without any complication of nerve injury from 90 consecutive limbs.17\n\nWe used a similar method with two steps of ablation. We started using energy at 6 watts with LEED 50 J/cm from the proximal part of GSV above the knee until the distal above the knee. Then we continued with lower energy and LEED until the distal part of GSV below the knee. The speed of fiber traction was persistent at one centimeter every seven seconds.\n\nAfter performing ablation of the incompetent saphenous vein, collateral varices resection by stab avulsion method is regularly performed. Although the stab avulsion method is widely accepted, it may cause many adverse events, such as postoperative bleeding, pain, neuropathy, and wound infection, even though it involves only a few millimeters of the incision. Conversely, sclerotherapy is one option for treating varicose without skin incision. However, thrombophlebitis and other problems happen, such as pain, induration, and skin pigmentation. It is also yet to be available in our cases, she already had experience with stab avulsion, and she felt prolonged pain after the procedure, although the varicose was completely obliterated.\n\nVaricose vein ablation with Utoh’s ablation technique had recently been used as an alternative to the stab avulsion method, which did not require skin incision, had fewer adverse events, and could be done after EVLA treatment. 66% of a side branch varicose vein may collapse or spasm right after GSV main trunk ablation. Thus, they didn’t need an additional procedure. However, there are some uncertainties regarding whether the residual varicose will spontaneously be regressed. If left untreated, postoperative thrombophlebitis would be a risk, which could trigger long-term recurrence after the procedure. Therefore, EVLA on varicose veins was still recommended.8\n\nFor our patient, after the regular procedure, we punctured the varicose using Utoh’s ablation technique under ultrasound guidance with a 16 G needle; then the slim radial fiber was inserted without using any sheath. A tumescent solution was given to protect the surrounding tissue. Low energy was used to ablate the varicose because the diameter was 3 mm; the energy should be set based on diameter according to the latest study.17\n\nThe fiber was retracted with constant speed, similar to GSV ablation. The result was good, with the varicose vein completely obliterated, and she could walk not long after the procedure. No complications were observed; the next day, the patient underwent post-procedure evaluation using duplex ultrasound. The right GSV was completely obliterated from the proximal above the knee until the distal part below the knee without visualizing the varicose vein. There was no thrombus in the deep vein, as we were concerned about EHIT after the EVLA procedure.\n\nThis procedure showed that varicose ablation using the Utoh’s direct varix ablation technique was an ideal option and seriously challenged stab avulsion method with similar efficacy but more comfortable for the patient and fewer adverse event. The possible indication was (not limited to) a patient with a history of thrombophlebitis, varicose on the anterior tibial region, static dermatitis, and patients undergoing anticoagulant therapy in which stab avulsion was not recommended.8 At this early stage of clinical application, the selection of cases was appropriate regarding the complexity of varicose veins. However, we still believe there is room for improvement and expanding the indication of this procedure.\n\nBased on previous experience with stab avulsion, skin incisions for varicose are often performed in patients with sizeable varicose, leading to postoperative bleeding, nerve damage, and risk of scar formation. However, surgical stab avulsion might not be avoided significantly in some conditions when the varicose lumen narrows due to spasm or collapse and is difficult to puncture.8\n\n\nConclusions\n\nA case of CVI with varicose veins as a clinical manifestation has been reported. The current therapeutic strategy was EVLA on GSV with additional stab avulsion or ambulatory phlebectomy. Utoh’s direct varicose ablation technique was proposed as a better alternative with an enormously successful rate and as effective as phlebectomy with reduced risk of bleeding, pain, neuropathy, or wound infection. It can be totally managed with EVLA without a scalpel, incision, avulsion, or phlebectomy.\n\n\nPatient consent\n\nWritten informed consent has been obtained from the patient to publish the case report and accompanying images.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nAcknowledgements\n\nWe want to thank the patient for allowing us to have their case published.\n\n\nReferences\n\nRobertson L, Evans C, Fowkes FGR: Epidemiology of chronic venous disease. Phlebol. J. Venous Dis. 2008 Jun; 23(3): 103–111. Publisher Full Text\n\nRabe E, Berboth G, Pannier F: Epidemiologie der chronischen Venenkrankheiten. Wien. Med. Wochenschr. 2016 Jun; 166(9–10): 260–263. PubMed Abstract \| Publisher Full Text\n\nPiazza G: Varicose Veins. Circulation. 2014 Aug 12; 130(7): 582–587. Publisher Full Text\n\nEberhardt RT, Raffetto JD: Chronic Venous Insufficiency. Circulation. 2014 Jul 22; 130(4): 333–346. Publisher Full Text\n\nYamamoto T, Sakata M: Influence of fibers and wavelengths on the mechanism of action of endovenous laser ablation. J. Vasc. Surg. Venous Lymphat. Disord. 2014 Jan; 2(1): 61–69. PubMed Abstract \| Publisher Full Text\n\nZhan HT, Bush RL: A Review of the Current Management and Treatment Options for Superficial Venous Insufficiency. World J. Surg. 2014 Oct; 38(10): 2580–2588. PubMed Abstract \| Publisher Full Text\n\nPark SW, Yun IJ, Hwang JJ, et al.: Endovenous Laser Ablation of Varicose Veins after Direct Percutaneous Puncture: Early Results. Dermatol. Surg. 2007 Oct; 33(10): 1243–1249. PubMed Abstract \| Publisher Full Text\n\nUtoh J, Tsukamoto Y: Endovenous Laser Ablation of Varicose Veins Using Radial Slim Fibers. Jpn. J. Phlebol. 2020 Sep 28; 31(3): 113–118. Publisher Full Text\n\nYoun YJ, Lee J: Chronic venous insufficiency and varicose veins of the lower extremities. Korean J. Intern. Med. 2019 Mar 1; 34(2): 269–283. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHamdan A: Management of Varicose Veins and Venous Insufficiency. JAMA. 2012 Dec 26; 308(24): 2612. Publisher Full Text\n\nGawas M, Bains A, Janghu S, et al.: A Comprehensive Review on Varicose Veins: Preventive Measures and Different Treatments. J. Am. Nutr. Assoc. 2022 Jul 4; 41(5): 499–510. PubMed Abstract \| Publisher 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): 2S–48S. Publisher Full Text\n\nUtoh J, Tsukamoto Y, Nobuoka H: Changes of Surgical Procedure for Primary Varicose Veins: Stripping Surgery to Endovenous Thermal Ablation Therapy. Jpn. J. Phlebol. 2017 Sep 8; 28(3): 317–321. Publisher Full Text\n\nPavlović MD, Schuller-Petrović S, Pichot O, et al.: Guidelines of the First International Consensus Conference on Endovenous Thermal Ablation for Varicose Vein Disease – ETAV Consensus Meeting 2012. Phlebol. J. Venous Dis. 2015 May; 30(4): 257–273. PubMed Abstract \| Publisher Full Text\n\nSadek M, Kabnick LS, Rockman CB, et al.: Increasing ablation distance peripheral to the saphenofemoral junction may result in a diminished rate of endothermal heat-induced thrombosis. J. Vasc. Surg. Venous Lymphat. Disord. 2013 Jul; 1(3): 257–262. PubMed Abstract \| Publisher Full Text\n\nDickson R, Hill G, Thomson IA, et al.: The valves and tributary veins of the saphenofemoral junction: ultrasound findings in normal limbs. Veins Lymphat. 2013 Aug 2; 2(2): 18. Publisher Full Text\n\nUtoh J, Tsukamoto Y: Prevention of Saphenous Nerve Injury after Endovenous Laser Ablation of Incompetent Great Saphenous Veins: 2 Step Ablation. Jpn. J. Phlebol. 2021 Dec 24; 32(3): 355–357. Publisher Full Text" }	[ { "id": "175846", "date": "19 Jun 2023", "name": "Lars Mueller", "expertise": [ "Reviewer Expertise General surgery", "phlebology", "endovenous thermal ablation", "vein surgery", "ultrasound" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present an endovenous technique of treatment of varicose veins on the basis of a case. More specifically, they address the issue of removal of side branches in the context of thermal treatment of truncal venous insufficiency. In this regard, the authors present a method of eliminating such varicose veins through tributaries of the great saphenous vein by means of cannulation and laser ablation with a radially emitting laser. This appears potentially gentler than open surgical removal by phlebectomies, which is often used in such situations.\nThe case description is detailed. Nevertheless, technical details are missing in important places. More importantly, it seems that existing evidence from other publications is not sufficiently mentioned or discussed. Also, observational studies with quite large cohorts have recently been published by one of the authors, fitting the particular case presented. Therefore, I have reservations about publishing this case report.\nI have expanded upon on my views below:\nIs the background of the case’s history and progression described in sufficient detail?\n\nYes, the clinical history is well reported\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes?\nNot complete. The diameter of the great saphenous vein and the varicose tributaries would be interesting. Also, it would be important to know exactly the level to which the venous valves are defective or the length to which the reflux of the great saphenous vein exists before it is then transmitted via the side branch, if applicable. It would also be valuable to know the total energy delivered. Was the same laser fiber used for the tributaries/varices also used to ablate the trunk? Also, to establish reproducibility of the method, the manufacturer of the lasers used here should be accurately stated. In the discussion section, the authors (correctly) mention the need for tumescent infusion. However, this step was not described in the case report. This should be clarified.\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis, or treatment?\nThere are some deficits here. First of all, it is not sufficiently mentioned that there are indeed scientific studies and descriptions of the direct ablation of varicosities/tributaries by other working groups. As an example, we refer to the work of Wang et al. (DOI: 10.1016/j.jvir.2018.01.774) and Myers et al. (DOI: 10.1258/phleb.2011.011088). It is conceivable that there is additional literature on the topic.\nIt is also not clear what purpose this case report serves in relation to other previous work. On the one hand, reference is correctly made to the prior papers, which, however, were published in a Japanese-language journal by one of the authors (Junichi Utoh), who has apparently already treated hundreds of cases with the described technique. On the other hand, however, it is not mentioned that in early June 2023, two case series studies were published by the same author (Junichi Utoh) in the journal Phlebology, also involving hundreds of patients treated with the techniques described.\nIs the case presented with sufficient detail to be useful for other practitioners?\nYes, it is. The Author report a good practice management.\nI would like to express that there are deficiencies in this paper in terms of the scientific approach to the subject. Such a description of a technique, which is elsewhere thematized in large case series, may make sense, considering the detail with which this single case is described. However, the rationale for such a separate case description should also emerge from this; here, further arguments are needed.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [ { "c_id": "9845", "date": "13 Jul 2023", "name": "Taofan Taofan", "role": "Author Response", "response": "We would like to thank the reviewer for the brief review of our article. Here we mentioned some of the revisions we made to the article according to the reviewer’s points: Are enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Not complete. The diameter of the great saphenous vein and the varicose tributaries would be interesting. Also, it would be important to know exactly the level to which the venous valves are defective or the length to which the reflux of the great saphenous vein exists before it is then transmitted via the side branch, if applicable. It would also be valuable to know the total energy delivered. Was the same laser fiber used for the tributaries/varices also used to ablate the trunk? Also, to establish reproducibility of the method, the manufacturer of the lasers used here should be accurately stated. In the discussion section, the authors (correctly) mention the need for tumescent infusion. However, this step was not described in the case report. This should be clarified. We’ve added more detail about the examination, diagnostic test, and treatment given to the article: Lower extremity duplex ultrasound investigation revealed severe incompetence of the right GSV above and below the knee (reflux >500 ms), deep vein, and varicose vein in the mid part of the proximal GSV below the knee. The diameter of the right Sapheno-femoral junction (SFJ) was 8.0 mm, proximal above-the-knee (ATK) was 8.2 mm, mid ATK was 5.0 mm, distal ATK was 4.0 mm, proximal below-the-knee (BTK) was 4.0 mm, and distal BTK was 1.8 mm. The diameter of the varicose vein was approximately 4.5 mm. The left GSV was utterly obliterated. There was no DVT in both legs. The arterial flow was normal in both legs. The procedure was using 1470-nano meter wavelength laser device and ELVeS radial slim-type fiber (Biolitec, Bonn, Germany). The initial puncture was done with 6F Radiofocus introducer kit (Terumo Medical Corp., Piscataway, NJ, USA) at right distal BTK GSV and laser fiber was introduced until 2.5 cm distal from SFJ. Tumescent anesthesia was applied along the GSV. EVLA was done with laser power of 6 W linear endovenous energy density (LEED) 50 J/cm in proximal until distal ATK GSV, 5 W LEED 40 J/cm in distal ATK GSV until mid BTK GSV, and 2 W LEED 20 J/cm in mid until distal BTK. The laser fiber pullback speed was 0.14 cm/s. For the varicose vein, we used the same laser fiber, and puncture was done with a curved-like 16G IV catheter (Terumo Corp., Tokyo, Japan). We punctured the varicose vein with the ultrasound-guided method and inserted the fiber into the lumen. Tumescent anesthesia was applied along the varicose vein. The laser power used for varicose ablation was 3 W with LEED 20 J/cmJoule. With a similar technique, the fiber was slowly withdrawn with the speed of 0.14 cm/s. The total ablated length was ± 40 cm with a total tumescent anesthesia amount was 650 mL. Is sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis, or treatment? There are some deficits here. First of all, it is not sufficiently mentioned that there are indeed scientific studies and descriptions of the direct ablation of varicosities/tributaries by other working groups. As an example, we refer to the work of Wang et al. (DOI: 10.1016/j.jvir.2018.01.774) and Myers et al. (DOI: 10.1258/phleb.2011.011088). It is conceivable that there is additional literature on the topic. It is also not clear what purpose this case report serves in relation to other previous work. On the one hand, reference is correctly made to the prior papers, which, however, were published in a Japanese-language journal by one of the authors (Junichi Utoh), who has apparently already treated hundreds of cases with the described technique. On the other hand, however, it is not mentioned that in early June 2023, two case series studies were published by the same author (Junichi Utoh) in the journal Phlebology, also involving hundreds of patients treated with the techniques described. We’ve added more scientific studies to the discussion including article by Wang, et al., Myers, et al., and Utoh. The purpose of this case report is to describe the detailed procedure of the first successful direct varicose ablation with Utoh’s technique using EVLA without any surgical incision in a 71-year-old female presenting varicose vein at the National Cardiovascular Centre Harapan Kita, Jakarta, Indonesia. We hope that our revision can provide answers for the reviewer. Please let us know if further revision or detailed information according to our article is needed. Once again, we would like to thank you for the opportunity given to publish our case. Hope that our article can give new insights about the direct varicose vein ablation using EVLA." } ] } ]	1	https://f1000research.com/articles/12-451
https://f1000research.com/articles/12-824/v1	13 Jul 23	{ "type": "Research Article", "title": "A comparative evaluation of different scores in predicting severity and outcome in acute pancreatitis", "authors": [ "Ojas Mahajan", "Satish Mahajan", "Sourya Acharya", "Anil Wanjari", "Sunil Kumar", "Shilpa Bawankule", "Anamika Giri", "Kashish Khurana", "Ojas Mahajan", "Sourya Acharya", "Anil Wanjari", "Sunil Kumar", "Shilpa Bawankule", "Anamika Giri", "Kashish Khurana" ], "abstract": "Background: Acute pancreatitis (AP) is an inflammatory condition usually caused by alcohol or gallstones. Our goal was to prospectively compare the diagnostic efficacy of the Acute Physiology & Chronic Health Evaluation (APACHE) II, the Bedside Index of Severity in Acute Pancreatitis (BISAP), the Ranson's score & the Modified Glasgow Score (MGS) in determining the severity & outcome of Acute pancreatitis in a tertiary care facility in central India. Methods: Between December 2020 & December 2022, this prospective observational study was done in rural area of Wardha district. 110 subjects were included, and the diagnosis of acute pancreatitis was done using Atlanta criteria. APACHE II, MGS, Ranson score on admission, Ranson score 48 hours after admission & BISAP were used to evaluate each subject. The reciever operating curve was used to measure the specificity, sensitivity, NPV, PPV, diagnostic accuracy, area under the curve (AUC) & these scoring methods were then prospectively compared. Results: When a cut-off based on the literature was used, the APACHE II score could accurately diagnose severe cases of AP (n=110) in 69 patients, BISAP in 68 patients, MGS in 49, Ranson score on admission in 48 patients & after 48 hours in 48 patients. This study showed that Ranson score 48 hours after admission had a AUC (0.991), Ranson score at admission (AUC 0.989) & Modified Glasgow Scale (AUC 0.6486) had fair accuracy as compared to APACHE II (AUC 0.974) & BISAP (AUC 0.896) for determining the level of severity among AP patients based on ROC curves. Conclusion: To predict the severity of AP, the Ranson score after 48 hours showed the highest NPV, PPV, sensitivity, specificity, and diagnostic accuracy of all the scoring methods tested. The BISAP score had the highest specificity, sensitivity, PPV& NPV for determining the outcome of AP.", "keywords": [ "Acute Pancreatitis", "APACHE II", "BISAP", "Ranson’s score", "MGS" ], "content": "Introduction\n\nThe pancreas is a unique endocrine & exocrine organ. The exocrine glands discharges enzymes into the digestive system, while the endocrine glands secrete hormones into the circulatory system.1 According to Claude Bernard's theory from 1856, acute pancreatitis was brought on by bile reflux into the common pancreatic duct. However, the controversy did not begin to be settled until 1901, when Eugene Opie proposed that gallstone immigration into the common bile duct was the major cause of acute pancreatitis.2 When intracellular defences that stop trypsinogen activation or lessen trypsin activity are overpowered, AP results. Pancreatic enzyme activation causes the gland to digest itself & causes localised inflammation.3 Necrotizing pancreatitis & interstitial oedematous pancreatitis are two types of acute pancreatitis. Inflammation & edema are present in the peripancreatic tissues and pancreatic parenchyma in interstitial edematous pancreatitis. Necrotizing pancreatitis appears when this condition deteriorates to the point of peripancreatic or pancreatic tissue death.4 Most patients have localised inflammation, but about one-fifth of them go on to develop multiple organ dysfunction syndrome (MODS), which is linked to a significant increase in mortality. A diagnosis of acute pancreatitis requires abdominal pain, high pancreatic amylase and/or lipase values that are at least three times above normal, & imaging studies that show anomalies unique to acute pancreatitis. The Atlanta Classification has been used to gauge the severity of acute pancreatitis ever since its establishment in 1992.5 The original classification's boundaries given by Atlanta, notably the definition of severity is unclear. In 2012, the Atlanta classification was revised to include chronic organ failure.6 Early diagnosis of acute pancreatitis is crucial for lowering morbidity & mortality caused by the condition. To determine the severity of AP, many biochemical, radiological & clinical scores had been devised in the past. Ranson's score, the CT-severity index (CTSI), the bedside index of severity in acute pancreatitis (BISAP), the Modified Glasgow Score, & APACHE-II are some of them.7 Acute pancreatitis severity can now be determined with the use of these forecasting methods. Though complex & difficult to use in clinical settings, it has been shown that these multi-factorial scoring systems work with a high negative predictive value but a meagre overall sensitivity.8 In this study, we aim to determine which scoring method best predicted acute pancreatitis severity. Its secondary aim was to determine which scoring method best predicted the outcome of AP.\n\n\nMethods\n\nThis observational and prospective research work was conducted for two years at a tertiary care centre in the rural area of Wardha district. Patients with significant abdominal pain, elevated serum amylase and serum lipase levels more than three times the upper limit of the normal range and abdominal ultrasonography findings suggestive of acute pancreatitis were included in the study. 110 subjects were studied. The Atlanta Criteria was used for the diagnosis of acute pancreatitis. The study was approved by Institutional Ethical Committee, Datta Meghe Institute of Medical Science (Deemed to be University) with Ref.No. DMIMS (DU)/IEC/2020-21/9284.\n\nThe enrolment of the subjects was started after approval from the ethics committee. The study included subjects over the age of 18 who provided written consent. The study excluded all subjects with chronic pancreatitis and those who received outside treatment prior to coming to the emergency room.\n\nAll subjects admitted for acute pancreatitis had their prospectively gathered demographic, clinical, biochemical, & radiological data. One can determine if they have acute pancreatitis if they meet two out of the following three criteria: (i) AP-specific abdominal pain, (ii) Serum amylase and serum lipase levels that are at least three times above normal (iii) Radiological abnormalities on abdominal ultrasonography and/or computerized tomography (CT) scan characteristic of acute pancreatitis. Patients with features of chronic pancreatitis, such as dilated pancreatic ducts, pancreatic calcifications, pseudocysts & areas of atrophy, discovered during radiological examinations performed while they were hospitalised or who had chronic pancreatitis based on their prior hospital records were excluded from the research.\n\nAfter a thorough history & physical examination, several clinical & biochemical factors were assessed. All subjects underwent abdominal ultrasonography at the time of admission. Subjects with mild AP did not experience any local consequences or organ failure, however those with severity did. The local sequelae included pseudocyst, pancreatic necrosis, walled off necrosis, & acute fluid collections. MGS, BISAP, APACHE II score, Ranson score on admission & 48 hrs after were the grading systems used for assessment of all the subjects. Subjects were followed until they were discharged or died.\n\nIBM's SPSS version 23.0 in Chicago, United States, was used to do the analysis. We used the ROC curve to establish a cut-off for the APACHE II score, the BISAP score, the Modified Glasgow score, the Ranson score at admission & after 48 hours, all of which predict outcome and severity. The diagnostic accuracy, sensitivity, and specificity of the four scores were evaluated for their ability to foretell the likelihood of severe outcomes or death.\n\n\nResults\n\nAccording to the classification given by Atlanta, 110 subjects displayed symptoms of acute pancreatitis. Out of them, 60 (54.54%) had mild and 50 (45.46%) had severe acute pancreatitis. nine (0.08%) of them died while being treated in the hospital (Tables 1 and 2; Figures 1 and 2; Table 3).\n\n\nDiscussion\n\nAcute pancreatitis is pancreatic inflammation which can range from mild to severe. The majority of patients suffer with mild condition with low morbidity, while the others have severe acute pancreatitis, which has a mortality rate of 10% to 20%.9 In present study mean age of the subjects was 40.49±12.12 years and maximum i.e. 38 (34.5%) of the participants were in the age group of 31-40 years. 72 individuals, evaluated by Ajay K. Khanna et al., had mean age of 40.5 years, similar to our study.9 Similarly, in a study by Anubhav Kumar et al., 50 patients with acute pancreatitis had the mean age of 48.42 years.10 In our study there were 100 (90.9%) males and 10 (9.1%) of the subjects were females. Similar findings were reported by Lankisch PG et al., as they found, out of 274 patients 172 were males and 102 were females.11 We found that the mean value of Serum Amylase was 399.82±104.82 U/L and 680.06±157.54 U/L in Mild and Severe acute pancreatitis groups, respectively. Kiat et al, also found in their study that the mean serum amylase was 1151.1±753.5 U/L and 1484.6±736.5 U/L in Mild and Severe acute pancreatitis groups, respectively.12 In the present study, out of 110 subjects, 41 (37.3%) had APACHE II Score of <8 and 69 (62.7%) had APACHE II Score of ≥8. In their analysis of 161 Acute Pancreatitis patients, Cho J H et al., also observed that 52 (32.2%) of Severe Acute Pancreatitis patients had APACHE II score of <8 and 109 (67.8%) of Severe Acute Pancreatitis had APACHE II score of ≥8.13 In our study, 42 (38.2%) subjects had BISAP Score of <2 and 68 (61.8%) subjects had BISAP Score of ≥2. Cho et al., studied 161 subjects and found that 109 (67.70%) participants had BISAP Score of <2 and 52 (32.30%) participants had BISAP Score ≥2, which was in contrast to our study.13 In the present study, 62 (56.4%) subjects had Ranson score of <3 at admission and 48 (43.6%) subjects had Ranson score of ≥3 at admission. Similarly, Khanna et al. in their study of 72 participants showed that 37 (51.4%) participants had Ranson score of <3 and 35 (48.6%) participants had Ranson of ≥ 3.9 In our study, 61 (55.5%) subjects had Modified Glasgow Score of <3 and 49 (44.5%) subjects had Modified Glasgow Score of ≥3. Similar results were reported by by Kiat TT et al. in their study of 669 participants which showed that 425 (63.52%) participants had Modified Glasgow Score of <3 and 244 (36.48%) participants had Modified Glasgow Score ≥3.12\n\nIn present study, we found that Ranson score 48 hours after admission (AUROC=0.900) was better than Ranson score at admission, Modified Glasgow Score, APACHE II score and BISAP score in predicting severity of acute pancreatitis. According to Kiat TT et al., Ranson score had higher sentivity, negative predictive value and area under ROC curve (AUROC=0.848) for predicting severity in acute pancreatitis than Modified glasgow score, similar to our study.12 According to Arif A et al., Ranson score predicted Severe Acute Pancreatitis more correctly than BISAP score similar to our study.14 According to Wei Gao et al., Severe Acute Pancreatitis was predicted more correctly by Ranson's score than by BISAP score with area under ROC curve (AUROC) 0.83, sensitivity 66% and specificity 78%. This was consistent with our study.15 Similarly, Zhang J et al., revealed that the AUC for predicting severity by BISAP was 0.793, APACHE II was 0.836 and by Ranson score was 0.903.16\n\nIn our study, we found that BISAP score was best in predicting outcome of acute pancreatitis followed by APACHE II score then Modified Glasgow Score then Ranson score at admission and Ranson score 48 hours after admission. Wei Gao et al., reported that Ranson score had the area under ROC curve (AUROC) 0.92, sensitivity and specificity were 93% and 69% respectively. BISAP score had the area under ROC curve (AUROC) 0.82, sensitivity and specificity were 81% and 70% respectively. Compared with the Ranson criteria, BISAP score outperformed in specificity, but having a suboptimal sensitivity for mortality in Acute Pancreatitis. This was consistent with our study.15 Eachempati SR et al., found that Ranson score was a good predictor of outcomes in patients with Severe Acute Pancreatitis. Ranson score after 48 hours predicted outcomes in patients more accurately than Ranson score at admission with Severe Acute Pancreatitis.17 In 2013, Chen L. et al., reported that to accurately predict death in Severe Acute Pancreatitis patients, the BISAP score performed comparably to other scoring systems with area under ROC curve (AUROC) of 0.808, sensitivity of 83.3% and specificity of 67.4%.18 Zhang J et al., revealed that the AUC for mortality predicted by BISAP was 0.791, APACHE II was 0.812 and by Ranson score was 0.904. BISAP score was found as valuable source for prognostic prediction in Chinese patients with Acute Pancreatitis.16\n\n\nConclusion\n\nWe conclude that the best scoring system for predicting the severity of Acute Pancreatitis is Ranson Score after 48 Hours with area under the curve, 0.900 (0.841 – 0.960), at 95% CI with p value <0.001 which was found to have the highest sensitivity and specificity of 87% and 86%, respectively. That was followed by Ranson score at admission with area under the curve 0.885, sensitivity of 85%, specificity of 75%. Then Modified glasgow scale with area under the curve 0.812, sensitivity of 77%, specificity of 72% then APACHE II score with area under the curve 0.812, sensitivity of 75%, specificity of 72% and lastly BISAP score with area under the curve 0.751, sensitivity of 73%, specificity of 67%.\n\nWe also conclude that BISAP Score was best with area under the curve, 0.841 (0.724 – 0.958) at 95% CI, with p<0.001 was found to have the highest sensitivity and specificity of 83% and 94%, respectively for predicting the outcome of Acute Pancreatitis as compared to Ranson score at admission with area under the curve 0.824, sensitivity of 70%, specificity of 73%, Modified glasgow scale with area under the curve 0.819, sensitivity of 66%, specificity of 75%, APACHE II with area under the curve 0.812, sensitivity of 75%, specificity of 60% and Ranson score after 48 hours with area under the curve 0.736, sensitivity of 70%, specificity of 80%.", "appendix": "Data availability\n\nZenodo. A Comparative Evaluation of Different Scores in Predicting Severity and Outcome in Acute Pancreatitis. DOI: https://doi.org/10.5281/zenodo.7777706. 19\n\nThis project contains the following data:\n\n- This dataset is regarding my study which I conducted on 110 subjects\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo. STROBE checklist. DOI: https://doi.org/10.5281/zenodo.7777876\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe thank all the participants who have contributed to this study.\n\n\nReferences\n\nFrantz E, Souza-Mello V, Mandarim-de-Lacerda C: Pancreas: Anatomy, diseases and health implications. Pancreas. 2012; 41: 1–9. Publisher Full Text\n\nFrossard JL, Steer ML, Pastor CM: Acute pancreatitis. Lancet. 2008; 371: 143–152. Publisher Full Text\n\nWang GJ, Gao CF, Wei D, et al.: Acute pancreatitis: etiology and common pathogenesis. World J. Gastroenterol: WJG. 2009 Mar 3; 15(12): 1427–1430. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFoster BR, Jensen KK, Bakis G, et al.: Revised Atlanta classification for acute pancreatitis: a pictorial essay. Radiographics. 2016 May; 36(3): 675–687. PubMed Abstract \| Publisher Full Text\n\nBradley EL: A clinically based classification system for acute pancreatitis: summary of the International Symposium on Acute Pancreatitis, Atlanta, Ga, September 11 through 13, 1992. Arch. Surg. 1993 May 1; 128(5): 586–590. Publisher Full Text\n\nBanks PA, Bollen TL, Dervenis C, et al.: Classification of acute pancreatitis—2012: revision of the Atlanta classification and definitions by international consensus. Gut. 2013 Jan 1; 62(1): 102–111. PubMed Abstract \| Publisher Full Text\n\nWu BU, Johannes RS, Sun X, et al.: The early prediction of mortality in acute pancreatitis: a large population-based study. Gut. 2008 Dec 1; 57(12): 1698–1703. PubMed Abstract \| Publisher Full Text\n\nPapachristou GI, Muddana V, Yadav D, et al.: Comparison of BISAP, Ranson's, APACHE-II, and CTSI scores in predicting organ failure, complications, and mortality in acute pancreatitis. Am. J. Gastroenterol. 2010 Feb 1; 105(2): 435–441. PubMed Abstract \| Publisher Full Text\n\nKhanna AK, Meher S, Prakash S, et al.: Comparison of Ranson, Glasgow, MOSS, SIRS, BISAP, APACHE-II, CTSI Scores, IL-6, CRP, and procalcitonin in predicting severity, organ failure, pancreatic necrosis, and mortality in acute pancreatitis. HPB Surg. 2013 Sep 24; 2013: 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarshit Kumar A, Singh GM: A comparison of APACHE II, BISAP, Ranson’s score and modified CTSI in predicting the severity of acute pancreatitis based on the 2012 revised Atlanta Classification. Gastroenterol. Rep. 2018 May; 6(2): 127–131. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLankisch PG, Assmus C, Lehnick D, et al.: Acute pancreatitis: does gender matter? Dig. Dis. Sci. 2001 Nov; 46: 2470–2474. Publisher Full Text\n\nKiat TT, Gunasekaran SK, Junnarkar SP, et al.: Are traditional scoring systems for severity stratification of acute pancreatitis sufficient? Ann. Hepatobiliary Pancreat. Surg. 2018 May 1; 22(2): 105–115. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBollen TL, Singh VK, Maurer R, et al.: A comparative evaluation of radiologic and clinical scoring systems in the early prediction of severity in acute pancreatitis. Am. J. Gastroenterol. 2012 Apr 1; 107(4): 612–619. PubMed Abstract \| Publisher Full Text\n\nArif A, Jaleel F, Rashid K: Accuracy of BISAP score in prediction of severe acute pancreatitis. Pak. J. Med. Sci. 2019 Jul; 35(4): 1008–1012. PubMed Abstract \| Publisher Full Text\n\nGao W, Yang HX, Ma CE: The value of BISAP score for predicting mortality and severity in acute pancreatitis: a systematic review and meta-analysis. PLoS One. 2015 Jun 19; 10(6): e0130412. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang J, Shahbaz M, Fang R, et al.: Comparison of the BISAP scores for predicting the severity of acute pancreatitis in Chinese patients according to the latest Atlanta classification. J. Hepatobiliary Pancreat. Sci. 2014 Sep; 21(9): 689–694. PubMed Abstract \| Publisher Full Text\n\nEachempati SR, Hydo LJ, Barie PS: Severity scoring for prognostication in patients with severe acute pancreatitis: comparative analysis of the Ranson score and the APACHE III score. Arch. Surg. 2002 Jun 1; 137(6): 730–736. PubMed Abstract\n\nChen L, Lu G, Zhou Q, et al.: Evaluation of the BISAP score in predicting severity and prognoses of acute pancreatitis in Chinese patients. Int. Surg. 2013; 98(1): 6–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMahajan O: A Comparative Evaluation of Different Scores in Predicting Severity and Outcome in Acute Pancreatitis. [Data set]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "209095", "date": "20 Oct 2023", "name": "Wenjian Mao", "expertise": [ "Reviewer Expertise Acute pancreatitis" ], "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 Abstract and the results section, cut-off value of each scoring system should be given.\n\nAt present, the revised Atlanta Criteria was widely used to define or classify acute pancreatitis (AP) over the world. Out of the 110 AP patients, 60 (54.54%) had mild and 50 (45.46%) had severe acute pancreatitis. It is unbelievable that there are no patients diagnosed with moderate severe acute pancreatitis (MSAP) according to the revised Atlanta Criteria. Please check and make some revision.\n\nWhat's the outcome of AP. It should be given definitely in the methods section. All definition should not be ambiguous.\n\nAP patients' severities are affected by various factors. To compare the predictive value of each scoring system, multivariate logistic regression models are recommended to evaluate them.\n\nSome attention should be paid to the writing style and grammar.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] } ]	1	https://f1000research.com/articles/12-824
https://f1000research.com/articles/12-823/v1	13 Jul 23	{ "type": "Research Article", "title": "Diagnostic utility of mast cell analysis in hypoplastic bone marrows for differentiation of aplastic anaemia from hypoplastic myelodysplastic neoplasm: A retrospective study", "authors": [ "Chaithra G V", "Soumya Gupta", "Ranjitha Rao", "Sharada Rai", "Nirupama Murali", "Sunita Hegde", "Chaithra G V", "Ranjitha Rao", "Sharada Rai", "Nirupama Murali", "Sunita Hegde" ], "abstract": "Background: Haematological disorders characterized by hypocellular marrow like aplastic anaemia (AA) and hypocellular myelodysplastic neoplasm (MDS-h) are diagnostic challenges as the clinical and morphological features overlap, while the treatment and prognosis differ. Bone marrow mast cell quantification is proposed as a supplementary diagnostic and prognostic tool to differentiate AA from MDS-h. We aim to study the distribution of mast cells in hypoplastic marrow and determine its role in differential diagnosis of AA and MDS-h. Methods: We analysed bone marrow biopsies of 65 cases of hypoplastic/aplastic marrow received during the year 2015-2021 for the distribution of mast cells using Toluidine Blue special staining. Hematopoietic stem cells were assessed with the help of CD34 immunohistochemistry. Results: Increased mast cells were noted in 55.4% of all the cases, of which 48% were cases of AA and 21% were cases of MDS-h (P: 0.04). Overall, 76% of AA and 33% of MDS-h cases showed increased numbers of mast cells. Reduced hematopoietic stem cells were noted in 69.4% of the cases with elevated mast cells (P: 0.1). Conclusions: Mast cell quantification in trephine biopsy of AA and MDS-h can act as a supplementary diagnostic tool and guide the management of the respective entities. Understanding its role in the bone marrow niche can enhance stem cell transplant treatment.", "keywords": [ "Mast cell", "Aplastic anaemia", "MDS-h", "Hypocellular marrow", "Bone marrow niche", "CD34", "Hematopoietic stem cell." ], "content": "Introduction\n\nHaematological disorders characterised by hypocellular marrows like aplastic anaemia (AA) and hypocellular myelodysplastic neoplasm (MDS-h) are diagnostic challenges for haematologists as AA, MDS-h, other immune cytopenias, paroxysmal nocturnal haemoglobinuria (PNH), and inherited bone marrow (BM) failure disorders are all considered BM failure states with significant clinicopathological overlap.1–3 However, the differentiation is critical as both AA and MDS-h have different management protocols with varying outcomes and prognoses. Compared to patients with AA, those with MDS-h have shorter median survival rates and exhibit a lower response to immunosuppressive therapy.4,5\n\nAA is defined as pancytopenia in the peripheral blood secondary to BM hypocellularity and is a diagnosis of exclusion.6 MDS is a diverse collection of clonal disorders that affect the hematopoietic stem cells (HSCs) and are characterised by cytopenias of varying degrees in the peripheral blood and inefficient haematopoiesis with BM dysplasia. Myelodysplasias with hypocellular BM (MDS-h) comprises around 10–15% of all MDS cases and are characterized by BM hypocellularity. Both AA and MDS-h share a common pathophysiological pathway with CD34 positive progenitor cells being fundamental in the pathogenesis of both these entities. CD34 positive HSCs are the target of autoimmune attack in AA making its count significantly decreased in the BM of AA. Whereas CD34 progenitor cells are the cells from which MDS originates. This explains the elevated quantity of CD34 positive cells in the BM of patients with MDS as a result of neoplastic clonal expression.3\n\nRecent studies have proposed an additional mechanism exploring the possibility of the role of BM niche in the pathogenesis of AA. The BM microenvironments also known as the stem cell niche comprises endosteal cells, macrophages, fat cells, fibroblasts, mast cells and microvascular endothelial cells.7 The stem cell microenvironment transmits signals to maintain the fundamental features of the HSCs such as the ability to self-regenerate and the capacity to reproduce all the lineages. Thus, alteration in the BM niche was considered as a potential cause of hematopoietic impairment; however, the ways in which these changes affect the development of the disease remains unclear.8\n\nSeveral researchers have studied the correlation between the BM microenvironment and dysregulated haematopoiesis. Alterations in the components of the microenvironment in the BM, including lymphocytes, mast cells, macrophages, and stromal cells, may be associated with the impaired haematopoiesis leading to AA and/or myeloproliferative neoplasms. The quantitative increase of mast cells in AA cases has been demonstrated in several studies and has resulted in the hypothesis that mast cells can cause cytotoxic effects on the hematopoietic cells in the marrow.8\n\nMast cells originate from BM progenitor cells and migrate into various tissues to complete their maturation. BM mast cell quantification is proposed as a supplementary diagnostic and prognostic tool to differentiate AA from other BM failure conditions like MDS-h.5\n\nThe percentage of mast cells in the BM is generally less than 1% of all the nucleated cells in the marrow and is distributed singly.9 Mast cells stain metachromatically with Toluidine blue (TB), which stains the granules of mast cells purple to red. Histological staining with TB is a highly effective, rapid, direct and antibody-free technique to detect mast cells in tissue sections.10,11 Mast cells have longer life spans and are not directly targeted by the autoimmune attack on the stem cell compartment, resulting in the relative increase in its number in the BM of patients with AA. The quantitative increase in mast cell is clonal in mastocytosis and benign in acquired AA. However, its nature is not completely understood in AA and MDS-h.12,13\n\nIn AA, lower mast cell count is related to better prognosis, but no such relation exists in MDS.5 Several researchers have shown increased numbers of mast cells in cases of AA and have proposed an association between the increased mast cells in the BM with the poor outcome of the patients.14,15 Irrespective of the involved mechanism, a surge in the quantity of mast cells is assumed to be a factor responsible for the reduced cellularity observed in AA and MDS-h.16,17 Therefore, the present study aimed to evaluate the diagnostic utility of mast cell quantification in hypoplastic marrow (HM) to distinguish AA from MDS-h. Furthermore, the association of increased mast cells with decreased HSC in the BM of such entities was analysed.\n\n\nMethods\n\nAll procedures performed in the current study were approved by Institutional Ethical Board, Kasturba Medical College, Mangalore (reference no.: IEC KMC MLR 12-2020/452 date: 24/12/2020). Formal written informed consent was not required since this study used retrospective biopsy samples and we received a waiver by the Institutional Ethical Board, Kasturba Medical College, Mangalore.\n\nA time bound retrospective study was conducted at the Department of Pathology, Kasturba Medical College, Mangalore, MAHE, from 25th December 2020 to September 2022, after ethical clearance.\n\nCases of hypoplastic/aplastic BM biopsies received from January 2015 to December 2021 were included in the study. We calculated a minimum sample size of 58, considering 80% power, 95% confidence level and a relative precision of 10%. Overall, 65 cases met the inclusion criteria of adequate marrow biopsy measuring at least 1 cm in length with minimum four marrow spaces. Cases with measurable disease positive leukaemia, those with poorly preserved paraffin blocks and inadequate biopsies were excluded. Clinical data like age, sex and any other significant details were obtained from the laboratory information system and the medical records department. Our study follows the Sager guidelines for reporting sex and gender information. Sex and gender differences were not taken into consideration for the design of the study. The information regarding the sex of the cases was collected from the lab information system and not determined by the investigators as it is a retrospective study done on archived slides and blocks. The slides and paraffin blocks of all the cases were retrieved and reviewed and the diagnosis of hypoplasia/aplasia was confirmed.\n\nThe H&E-stained tissue sections were studied to assess the cellularity and to identify the morphology of the marrow. All the cases were categorised into three categories namely, AA, MDS-h and HM due to any other cause according to their cytomorphological and haematological features.\n\nThe special staining was done on paraffin embedded, formalin fixed tissue that was assessed for morphology. A representative block was selected in every case and TB special staining was performed, where 1% TB stain (1 gm TB in 100 ml H2O) was poured over the slides and kept for 90 seconds. The slides were then washed, dried and mounted.\n\nQuantification of mast cells was done by identifying the metachromatic granules in mast cell cytoplasm. Total number of mast cells was counted per 200 nucleated cells in 5-10 randomly selected high power fields. Mast cell percentage amongst all nucleated cells was calculated. Mast cell percentage of more than one was quantified as increased.\n\nImmunohistochemistry (IHC) for CD34 was performed on paraffin embedded, formalin fixed tissue that was assessed for morphology. A representative block was selected in every case. IHC staining was performed with a mouse monoclonal antibody against CD34 (Diagnostic BioSystems Cat# PDM050, RRID:AB_2934004). SITVue/DAB Detection System (Diagnostic BioSystems Cat# SIT-100D) was used as an intensification system to enhance the chromogenic signals of the primary antibody. The detailed description of all the procedural steps is available in Figshare.25 Evaluation for CD34 was done in the cytoplasm of the hematopoietic progenitor cells and the number of positive cells was counted and assessed as less than or more than 0.5% of the total hematopoietic cells.\n\nData were analysed using IBM SPSS Statistics (RRID:SCR_016479) 25.0 version. The statistical significance of all variables was calculated using the Chi-squared test and Fisher’s exact test. P<0.05 was taken to be significant.\n\n\nResults\n\nThis study included a total of 65 cases of hypoplastic and aplastic marrows that met the inclusion and exclusion criteria, of which 21 (32.3%) cases were AA, 12 cases were MDS-h (18.5%) and 32 (49.2%) cases were diagnosed as HM.\n\nA bimodal peak was noticed in the age distribution pattern with the majority of the population being from the paediatric and adolescent age group (32.3%) and the second peak comprising of people above 60 years of age (28.7%). The rest of the cases belonged to the age group of 20-60 years old. Slight male predilection was noted with M: F ratio being 1.6:1. Overall, 38% (25) of the total population were female and 62% (40) of the population were male. The demographic data of the individual cases are available as Underlying data.25\n\nMast cells in the BM were highlighted by staining them with TB. Mast cells were counted amongst 200 nucleated cells. More than 1% of mast cells were seen in 36 (55.4%) of the total cases. Seven (10.8%) cases showed more than 10% of mast cells. Mast cell count of more than 1% was considered as increased. Increased numbers of mast cells were observed in most of the cases of AA (31, 48%) followed by HM (20, 31%), and MDS-h (14, 21%), while the rest of the cases showed less than 1% of mast cells in their marrow. The Chi squared test was done with respect to the increased number of mast cells and the different entities of AA, MDS-h and other causes of HM was significant (P: 0.040). The distribution of the increased mast cells amongst the various differentials in the contingency table is depicted in Table 1. Metachromatically stained mast cells in light microscopy in a case of AA and MDS-h are depicted in Figure 1 and Figure 2, respectively. These microphotographs are annotated and minimally cropped. The original unprocessed microphotographs are available as Underlying data.25\n\nAA, aplastic anaemia; HM, hypoplastic marrow; MDS-h, hypocellular myelodysplastic neoplasm.\n\nA: In low power view aplastic marrow is seen with cellularity less than 10% in the marrow spaces (magnification, 20×, H&E). B: Toluidine blue special staining in low power view shows metachromatically stained mast cells (magnification, 20×, Toluidine blue staining). C: Toluidine blue special staining in high power view shows six metachromatically stained mast cells in around 20-22 nucleated cells (magnification, 40×, Toluidine blue staining).\n\nToluidine blue special staining in high power view shows four metachromatically stained mast cells in around 200 nucleated cells (magnification, 40×, Toluidine blue staining).\n\nCD34 IHC expression was assessed to calculate HSCs and categorised as more than and less than 0.5% of positive cells (decreased) amongst all the hematopoietic cells of the marrow. Decreased expression was noted in 45 (69.2%) of the cases.\n\nAn increased number of mast cells was seen in 36 (55.45%) cases of the total study population while significantly decreased/absent HSCs were seen in 45 (69.2%) cases. A total of 25 (69.4%) of the cases that showed an increased number of mast cells also showed significantly decreased HSCs. Whereas 26 (57.7%) of the cases that had decreased HSCs showed an increased number of mast cells. However, the association between decreased HSCs and increased mast cells was statistically insignificant (Chi squared test, P: 0.10). The contingency table of the same is depicted in Table 2.\n\nHSC, hematopoietic stem cell.\n\n\nDiscussion\n\nBM failure conditions with marrow that is hypocellular for age embodies a broad spectrum of acquired and inherited conditions. Patients with MDS-h are known to have a worse prognosis than those with AA because they are more prone to neoplastic progression.18\n\nHaematologists still continue to struggle in making a precise diagnosis due to the blurred lines between AA, other mimicking conditions like MDS-h and the various inherited BM failure syndromes. Identifying the exact disorder leading to a HM is critical as the cause of the disease significantly affects the choice of therapy.19,20\n\nBM evaluation, comprising of both trephine biopsy and aspirate, is obligatory to ascertain the diagnosis. There is convincing evidence that these discrete haematological conditions share a conjoint pathophysiological pathway centred at the alteration and/or damage of the hematopoietic stem and progenitor cells (HSPCs) by the cytotoxic effect of T cells. Increased T cells produce excessive proinflammatory cytokines (interferon-γ and tumor necrosis factor-α), leading to the reduced proliferation and increased apoptosis of the HSPCs.21\n\nThe distinction between AA and MDS-h is mostly dependent on the histomorphological and IHC features of the BM but in HMs it is challenging due to the scarcity of the hematopoietic cells present in the BM and the overlapping of the cytomorphological features of both the entities.4 Erythroid dysplasia is not uncommon in AA and thus cannot be used as a sole distinguishing feature.\n\nMast cell quantification in the BM was performed by several researchers and a common finding of increased number of mast cells in HMs was observed.14–16,22 In our study we considered more than 1% of mast cells per 200 nucleated cells as the cut off for defining increase in the quantity of mast cells. The results in our study were similar to other studies with elevated mast cells seen in 55.4% of the total cases out of which the majority of the cases were AA (P<0.05). The quantity of mast cells ranged from 0-100 mast cells per 200 nucleated cells. The case with the highest number of mast cells belonged to the category of AA. However, the variation in the quantity of mast cells in both AA and MDS-h lies in the same range. This is consistent with the findings of Ingrid Fohlmeister22 done on 48 cases of different forms of MDS and 59 cases of AA. They demonstrated that there was overlap in the number of mast cells found in the BM of individuals with AA and MDS-h. The number of mast cells varied from 0-205/mm2.\n\nComplex interactions between the hematopoietic cells and the BM niche occur during haematopoiesis, although the exact cause and mechanism involved in the deregulated haematopoiesis is unknown. HSCs reside in a specialized microenvironment (niche) in the BM. BM microenvironment is important in maintaining the function of HSC as it is thought to transmit signals sustaining key HSC properties like regenerating capability and multilineage reproducing capacity. Thus, alteration in the BM niche can be a potential factor associated with hematopoietic impairment. However, it is still unclear how these changes contribute to the development of the disease.\n\nIn cases of idiopathic AA, the ineffective haematopoiesis can be considered as a result of some unknown changes in the BM microenvironment. Mast cells are considered by some researchers as a cause of the ineffective haematopoiesis in AA as it stimulates apoptosis and auto immune attack by cytotoxic killer cells. Studies have demonstrated that the BM of patients with AA shows increases in the quantity of mast cells and natural killer (NK) cells reflecting the cytotoxic or immune-mediated damage of the marrow.8,11 Our study strengthens this hypothesis as 17 (48%) of the cases that showed an increased number of mast cells belonged to the patients with AA. Thus, increases in the numbers of mast cells can be considered as a causative factor for the insufficient haematopoiesis. However, in our study the association between increased mast cells and reduced HSCs was statistically insignificant.\n\nPatients with AA may have altered BM niches that contribute to the disease pathophysiology or cause ineffective haematopoiesis. Quantification of mast cell can help in identifying the prognosis of the cases of AA. Reduced numbers of mast cells are a good prognostic indicator in AA while no such relation is observed in cases of MDS.16\n\nAlthough hematopoietic stem cell transplantation plays a frontline role in the treatment of haemato-oncological conditions, there are still significant issues that need to be resolved, including the difficulty in finding matched donors and the ineffective engraftment of HSCs into the BM. An improved comprehension of the interactions amongst each component of the BM niche can help in identifying the potential therapeutic targets in cases of BM failure as well as myeloproliferative disorders.23\n\nSimulating the hematopoietic niche is a promising method for effectively increasing the number of HSPCs and fine-tuning their features ex vivo. The creation of a functioning hematopoietic microenvironment in vitro is still constrained by attempts to replicate it without a thorough grasp of the specific roles played by individual components involved in the hematopoietic setting. Detailed knowledge of the crucial cells in the BM microenvironment and the way they affect the regulation of HSCs can aid in establishing an ex vivo structural arrangement for the expansion of HSCs to provide a novel source of therapeutic blood cells for haematological disorders.23,24\n\nIn conclusion, mast cell quantification in the BM biopsies with the help of TB special stain can act as a supplementary tool to distinguish the two entities as mast cells are increased in the majority of the cases of AA, while it is increased only in a few cases of MDS-h. The knowledge of the association between the increased number of mast cells with decreased HSCs can help in establishing an ex vivo environment mimicking the normal BM. This can aid in cultivating HSPCs for therapeutic purposes as well as in identifying the targets for targeted therapies in disorders like AA and other haematological malignancies.", "appendix": "Data availability\n\nFigshare: mast cell quantification raw data.xlsx. https://doi.org/10.6084/m9.figshare.21966848. 25\n\nThis project contains the following underlying data:\n\n1. Excel sheet of complete data: rawdata.xlsx\n\n2. STROBE_checklist. Mast cell quantification.docx\n\n3. Unprocessed microphotographs: 1.jpeg, 2.jpeg, 3.jpeg, 4.jpeg, 5.jpeg, 6.jpeg\n\n4. Procedure of CD34 IHC staining.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\n\nReferences\n\nTuzuner N, Cox C, Rowe JM, et al.: Hypocellular myelodysplastic syndromes (MDS): new proposals. Br. J. Haematol. 1995 Nov; 91(3): 612–617. PubMed Abstract \| Publisher Full Text\n\nTuzuner N, Bennett JM: Reference standards for bone marrow cellularity. Leuk. Res. 1994 Aug; 18(8): 645–647. PubMed Abstract \| Publisher Full Text\n\nMatsui WH, Brodsky RA, Smith BD, et al.: Quantitative analysis of bone marrow CD34 cells in aplastic anemia and hypoplastic myelodysplastic syndromes. Leukemia. 2006 Mar; 20(3): 458–462. PubMed Abstract \| Publisher Full Text\n\nBarrett J, Saunthararajah Y, Molldrem J: Myelodysplastic syndrome and aplastic anemia: distinct entities or diseases linked by a common pathophysiology? Semin. Hematol. 2000 Jan; 37(1): 15–29. Publisher Full Text\n\nMaciejewski JP, Risitano A, Sloand EM, et al.: Distinct clinical outcomes for cytogenetic abnormalities evolving from aplastic anemia. Blood. 2002 May 1; 99(9): 3129–3135. PubMed Abstract \| Publisher Full Text\n\nPeslak SA, Olson T, Babushok DV: Diagnosis and treatment of aplastic anemia. Curr. Treat. Options Oncol. 2017; 18(12): 70. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYoung NS, Barrett AJ: The treatment of severe acquired aplastic anemia. Blood. 1995; 85: 3367–3377. Publisher Full Text\n\nGiudice V, Selleri C: Aplastic anemia: pathophysiology. Semin. Hematol. 2022 Jan; 59(1): 13–20. PubMed Abstract \| Publisher Full Text\n\nOrfao A, Escribano L, Villarrubia J, et al.: Flow cytometric analysis of mast cells from normal and pathological human bone marrow samples: identification and enumeration. Am. J. Pathol. 1996; 149(5): 1493–1499. PubMed Abstract\n\nRibatti D: The staining of mast cells: A historical overview. Int. Arch. Allergy Immunol. 2018; 176(1): 55–60. PubMed Abstract \| Publisher Full Text\n\nPuebla-Osorio N, Sarchio SNE, Ullrich SE, et al.: Detection of infiltrating mast cells using a modified toluidine blue staining. Methods Mol. Biol. 2017; 1627: 213–222. PubMed Abstract \| Publisher Full Text\n\nNatkunam Y, Rouse RV, Zhu S, et al.: Immunoblot analysis of CD34 expression in histologically diverse neoplasms. Am. J. Pathol. 2000; 156(1): 21–27. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDasgupta S, Mandal PK, Chakrabarti S: Etiology of pancytopenia: an observation from a referral medical institution of eastern region of India. J. Lab. Phys. 2015; 7(2): 090–095. Publisher Full Text\n\nOrazi A, Albitar M, Heerema NA, et al.: Hypoplastic myelodysplastic syndromes can be distinguished from acquired aplastic anemia by CD34 and PCNA immunostaining of bone marrow biopsy specimens. Am. J. Clin. Pathol. 1997 Mar; 107(3): 268–274. PubMed Abstract \| Publisher Full Text\n\nÖzdemir Ö, Ravindranath Y, Savaşan S: Evaluation of long-term liquid culture grown human bone marrow mast cell cytotoxicity against human leukemia cells. Blood. 2002; 100: 3690–3697. PubMed Abstract\n\nOzdemir O, Savaşan S: The role of mast cells in bone marrow diseases. J. Clin. Pathol. 2004 Jan; 57(1): 108–109. PubMed Abstract \| Publisher Full Text\n\nSkibenes ST, Clausen I, Raaschou-Jensen K: Next-generation sequencing in hypoplastic bone marrow failure: what difference does it make? Eur. J. Haematol. 2021 Jan; 106(1): 3–13. PubMed Abstract \| Publisher Full Text\n\nKhoury JD, Solary E, Abla O, et al.: The 5th edition of the World Health Organization Classification of Haematolymphoid Tumours: myeloid and Histiocytic/Dendritic Neoplasms. Leukemia. 2022 Jul; 36(7): 1703–1719. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRohira N, Meenai FJ: A cross sectional study of clinical and aetiological profile of pancytopenia at a tertiary care hospital in Bhopal. Indian J. Pathol. Oncol. 2019; 6(1): 67–74. Publisher Full Text\n\nDrexler B, Tichelli A, Passweg JR: Bone marrow failure. Ther. Umsch. 2019; 76(9): 523–529. PubMed Abstract \| Publisher Full Text\n\nDhanjal TS, Pendaries C, Ross EA, et al.: A novel role for PECAM-1 in megakaryocytokinesis and recovery of platelet counts in thrombocytopenic mice. Blood. 2007 May 15; 109(10): 4237–4244. PubMed Abstract \| Publisher Full Text\n\nFohlmeister I, Reber T, Fischer R, et al.: Bone marrow mast cell reaction in preleukaemic myelodysplasia and in aplastic anaemia. Virchows Arch. A Pathol. Anat. Histopathol. 1985; 405(4): 503–509. PubMed Abstract \| Publisher Full Text\n\nCosta MHG, de Soure AM , Cabral JMS, et al.: Hematopoietic niche - exploring biomimetic cues to improve the functionality of hematopoietic stem/progenitor cells. Biotechnol. J. 2018 Feb; 13(2). PubMed Abstract \| Publisher Full Text\n\nNegendank W, Weissman D, Bey TM, et al.: Evidence for clonal disease by magnetic resonance imaging in patients with hypoplastic marrow disorders. Blood. 1991 Dec 1; 78(11): 2872–2879. PubMed Abstract \| Publisher Full Text\n\nGupta S: mast cell quantification raw data.xlsx. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "198788", "date": "01 Nov 2023", "name": "Dijiong Wu", "expertise": [ "Reviewer Expertise Hematologist" ], "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 differentiation of AA and hypo-MDS remains a challenge in clinical. Chaithra, et al. try to make a differentiation diagnosis based on the IHC count of CD34+ hematopoietic stem cell and TB+ mast cells. Totally 21 AA, 12 hypo-MDS and 32 HM were included. Based on the report, there are many concern need to clarified and better explained:\nThe differentiation of AA and hypo-MDS is quite difficulty in clinical, how the authors make the specific diagnosis of 21 AA and 12 MDS? Please explain in detail. Also, the accurate number of the AA and MDS are quite limited, which may contribute to the deviation.\n\nThe distribution of hematopoietic cells in BM biopsy is not uniformly. The method of IHC may not practically represent the haematopoiesis, better adding the result of flow cytometry result, especially CD34+ cells.\n\nResult showed that there is a big different in the count of mast cell in AA, some case over 10%. Is there any difference in IST or HSCT response in AA with different range of mast cells?\n\nThe conclusion in ABSTRACT showed that \" Understanding its role in the bone marrow niche can enhance stem cell transplant treatment\". Based on the data and analysis, its hard to get the conclusion, and the response of IST or HSCT were missing.\n\nAuthors found that there are more mast cells in AA but not MDS, but there is still patient with gray expression. It would be better to have the probably rang to help the distinguish diagnosis.\n\nIn the discussion part, authors clarified that \"An improved comprehension of the interactions amongst each component of the BM niche can help in identifying the potential therapeutic targets\", please name the potential therapies specially as example.\n\nActually, with the development of HSCT, especially haploidentical HSCT, the donor of HSCT no longer a very big problem in the treatment of AA.\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? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "211585", "date": "01 Nov 2023", "name": "Valentina Giudice", "expertise": [ "Reviewer Expertise Bone marrow failure syndromes", "flow cytometry immunophenotyping" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this manuscript, Gupta et al. have investigated frequency of bone marrow mast cells in aplastic anemia (AA) and hypoplastic myelodysplastic syndromes (hMDS), as have proposed this cellular marker for differential diagnosis of these bone marrow failure syndromes. However, several issues are present:\nThis is a case series study and should be clearly stated also in the title. Indeed, to claim a \"diagnostic utility\" of a marker, more cases are required. In this case, the analysis is carried out on a total of 21 AA and just 12 hMDS, without a control cohort of non hypoplastic MDS.\n\nDiagnostic criteria used for AA and hMDS are not stated.\n\nMastocytosis was ruled out? c-Kit mutations were excluded?\n\nNo additional information on mast cell phenotype was reported, as mast cell related (tryptase, chymase, CD25, and CD117) antigens can be investigated also by IHC.\n\nMast cells have been associated with neoangiogenesis also in MDS1, and could be increased in higher-risk MDS; therefore, some indications on clinical features of those patients should be clearly indicated at least in a table.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-823
https://f1000research.com/articles/12-820/v1	13 Jul 23	{ "type": "Research Article", "title": "Mapping capacity building programs in health diplomacy: Relevance and application in an uncertain world", "authors": [ "Sanjay Pattanshetty", "Aniruddha Inamdar", "Kiran Bhatt", "Viola Savy Dsouza", "Anirudh Prem", "Helmut Brand", "Aniruddha Inamdar", "Kiran Bhatt", "Viola Savy Dsouza", "Anirudh Prem", "Helmut Brand" ], "abstract": "Background: Health diplomacy is one of the emerging avenues for academics where foreign policy dynamics and global health meet. Its relevance has augmented especially after the COVID-19 pandemic that brought the world to a halt. International organization and national entities that are responsible for health governance as well as its socio-economic determinants have been increasingly involved in the negotiations for a collective action towards a better health infrastructure and preparedness. However, the approach to health diplomacy seems to vary with whether health is looked through diplomacy lens or vice versa. Thus, inculcating adequate and appropriate competencies of both fields to conduct negotiations for health while keeping national interests and international commitments intact is imperative. Methods: This study investigates 50 programmes/courses that have been currently offered around the globe to understand the competencies that have been identified as essential for a health diplomat. We examined four aspects: i) geographical distribution of programme/course (ii) the type of global health diplomacy programme being offered and their duration (iii) mode of teaching and (iv) cross-cutting themes that the programme offers. Results: We found that the courses/programmes have been mostly provided by the countries of the Global North who play a key part in international negotiations. Although there were diverse types of certifications identified, they can be classified into two groups - core health diplomacy and inclusive health diplomacy programmes. The health diplomacy training is preferred to be provided in-person due to the nature of the work. Conclusions: While competencies for health governance and international relation have been dominant among the current programmes, other cross-cutting themes such as economics, politics, law, public policy, crisis management, environment and public health have been considered essential. The article concludes with a proposal of a framework to streamline the sectors and the competencies that is required in health diplomats.", "keywords": [ "Health Diplomacy", "Capacity Building Programs", "Review", "Global North", "Global South", "Global Health Diplomacy Programme" ], "content": "Introduction\n\nThe contemporary world is experiencing uncertainty and adaptability challenges considering the disruptive development and globalization of diverse sectors. Globalization has made it evident that any given sector cannot function in silos.1–3 Interdependence as a theory and practice is a necessity to be implemented in complex adaptive systems, which by nature are unpredictable. The health sector is no different in this context.4 Emerging and re-emerging diseases have challenged the transnational health systems, services, infrastructure, leadership, and governance set by the institutions established after World War II.5,6 The World Health Organization (WHO) was set up in 1948 as a progressive agency that set norms, standards, and guidelines to promote health and well-being, established partnerships through successful diplomatic and political negotiation with nations, partners, and people to ensure safety and protection of the vulnerable segments of the population. However, the growing discontent of globalization, political upheaval, food crisis, economic crisis, energy crisis, conflicts, cyber security, trade, intellectual property tensions, and technology wars have cornered the international organization to revisit their strategy in handling social, economic, political, and commercial determinants of health outcomes.7 The current health challenges are not confined to a nation alone but are international, inter-sectoral, multi-level, and multi-scalar with COVID-19 being an ideal case study.8,9\n\nAn approach to solving such health issues and determinants of health demands an intervention that is futuristic, context-specific, and resilient in nature and actions. Such interventions necessitate political commitment and diplomatic negotiations to reform member-driven institutions, economic reforms, cultural reforms, sensitiveness to the environment, and relevant capacity-building programs in educational institutions. The current health initiatives are issue specific with investments in addressing problems in health domains, predominantly. However, the Commission on Social Determinants of Health (CSDH) made it clear that policies for health equity involve diverse sectors with different core tasks and varied scientific traditions.10 Further, the Health in All Policies (HiAP) approach to public policy systematically articulated the health impacts of decisions made outside the health sector and advocated for synergies among various sectors to avoid harmful health impacts to improve population health and health equity. It is imperative to understand policies for trade, conflict, intellectual property, economics, political science, technology, labor market, transport, supply chain, international relations etc. to develop cross-border solutions to achieve health policy outcomes. Thus, from the socioecological perspective, to address the current health policy challenges a systemic inspection is an essential requirement.\n\nWith this backdrop, one question that stands tall is to ask if there are robust educational programs covering the aforementioned issues from a health lens. Whether programs in health diplomacy cover some of the cross-cutting issues? The importance and the relevance of concept of “Global Health Diplomacy” has been increasingly recognized and practiced by both the developed and developing countries. Figure 1 depicts the frequency of health diplomacy journal articles in the last few decades in PubMed database. The graph indicates a growing interest in the academia in recent years. However, a major criticism of global health diplomacy as concept is that the deliberations are exclusionary to low- and middle-income countries that cannot compete with the negotiating power of high-income countries.11 With power and influence, global health governance can potentially skew the framing of the global health agenda and marginalize issues relevant to LMICs. The increasing role of India, Indonesia and South-East Asia in global governance and health diplomacy in particular is relevant given the size of the population, disease burden and its strategic geographical location in the Indo-Pacific.\n\nHowever, growing interest and influence in global health governance needs to be supported and accompanied by the necessary capacity in health diplomacy and governance. LMIC should invest in initiatives to strengthen its diplomacy skills to enhance its involvement in the staging of global health diplomacy. In this context, in this paper, a narrative synthesis of existing health diplomacy programs across the globe was conducted.\n\n\nMethods\n\nThis narrative review article reviewed the data that was extracted using an extensive web and internet search from websites of universities, massive open online courses (MOOCS), and training centres, published in English. To search the articles, search terms mentioned in Table 1 were used. Using this search method, a list of 50 programmes were assessed for eligibility. A detailed Data Extraction Sheet (DES) is presented in the Extended data.12 Programmes that adopted a holistic and multidisciplinary approach to combine the fields of foreign affairs with health were included in the study. Similarly, dual degree and joint degrees programmes that aim to bring in the international relations element in public health, policy or law and vice versa were considered. The graphs and figures were derived using Microsoft Excel.\n\n\n\n• Global health\n\n\n\n• Global health and security courses\n\n\n\n• Health Diplomacy course\n\n\n\n• Public Health and international relations\n\n\n\n• Public Health\n\n\n\n• Health Diplomacy and specialisations degrees\n\n\n\n• International relations health course\n\n\n\n• Public health Policy and International Development\n\n\n\n• Health diplomacy programmes\n\n\n\n• Public Health and International relations Joint degrees\n\n\n\n• Health Policy\n\n\n\n• Dual Degrees and Health Diplomacy\n\n\n\n• Public health Policy\n\n\n\n• Health Diplomacy and Certifications\n\n\n\n• Health Policy Concentrations\n\n\n\n• International Affairs and Health Policy\n\n\n\n• Global health security courses India\n\n\n\n• Online courses and Global Health Diplomacy\n\n\n\n• Public Policy\n\n\n\n• Health Security and Global Health and International relations\n\n\n\n• Public Policy and Development\n\n\n\n• Global Health Diplomacy and Health Law\n\n\n\n• Global Health Policy\n\n\n\n• Community Health and International Aid and Diplomacy\n\nFurther, the programmes that were identified during the search have been divided into two broad categories:\n\n1. Core global health diplomacy programmes: This group of programs includes the ones that explicitly focuses on ‘global health diplomacy’ and is mentioned in its title.\n\n2. Inclusive health diplomacy programmes: This group comprises programmes that offer global health diplomacy related modules, certification, specialisation in Masters, joint or dual degrees but do not specifically mention the field in its title. The programmes identified were of various categories which the candidates would receive at its successful completion.\n\n\nResults\n\nIn the following section, the major findings have been discussed and analysed for: (i) The country where the programme/course is offered (ii) the type of global health diplomacy programme being offered and their duration (iii) Mode of teaching and (iv) The cross-cutting themes that the programme offers.\n\nAn overview of the geographical distribution of the global health diplomacy and the related programmes offered is depicted in Figure 2. We observe that most of the programmes/courses that deal with health diplomacy are offered in global north. The exception of the Egypt is due to the training certification offered by WHO Regional Committee for the Eastern Mediterranean Region. The highest concentration of 28 programmes and courses are in the United States of America, followed by nine in United Kingdom, five in Switzerland, and at most one offered by other countries. This state of education programmes in health diplomacy also highlights the issue of disproportionate involvement of global north in practicing health diplomacy while the global south faces greater health threats. Thus, it is imperative for the global south to train the diplomats according to the local challenges and solutions available and have an equal footing during negotiations of health-related issues at a global level.\n\nOverall, health diplomacy has been offered through various certification. Figure 3 depicts the type of certifications that are offer in the health diplomacy and related programmes and Table 2 provides the description of the classifications. It was seen that most of the programmes in health diplomacy and related courses were offered in the form of certificate courses. It was interesting to observe that out of the 50 programmes that were collected and examined, there were only seven programmes that could be included in the core health diplomacy programmes. This condition is interesting to ponder upon as despite the increase in the discussions of health diplomacy in academia as depicted in Figure 1, the progress in creating educational modules and training specifically for the field has been marginal. Out of the seven identified, five were certificate programmes, one was training certification, and one was in the form of an optional module. The duration allocated by these programmes was interesting to note as it had a range of highest being two months (training certification) and the lowest being 12 hours (optional module). Thus, there is need to revise the time dedicated to training of health diplomats as the relevance of this topic is in the rise more so after the COVID-19 pandemic.\n\nAs the mentioned in the previous section, the programmes were mainly classified into two categories, and the following sub-sections provides the description of the observations that emerged during analysis.\n\nCore global health diplomacy programmes\n\nThese courses were designed and delivered by USA, Canada, UK, Switzerland, Hungary, and Egypt. The curriculum in health diplomacy predominantly covered history, relevance, relevance of global institutions such as WHO, World Trade Organization (WTO), International Monetary Fund (IMF), concepts of diplomacy and governance, cross-cutting issues in relation to health in foreign policy, global health security, health system strengthening, determinants of health such as inequity, influence of trade, climate change, economics, human rights, and recent developments related to diverse health policy level challenges. Some of the competencies that are stressed were mostly cross cutting such as communication, negotiation, decision making, scenario planning, and analytical skills. Additionally, analysis of case studies and negotiation processes at the national, regional, and global levels were also covered as part of the curriculum. Table 3 provides the details regarding the seven core health diplomacy programmes offered across the world.\n\n* The fees in terms of USD was done according to the conversion rate on May 2, 2023.\n\nIn this category, pedagogy on health diplomacy was covered briefly as part of global health, international development, international affairs, global health security, global health policy, global health affairs, international governance, public health, public policy, Humanitarian Emergencies, Global Health Law and Health System Strengthening related programs. The curriculum in health diplomacy predominantly covered was related to mostly on global health with few topics related to global health governance, political analysis, geopolitics, conflict, regulatory challenges, diplomacy, and negotiation with different stakeholders. In few programs, biological weapons, new and re-emerging diseases, demographic and epidemiological transitions, and sustainable development were discussed. However, few programs stressed the importance of protection and promotion of population health in a globalising world, at both national and transnational level. In particular, the George Washington University (Elliott School of International Affairs), covered IHR, global pandemic disease; environmental health problems; international nutrition and malnutrition; disparities in access to health care; and global health regulations and economics. A course from London School of Economics and Political Science highlights the politics of global health at the time of pandemics and learning lessons from COVID-19. The impact of conflict, climate change and migration on health was also considered in the curriculum. The course stressed on critical discussion of health-focused targets and international indicators such as the Sustainable Development Goals, the pharmaceutical industry, multilateral and bilateral donors and universal health coverage policies. And the course from Harvard University (John F. Kennedy School of Government) using the combination of lectures, interactive discussions, case studies, and group work focussed on global health security, emerging health threats, its consequences in the context of weak health systems, identifying and analysing the connections between health systems, global security policies, and international responses during conflicts.\n\nDespite the incremental increase in the use of online mode of education during the pandemic, 80 per cent of health diplomacy and the related programmes were conducted in person as shown in Figure 4. Among the seven core health diplomacy programmes, the mode of teaching used were distributed by three being online, three in-person training, and one hybrid mode. As dialogue is a key component in practicing diplomacy, it the trainers and the learners may prefer the programme to be conducted in person than in an online mode.\n\nThe main component while examining in the programmes were the themes that have been included for being trained for a health diplomat by the existing programmes. Figure 5 depicts the radar diagram of the key themes that were identified in the learning outcome section of the programme/course description. We see that most of the educational content on health diplomacy has identified that health is a cross-cutting theme across various discipline such as international relations, health governance, law, politics, economics, crisis management, public policy, public health, and environment. We can observe that most health diplomacy programmes consider international relations and health governance are essential components that need to be included in the curriculum. Understanding the national and international regulations and laws were also considered to be an important for at least 23 programmes out of the 50 that were analysed.\n\n\nDiscussion and conclusion\n\nThe interconnected nature of global pandemics with socioeconomic, political, geopolitical, and environmental factors was recognized as a threat to the stability of nations. A collective commitment towards minimizing the impact of a potential global pandemic was emphasized by the Oslo Ministerial Declaration in 2007 where with both foreign and health policymakers came together and stated, “We have agreed to make an impact on health a point of departure and a defining lens that each of our countries would use to examine key elements of foreign policy and development strategies”.13 Foreign policy and global health were acknowledged to be interdependent for effective global health outcomes by the United Nations General Assembly (UNGA) resolutions.14 During the 64th session UNGA focused on pandemic preparedness, access to diagnostics, therapeutics, and human resource for health. Foreign Policy commitments to health issues is reflected in the negotiation and adoption of the International Health Regulations (2005), the WHO Framework Convention on Tobacco Control and intergovernmental negotiations on public health, innovation, and intellectual property, and currently the ratification of IHR and proposed Pandemic Treaty.\n\nAugmented globalization, occurrence of emerging, re-emerging diseases, COVID-19, climate change, changes in trade facilitation norms, intellectual property rights and global supply chain issues has influenced and produced uncertain conditions for negotiating global health challenges through diplomatic practices which otherwise was feasible to anticipate the solution for various global challenges including health. The current global health governance challenges are transcending both health and foreign policy dimensions. Global Health challenges have become increasingly well-known in the evolving global diplomacy agenda. There is shift in approach from “Global Health Governance to Governance of Global Health” due to recent events. Historically health was considered as “low politics” and a “mere humanitarian” endeavour in foreign policy priorities.15,16 However, pandemics such as SARS, pandemic influenza, MERS, Ebola, Zika, COVID-19, Monkeypox and recent Marburg virus disease are demanding for joint commitment, cooperation among health and foreign policymakers and to consider health as “High Politics” on par with the national interests of safety, security, power, and influence.7 Further, the Sustainable Development Goals, adopted in 2015, presented a major milestone in unifying efforts toward global development and partnership, thereby causing significant shift in health priorities.17 Having understood the drift in global challenges and political commitment, it is imperative to ask whether the existing capacity building programs for instance in global health, international relations, health policy cover diplomatic, financial, and geopolitical context that underlies global health decision-making? And whether existing programs have a component that builds competency to describe and analyze the opportunities, challenges, and limits of Global Health Diplomacy? How many programs in health diplomacy cover competencies related to international cooperation and global solidarity, global economy, trade and development, global health security, strengthening health systems and addressing inequities to achieve global health targets? Given the policy significance of health diplomacy, authors have tried to address, create demand and build a narrative on the need for health diplomacy programs using a narrative evidence synthesis approach. The narrative synthesis has captured existing evidence on capacity building programs in health diplomacy.\n\nGlobal Health Diplomacy has so far been principally defined by global institutions from developed countries. The current Global Health Diplomacy programs lack inclusivity and competency to tackle the challenges that are faced by developing countries such as access to diagnostics, vaccines and therapeutics. From the impact of COVID-19 on developing countries it was clear that health issues are transnational, and the reputed institutions in the global south should invest and put sincere effort to initiate capacity building programs in global health diplomacy in cooperation with national and international government and reputed international universities and global institutions.18\n\nThe pedagogy should focus on inter-disciplinary topics such as trade, intellectual property, innovation, public policy, conflict, and human rights. The innovative methods of teaching such as scenario planning, simulation exercises and negotiation techniques would be helpful. With newer development of digital infrastructure and the associated risk of cyber security, it becomes all the more important for the Global Health Diplomacy programs to design cross-cutting curriculum that can facilitate in building transferrable skills and competencies among diverse professionals. Finally, it is a moral obligation of government, institutions, and universities both in developed and developing countries to bridge the knowledge gap in global health diplomacy. This approach can enable leaders in global health to tackle both developing and developed country problems irrespective of location using the competencies acquired in Global Health Diplomacy programs.\n\nThe Figure 5 depicts the binary approach of the current health diplomacy programmes and courses. While multi-disciplinary has been vocalized in health diplomacy trainings, the potential approach to inculcate it has not been mapped in the current literature. Studies such as Bond (2008), Katz et al. (2011), Cooper & Farooq (2015), and Kickbusch et al. (2021), have highlighted the importance of including the security, trade, social justice, and development issues during the health diplomacy training.19–22 Additionally, Brown et al. (2014) provided a description of the levels and the actors involved in conducting health diplomacy.23 An amalgamation of the previously proposed models and the outcomes of the current study, Table 4 is a proposed framework to streamline the sectors and the competencies that is required in health diplomats.", "appendix": "Data availability\n\nOpen Science Framework: Mapping Capacity Building Programs in Health Diplomacy – Relevance and Application in Uncertain World, https://doi.org/10.17605/OSF.IO/TECPS. 12\n\nThis project contains the following underlying data:\n\n‐ Appendix 1: Data Extraction Sheet (DES)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nWe would like to acknowledge Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, for the logistics and administrative support.\n\n\nReferences\n\nIMF Staff: Globalization: Threat or Opportunity? An IMF Issues Brief. International Monetary Fund; 2000; published online April 12. (accessed May 2, 2023). Reference Source\n\nReeves M, Deimler M: Adaptability: The New Competitive Advantage. Harv. Bus. Rev. 2011. (accessed May 2, 2023). Reference Source\n\nSharma P, Leung TY, Kingshott RPJ, et al.: Managing uncertainty during a global pandemic: An international business perspective. J. Bus. Res. 2020; 116: 188–192. Publisher Full Text\n\nMcDaniel RR, Lanham HJ, Anderson RA: Implications of complex adaptive systems theory for the design of research on health care organizations. Health Care Manag. Rev. 2009; 34: 191–199. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nElston JWT, Cartwright C, Ndumbi P, et al.: The health impact of the 2014–15 Ebola outbreak. Public Health. 2017; 143: 60–70. Publisher Full Text\n\nOECD: Strengthening health systems during a pandemic: The role of development finance.2020; published online June 25. (accessed May 2, 2023). Reference Source\n\nPattanshetty S, Inamdar A, Brand H: Global Health Governance in an Uncertain World: A Proposed Framework for the G20. Observer Research Foundation; 2023; published online Jan 30. (accessed May 1, 2023). Reference Source\n\nFinch H, Hernández Finch ME, Mytych K: Not One Pandemic: A Multilevel Mixture Model Investigation of the Relationship Between Poverty and the Course of the COVID-19 Pandemic Death Rate in the United States. Front. Sociol. 2021; 6: 158.\n\nSovacool BK, Furszyfer Del Rio D, Griffiths S: Contextualizing the Covid-19 pandemic for a carbon-constrained world: Insights for sustainability transitions, energy justice, and research methodology. Energy Res. Soc. Sci. 2020; 68: 101701. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: Closing the gap in a generation: health equity through action on the social determinants of health - Final report of the commission on social determinants of health.2008; published online Aug 27. (accessed May 1, 2023). Reference Source\n\nReidpath DD, Allotey P: The problem of ‘trickle-down science’ from the Global North to the Global South. BMJ Glob. Health. 2019; 4: e001719. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPattanshetty S, Inamdar A, Bhatt K, et al.: Mapping Capacity Building Programs in Health Diplomacy – Relevance and Application in Uncertain World. OSF. 2023; published online May 2. Publisher Full Text\n\nMinisters of Foreign Affairs of Brazil FINSSA and T. Oslo Ministerial Declaration-global health: a pressing foreign policy issue of our time. Lancet. 2007; 369: 1373–1378. Publisher Full Text\n\nSecretary-General UN, Director-General WHO: Global health and foreign policy:: strategic opportunities and challenges: note/: by the Secretary-General.2009; published online Sept 23. (accessed May 1, 2023). Reference Source\n\nPattanshetty S, Brand H: Health in Foreign Policy in the Context of COVID-19.Udupi N, Seetharam RN, Mukhopadhyay C, editors. COVID-19: A Multidimensional Response. Manipal Universal Press (MUP); 2021; pp. 375–392.\n\nFidler DP: Health as foreign policy: harnessing globalization for health. Health Promot. Int. 2006; 21: 51–58. PubMed Abstract \| Publisher 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: e1196–e1252. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTaghizade S, Chattu VK, Jaafaripooyan E, et al.: COVID-19 Pandemic as an Excellent Opportunity for Global Health Diplomacy. Front. Public Health. 2021; 9: 655021. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBond K: Commentary: health security or health diplomacy? Moving beyond semantic analysis to strengthen health systems and global cooperation. Health Policy Plan. 2008; 23: 376–378. Publisher Full Text\n\nKatz R, Kornblet S, Arnold G, et al.: Defining Health Diplomacy: Changing Demands in the Era of Globalization. Milbank Q. 2011; 89: 503–523. Publisher Full Text\n\nCooper AF, Farooq AB: Stretching health diplomacy beyond ‘Global’ problem solving: Bringing the regional normative dimension in. Glob. Soc. Policy. 2015; 15: 313–328. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKickbusch I, Nikogosian H, Kazatchkine M, et al.: Conducting global health negotiations. A Guide to Global Health Diplomacy. Geneva, Switzerland: Global Health Centre; 2021; pp. 153–164.\n\nBrown MD, Mackey TK, Shapiro CN, et al.: Bridging Public Health and Foreign Affairs -The Tradecraft of Global Health Diplomacy and the Role of Health Attachés. Sci. Dipl. 2014; 3: 1–12." }	[ { "id": "188144", "date": "01 Nov 2023", "name": "Shyam Sundar Budhathoki", "expertise": [ "Reviewer Expertise Global Health practice and education" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper is well-written account of an important area of Global Health.\nSome minor comments:\nThe title mentions ‘uncertain world’. I am not sure how that is reflected in the main text. Perhaps a more neutral word/phrase could be an alternative to describe the world?\n\nWhile it is clear what the article has intended to do after reading the full paper, I feel the aims as mentioned in the main text could be a bit more elaborative. Currently it just says that ‘this paper is a narrative synthesis of existing health diplomacy programs…’. ‘Narrative Synthesis’ could be unfolded for use in aims.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "188131", "date": "01 Nov 2023", "name": "Rajib Dasgupta", "expertise": [ "Reviewer Expertise Public health policy", "evalution and national health programmes" ], "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 is an excellent review of 50 programmes/courses currently offered around the globe and four principal dimensions have been explored: i) geographical distribution; (ii) type of global health diplomacy programme; (iii) mode of teaching and; (iv) cross-cutting themes. The study makes an important observation that these are almost exclusively limited to the global north and that cross cutting themes such as trade, law or environment need further strengthening. This article is recommended as an important contribution and a valuable addition to the discourse.\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": "188153", "date": "02 Nov 2023", "name": "Garry Aslanyan", "expertise": [ "Reviewer Expertise Global health", "global health diplomacy" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is a good attempt to bring together current programs and course in the ever emerging area of global health diplomacy.\nThere are some limitations to this review which will affect the conclusions. These include, lack of information how many of the programs/courses cited actually include simulation practical negotiation modules which are critical for diplomacy skill development?\nHow many of the course participants are from global north and how many are from global south? Also, there are diplomacy courses, in various countries, that include global health as one of the subjects only - these were not included.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-820
https://f1000research.com/articles/10-891/v1	06 Sep 21	{ "type": "Research Article", "title": "Attrition of methylnaltrexone treatment-emergent adverse events in patients with chronic noncancer pain and opioid-induced constipation: a post hoc pooled analysis of two clinical trials", "authors": [ "Neel Mehta", "Neal E. Slatkin", "Robert J. Israel", "Nancy Stambler", "Neal E. Slatkin", "Robert J. Israel", "Nancy Stambler" ], "abstract": "Background: Opioids prescribed for the management of chronic noncancer pain are associated with nausea, vomiting, and constipation. Methylnaltrexone, a peripherally acting µ-opioid receptor antagonist, has demonstrated robust efficacy and was well-tolerated in treating opioid-induced constipation without affecting central analgesia. Our objective was to assess changes in the frequency of adverse events after the first or second dose of methylnaltrexone or placebo. Methods: This post hoc analysis pooled data from two randomized, placebo-controlled clinical trials assessing methylnaltrexone for opioid-induced constipation in the outpatient setting. Patients received subcutaneous methylnaltrexone (12 mg once daily or 12 mg once every other day), oral methylnaltrexone (150, 300, or 450 mg daily), or placebo. Adverse events, opioid withdrawal symptoms, pain intensity, and rescue-free bowel movements (RFBMs) within 4 hours of the first dose (i.e., RFBM responders) were assessed. Associations between adverse event frequencies and RFBM response were also evaluated. Results: The analysis included 1263 adult patients with chronic noncancer pain. Treatment-emergent adverse event rates declined from treatment day 1 to 2 (methylnaltrexone: 16.2%–5.3%; placebo: 6.6%−5.4%). Among methylnaltrexone-treated patients, significantly greater proportions of RFBM responders versus nonresponders reported gastrointestinal adverse events on day 1. No associations between RFBM response and the frequency of adverse events were observed in the placebo group. No meaningful changes in opioid withdrawal symptoms or pain intensity were observed. Conclusions: Early-onset adverse events following methylnaltrexone treatment, particularly gastrointestinal adverse events, are at least partially due to laxation. Methylnaltrexone treatment effectively relieves opioid-induced constipation without affecting the central analgesic effects of opioids.", "keywords": [ "methylnaltrexone", "opioid analgesic", "constipation", "chronic pain", "adverse events" ], "content": "Introduction\n\nOpioids, despite their potential drawbacks, remain an analgesic mainstay for patients with a number of chronic refractory pain conditions, including appropriate patients with chronic noncancer pain. The use of opioids, even over the short-term, may be associated with gastrointestinal side effects such as nausea, abdominal pain, vomiting, and constipation.1–4 Of these, constipation has been ranked by patients as the most bothersome,2 and can have a demonstrably negative impact on quality of life.5,6 Opioid-induced constipation (OIC) occurs in as many as 80% of patients treated with opioids,7 frequently leading to dose reduction or discontinuation of therapy.1,2,4,8,9 Moreover, whereas other gastrointestinal side effects associated with opioids tend to dissipate over time, OIC is generally not subject to the development of tolerance and, therefore, presents a patient management challenge requiring ongoing assessment, monitoring, and treatment.1 Preventative measures and common constipation remedies, including lifestyle changes and over-the-counter or prescription laxatives, only provide limited relief from OIC.8,10,11\n\nMethylnaltrexone (Relistor®, Salix Pharmaceuticals, a division of Bausch Health US, LLC, Bridgewater, NJ) is a peripherally acting μ-opioid receptor antagonist that reverses opioid-induced effects in the gastrointestinal tract, such as delayed gastric emptying and prolonged oral-cecal transit time.12,13 Pain relief with opioid therapy, however, is maintained during methylnaltrexone treatment because the high polarity and low lipid solubility of the molecule inhibits its passage through the blood-brain barrier, thereby preserving centrally mediated opioid analgesia.14,15 Methylnaltrexone is available in subcutaneous and oral formulations, both of which are approved for the treatment of OIC in adults with chronic noncancer pain.16 Subcutaneous methylnaltrexone is also indicated for the treatment of OIC in patients with advanced illness or pain caused by active cancer.16\n\nIn clinical trials, the majority of adverse events (AEs) that occurred during methylnaltrexone treatment were gastrointestinal in nature (e.g., abdominal pain, diarrhea, nausea).15,17–19 As many of these events are also common during laxation, it is plausible that gastrointestinal AEs reported in patients who received methylnaltrexone, most of whom had not had an adequate response to their laxative regimens before entering the studies, are of short duration and may be linked to successful relief of OIC. To test this hypothesis, the frequency of AEs after multiple doses of methylnaltrexone in two randomized, placebo-controlled clinical trials were evaluated. Relationships between AE frequency and methylnaltrexone efficacy, measured by opioid withdrawal symptom frequency, changes in pain intensity, and rescue-free bowel movements (RFBMs) within four hours of the first study drug dose, were also evaluated.\n\n\nMethods\n\nA post hoc analysis was performed using pooled data from two randomized, double-blind, placebo-controlled clinical trials that evaluated the efficacy and safety of subcutaneous or oral methylnaltrexone for the relief of OIC in patients with chronic, noncancer pain (NCT00529087 [Study dates August 22, 2007 – November 25, 2008], NCT01186770 [Study dates September 1, 2010 – November 8, 2011). Study methodologies for both clinical trials have been previously published.15,17,18 Briefly, the studies enrolled adult patients who had chronic noncancer pain for at least two months and OIC for at least 30 days. The presence of OIC was confirmed during screening and defined as fewer than three RFBMs (no laxative use within 24 hours prior to the bowel movement) per week on average and one or more of the following symptoms: hard or lumpy stools, straining during bowel movements, or a sensation of incomplete evacuation after bowel movements. Patients were required to have been receiving an opioid for at least one month, with a daily dose of at least 50-mg oral morphine equivalents for 14 days prior to screening. Patients with a history of clinically significant bowel or rectal disease, chronic constipation, unstable hepatic, renal, pulmonary, cardiovascular, ophthalmologic, neurologic, psychiatric or any other medical condition that might compromise the study or put the patient at risk were excluded from the studies. Each study was approved by independent ethics committees at each participating institution and was conducted in accordance with the International Conference on Harmonisation Guideline for Good Clinical Practice and the Declaration of Helsinki. All patients provided written informed consent.\n\nPatients in the subcutaneous methylnaltrexone study were randomized 1:1:1 to receive treatment with methylnaltrexone 12 mg once daily, methylnaltrexone 12 mg every other day, or placebo for four weeks. Patients then entered an eight-week, open-label phase, during which methylnaltrexone was administered to all patients on an as-needed basis. Patients participating in the oral methylnaltrexone study were randomized 1:1:1:1 to receive treatment with methylnaltrexone 150 mg, 300 mg, 450 mg, or placebo once daily for 4 weeks, then as needed for an additional eight weeks during an open-label study phase. In both studies, patients discontinued use of laxatives prior to study enrollment. Rescue laxative use (one dose of up to 3 or 4 bisacodyl tablets) was permitted if the patient had no bowel movements for three consecutive days. Rescue laxative use was limited to a single dose within a 24-hour period administered four hours or more after study drug administration.\n\nSafety and tolerability on treatment days 1 and 2 were evaluated by treatment-emergent AE rates and severity. Opioid withdrawal symptoms were measured by the patient and by the clinician using the Subjective Opiate Withdrawal Scale (SOWS) and the Objective Opiate Withdrawal Scale (OOWS), respectively. For the SOWS, patients rated their perceived severity of 19 opioid withdrawal symptoms on a scale from 0 (not at all) to 4 (extremely), with a total possible score of 76. The original SOWS scale has 16 questions20; three questions were added for the purpose of this study to more accurately reflect withdrawal symptoms in a study population with OIC. The three additional statements regarding symptoms included: I have had trouble sleeping; My appetite has been poor; and I have had diarrhea. Additionally, the original SOWS statement of “I feel like shooting up now” was modified to “I have felt like taking more pain medication”. For the OOWS, clinicians assigned patients a score of 0 or 1 based on the absence or presence of 13 symptoms indicative of opioid withdrawal, with a total possible score of 13. In addition to SOWS and OOWS total scores, each scale was also evaluated without inclusion of cramping as a symptom, because cramping may also be associated with constipation and the process of laxation and, therefore, may confound the assessment of opioid withdrawal symptoms.14 Evaluations of SOWS and OOWS were performed at 1 hour postdose on day 1 and at weeks 2 and 4 during the double-blind treatment phases of the studies. Maintenance of analgesia was assessed via a pain intensity score reflecting patients’ ratings of the intensity of their pain on a scale from 0 (no pain) to 10 (worst pain possible) at each study visit.15 Efficacy was measured by the proportion of patients demonstrating a laxation response to treatment, defined for the purpose of this analysis as an RFBM within four hours of first study drug dose.\n\nThe analysis population consisted of all randomized patients pooled from both included studies. Demographics and AEs were summarized using descriptive statistics. Between-group comparisons in RFBM responders were performed using chi-square tests. Associations between individual AEs and the occurrence of an RFBM within four hours of the first study drug dose were evaluated using Fisher’s exact test. Changes from baseline in SOWS and OOWS between groups were assessed by analysis of covariance, with treatment as the main effect and the baseline value as a covariate. Statistical calculations compared the all methylnaltrexone group versus placebo. All p-values reported for between-group comparisons used a nominal value of 0.05 to denote statistical significance. There were no corrections for multiplicity performed in these exploratory analyses. Statistical analyses were performed using SAS version 9.4 software.\n\n\nResults\n\nA total of 1263 patients who received at least one dose of study medication were included in the pooled analysis: 900 had been randomized to methylnaltrexone (subcutaneous, n = 298; oral, n = 602) and 363 had been randomized to placebo. Patients in the subcutaneous methylnaltrexone treatment group were evenly divided between those who received 12 mg once daily (n = 150) and 12 mg every other day (n = 148). Among those in the oral methylnaltrexone treatment group, 201, 202, and 200 patients were randomized to treatment with methylnaltrexone 150 mg, 300 mg, and 450 mg once daily, respectively. Among all patients, 88% completed the double-blind phase. The discontinuation rate ranged from 10.0% to 18.8% depending on the methylnaltrexone dose and route of administration. The most common reasons for discontinuation were adverse events, patient request, and protocol violations. Patients who discontinued due to adverse events most commonly reported gastrointestinal complaints, such as abdominal pain, nausea, and vomiting (Table 1).\n\nDemographic and baseline characteristics were generally well balanced among treatment groups (Table 2). Patients in the oral methylnaltrexone treatment group reported modestly lower rates of baseline laxative use and a slightly greater mean number of RFBMs per week compared with patients who received subcutaneous methylnaltrexone. Baseline median daily morphine-equivalent doses and baseline mean pain scores were comparable among treatment groups.\n\nThe numbers of patients who experienced at least one AE decreased from day 1 to day 2 of treatment among all treatment groups with the greatest decrease occurring in the subcutaneous methylnaltrexone treatment group (Table 3). On treatment day 2, the overall incidence of AEs among all patients who received methylnaltrexone was similar to that of placebo.\n\na Reported by ≥2% of patients in any treatment group.\n\nb Treatment day 2 occurred on study day 3 for patients who received SC methlynaltrexone every other day.\n\nAEs reported on days 1 and 2 of treatment were predominantly gastrointestinal (e.g., abdominal pain, nausea, diarrhea, upper abdominal pain, and vomiting) (Table 3). All AEs were reported by fewer patients on treatment day 2 compared with day 1 among patients who received methylnaltrexone. Abdominal pain was the most common AE reported on treatment day 1 among patients who received methylnaltrexone or placebo. Among the patients treated with methylnaltrexone who experienced abdominal pain on day 1, the majority (83%, n = 43/52) reported mild-moderate abdominal pain and 17% (n = 9/52) reported severe abdominal pain. All patients in the placebo group who reported abdominal pain on day 1 experienced mild-moderate pain (100%, n = 3/3). Abdominal pain on day 1 led to treatment discontinuation in 0.4% (n = 4) of methylnaltrexone-treated patients and in none of the patients who received placebo.\n\nOn treatment day 2, the frequency of abdominal pain had decreased among patients treated with methylnaltrexone, whereas the frequency among patients who received placebo was unchanged. Among patients reporting abdominal pain on treatment day 2, pain severity was characterized as mild-moderate in most of the patients treated with methylnaltrexone (87.5%, n = 14/16) and in all of the patients who received placebo (100%, n = 4/4). Two methylnaltrexone-treated patients (12.5%, n = 2/16) reported severe abdominal pain on treatment day 2. Abdominal pain on treatment day 2 led to treatment discontinuation in 0.2% (n = 2) of methylnaltrexone-treated patients; none discontinued treatment in the placebo group due to abdominal pain on treatment day 2. Hyperhidrosis and nausea frequency also markedly decreased from day 1 to day 2 of treatment in methylnaltrexone-treated patients. The frequency of AEs reported after the second dose of methylnaltrexone treatment were comparable to or less than those reported after the second dose of placebo (Table 4).\n\na Reported by ≥2% of patients in any treatment group.\n\nThe proportion of patients who experienced an RFBM within four hours after the first dose of study treatment (i.e., RFBM responders) was significantly greater among all patients who received methylnaltrexone (25.1%, n = 226/900) compared with placebo (8.8%, n = 32/363; P < 0.0001). In addition, more patients treated with subcutaneous versus oral methylnaltrexone were RFBM responders (34.2%, n = 102/298 and 20.6%, n = 124/602, respectively).\n\nAssociations between RFBM response and the occurrence of AEs on day 1 were evaluated. Among all methylnaltrexone-treated patients, abdominal pain on day 1 was reported by a significantly greater proportion of RFBM responders compared with nonresponders (Table 5). Similarly, significantly greater proportions of RFBM responders versus nonresponders reported upper abdominal pain, diarrhea, and nausea on day 1 among all methylnaltrexone-treated patients. No statistically significant associations between the frequency of AEs and RFBM response were observed among patients who received placebo. Among the patients who received subcutaneous methylnaltrexone 12 mg daily or oral methylnaltrexone 450 mg daily (the doses currently approved by the US Food and Drug Administration for the treatment of OIC), greater proportions of patients who were responders (13.7%, n = 14/102 and 10.6%, n = 5/47, respectively) than nonresponders (7.7%, n = 15/196 and 5.2%, n = 8/153, respectively) reported abdominal pain on day 1.\n\na Reported by ≥2% of patients in any treatment group.\n\nIn all treatment groups, slight decreases in SOWS total scores were observed between baseline and the day 1 postdose assessment, with the least decline occurring in the subcutaneous methylnaltrexone treatment group (Figure 1A). The difference in decrease from baseline in SOWS total scores between treatment groups was statistically significant for the comparison of the combined methylnaltrexone treatment group versus placebo at day 1 (least-squares means, −3.6 and −2.6, respectively; P = 0.01), but was not statistically significant at weeks two or four. Similar results were observed for SOWS total scores without cramping (Figure 1B).\n\nData are presented as means ± standard deviations.P < 0.05 for the comparison of change from baseline in least-squares mean values in the all methylnaltrexone vs placebo treatment groups.\n\nMNTX = methylnaltrexone; PBO = placebo; SC = subcutaneous; SOWS = Subjective Opioid Withdrawal Scale.\n\nThe OOWS total scores increased slightly from baseline to the day 1 postdose assessment in all methylnaltrexone treatment groups, whereas the placebo score remained unchanged (Figure 2A). The difference in changes from baseline values between the combined methylnaltrexone treatment group and placebo was statistically significant at day 1 (least-squares means, 0.13 and −0.02, respectively; P=0.001), but not at weeks two or four. When cramping was omitted from the OOWS total score, the observed increases from baseline score in the methylnaltrexone treatment group lessened but remained significantly different from placebo at day 1 (Figure 2B).\n\nData are presented as means ± standard deviations. P = 0.001; †P < 0.05; for the comparison of change from baseline in least-squares mean values in the all methylnaltrexone vs placebo treatment groups.\n\nMNTX = methylnaltrexone; OOWS = Objective Opioid Withdrawal Scale; PBO = placebo; SC = subcutaneous.\n\nPain intensity scores did not change significantly from baseline for any treatment group throughout the study (Figure 3). Least-squares mean changes in pain intensity score ranged from −0.02 to −0.12.\n\nData are presented as means ± standard deviations. MNTX = methylnaltrexone; PBO = placebo; SC = subcutaneous.\n\n\nDiscussion\n\nIn this pooled analysis of patients with chronic, noncancer pain and OIC, rates of AEs decreased considerably between the first and second dosing days following treatment with methylnaltrexone and were comparable to placebo after the second dose. Abdominal pain, nausea, hyperhidrosis, and diarrhea were the most frequently reported AEs in the methylnaltrexone treatment group at day 1 and also demonstrated the most pronounced decreases in frequency after the second dose. The presence of abdominal pain was predominantly reported as mild or moderate in intensity, and very few patients discontinued due to abdominal pain. An association was detected between the presence of the gastrointestinal symptoms of abdominal pain, upper abdominal pain, nausea, and diarrhea on day 1 and the occurrence of an RFBM within 4 hours of the first methylnaltrexone dose. Together, these data demonstrate the rapid attrition of early-onset AEs occurring with methylnaltrexone treatment for OIC, and suggest that gastrointestinal symptoms may be due, in part, to resumption of bowel function/constipation relief.\n\nA similar decrease in abdominal pain frequency from the first to second dose of methylnaltrexone was reported in a prior post hoc analysis using data from two randomized, placebo-controlled clinical trials of subcutaneous methylnaltrexone in patients with advanced illness whose laxative therapy response was insufficient (N=288).21 In that study, abdominal pain was reported by 23% of patients following the first methylnaltrexone dose, by 13% of patients following the second dose, and by less than 10% of patients following the fifth dose, a rate similar to the frequency of abdominal pain reported by the placebo group (9.8%). The investigators also observed a relationship between abdominal pain and laxation response. In total, 80% of patients in the methylnaltrexone treatment group who experienced abdominal pain on study day 1 had an RFBM within four hours of the first study drug dose, whereas 47.2% of patients without abdominal pain on day 1 demonstrated an RFBM response. These data support the hypothesis that, in patients with OIC despite ongoing laxative use, the process of being rapidly induced to a bowel movement is initially accompanied by abdominal pain with the first dose, but once laxation has occurred, subsequent doses are generally not accompanied by such pain.\n\nIn the current study, safety and efficacy assessments were generally comparable between the subcutaneous and oral methylnaltrexone formulations, although the frequency of AEs after the first dose of study drug and the decrease in AE rates from day 1 to treatment day 2 were greater among patients treated with subcutaneous methylnaltrexone. There are intrinsic and study-design related factors that could contribute to this observed difference between formulations. First, patients who received subcutaneous methylnaltrexone had a greater response rate (i.e., RFBM within four hours of first study drug dose) compared with patients who received oral methylnaltrexone. It has been postulated that the greater initial response rate is due to a faster onset of effect with the subcutaneous formulation, which, unlike the oral formulation, does not require time for absorption.18 If the hypothesis that the frequencies of the observed gastrointestinal symptoms are partially due to OIC relief is correct, then a greater rate of RFBM response within four hours would naturally be linked to a greater frequency of early-onset gastrointestinal AEs consistent with laxation, such as abdominal pain and cramping. Second, the study of oral methylnaltrexone investigated three doses, the lower doses being one third (150 mg) and two thirds (300 mg) of the recommended methylnaltrexone dose (450 mg). As oral methylnaltrexone efficacy has been shown to be dose dependent,18 the inclusion of lower doses in this analysis may have influenced RFBM response and the frequency of any associated AEs. However, when the patients receiving the methylnaltrexone doses that are approved for OIC treatment (subcutaneous methylnaltrexone 12 mg/day or oral methylnaltrexone 450 mg/day) were analyzed separately, more patients who were responders than nonresponders reported having abdominal pain on day 1, indicating that treatment with the approved doses may have an effect on efficacy. In addition, when discontinuation rates were assessed for each dose and regimen, overall discontinuation rates and discontinuation rates due to AEs were consistent between the approved doses (methylnaltrexone subcutaneous 12 mg/day and oral methylnaltrexone 450 mg/day) and the other studied doses (subcutaneous methylnaltrexone 12 mg every other day and oral methylnaltrexone 150 or 300 mg/day), further supporting the safety profile of the approved doses.\n\nPooled data from the two included clinical trials indicate that methylnaltrexone does not induce symptoms of opioid withdrawal. Scores for SOWS and OOWS showed slight changes after the initial study drug dose but returned to baseline levels by the subsequent assessment and were stable thereafter. Early changes in SOWS and OOWS scores could be partially attributable to changes in gastrointestinal AE frequency, as several items in both assessments address gastrointestinal symptoms.20 Interestingly, the initial decrease from baseline in SOWS was greatest in the placebo group. The clinical significance of a decrease from baseline in SOWS score is not clear, as it insinuates that a patient had symptoms of opioid withdrawal prior to receiving methylnaltrexone that were lessened by treatment. As pain intensity scores were consistent throughout the 12-week study durations and compromised analgesia typically precedes symptoms of opioid withdrawal in patients with chronic pain,22,23 the clinical significance of the SOWS and OOWS score changes observed in this study are even more questionable. Further studies evaluating and validating the use of the OOWS and SOWS in patients taking opioids for chronic nonmalignant pain without an opioid addiction are needed. However, data from this analysis affirm that neither subcutaneous nor oral methylnaltrexone negatively influences opioid-mediated analgesia. Lack of opioid withdrawal symptoms and maintenance of analgesia are consistent with methylnaltrexone’s pharmacologic profile and lack of effect on centrally mediated analgesia.14,15\n\nThere are limitations that need to be considered when interpreting the findings from this analysis. The designs of the two studies were similar, but not identical, which adds potential confounding factors to the analysis. As mentioned above, the oral methylnaltrexone formulation needs time to be absorbed prior to producing any effects not required by the subcutaneous formulation, which could influence the timing of treatment effects. In addition, individual subcutaneous and oral dose groups were combined for the purposes of this analysis, and oral methylnaltrexone efficacy has been shown to be dose dependent.18 However, in the individual published studies, the total numbers of AEs did not vary appreciably among dose groups17,18 thus any influence on the AE attrition assessment is likely to be minimal. The observation period of both studies was limited: opioid withdrawal symptoms were only reported during the four-week, double-blind treatment period, and pain intensity over 12 weeks. Longer-term data regarding the impact of methylnaltrexone on these parameters is available from a 48-week, open-label study, in which no indications of opioid withdrawal, loss of opioid-mediated analgesia, or alteration in median morphine equivalent dose were observed during methylnaltrexone treatment.19\n\n\nConclusion\n\nThe attrition of AEs after the first dose of methylnaltrexone and the association between gastrointestinal AEs and laxation response support the hypothesis that early-onset AEs experienced with methylnaltrexone treatment, particularly gastrointestinal AEs, are at least partially due to laxation. Treatment with methylnaltrexone was additionally shown to relieve OIC without inducing withdrawal symptoms or compromising analgesia. For patients with chronic pain and OIC, methylnaltrexone offers a well-tolerated and effective treatment option for constipation relief.\n\n\nData availability\n\nVivli: Attrition of TEAEs: Post Hoc Pooled Analysis, https://doi.org/10.25934/00007291.24\n\nPer the study sponsor’s policy, the datasets generated and/or analyzed for this study are not publicly available. Access to the data is provided to bona fide researchers subject upon submission of a research proposal and signing a Data Use Agreement. Interested researchers can request access to the data at the DOI by creating a free Vivli account and using the ‘Prepare to Request Vivli Study’ button on the ‘Administrative Details’ tab.", "appendix": "Acknowledgments\n\nTechnical editorial and medical writing assistance was provided under the direction of the authors by Dana A. Franznick, PharmD, of Echelon Brand Communications, LLC, an OPEN Health company, Parsippany, NJ, USA. Funding for this assistance was provided by Salix Pharmaceuticals.\n\n\nReferences\n\nBenyamin R, Trescot AM, Datta S, et al.: Opioid complications and side effects. Pain Physician. 2008; 11(2 Suppl): S105–S120. PubMed Abstract\n\nCook SF, Lanza L, Zhou X, et al.: Gastrointestinal side effects in chronic opioid users: results from a population-based survey. Aliment Pharmacol Ther. 2008; 27(12): 1224–1232. PubMed Abstract \| Publisher Full Text\n\nManchikanti L, Fellows B, Ailinani H, et al.: Therapeutic use, abuse, and nonmedical use of opioids: a ten-year perspective. Pain Physician. 2010; 13(5): 401–435. PubMed Abstract\n\nNoble M, Tregear SJ, Treadwell JR, et al.: Long-term opioid therapy for chronic noncancer pain: a systematic review and meta-analysis of efficacy and safety. J Pain Symptom Manage. 2008; 35(2): 214–228. PubMed Abstract \| Publisher Full Text\n\nBell T, Annunziata K, Leslie JB: Opioid-induced constipation negatively impacts pain management, productivity, and health-related quality of life: findings from the National Health and Wellness Survey. J Opioid Manag. 2009; 5(3): 137–144. PubMed Abstract \| Publisher Full Text\n\nMuller-Lissner S, Bassotti G, Coffin B, et al.: Opioid-induced constipation and bowel dysfunction: a clinical guideline. Pain Med. 2017; 18(10): 1837–1863. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBell TJ, Panchal SJ, Miaskowski C, et al.: The prevalence, severity, and impact of opioid-induced bowel dysfunction: results of a US and European Patient Survey (PROBE 1). Pain Med. 2009; 10(1): 35–42. PubMed Abstract \| Publisher Full Text\n\nCoyne KS, Margolis MK, Yeomans K, et al.: Opioid-induced constipation among patients with chronic noncancer pain in the United States, Canada, Germany, and the United Kingdom: laxative use, response, and symptom burden over time. Pain Med. 2015; 16(8): 1551–1565. PubMed Abstract \| Publisher Full Text\n\nManchikanti L, Kaye AM, Knezevic NN, et al.: Responsible, safe, and effective prescription of opioids for chronic non-cancer pain: American Society of Interventional Pain Physicians (ASIPP) guidelines. Pain Physician. 2017; 20(2s): S3–S92. PubMed Abstract\n\nArgoff CE, Brennan MJ, Camilleri M, et al.: Consensus recommendations on initiating prescription therapies for opioid-induced constipation. Pain Med. 2015; 16: 2324–2337. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFarmer AD, Holt CB, Downes TJ, et al.: Pathophysiology, diagnosis, and management of opioid-induced constipation. Lancet Gastroenterol Hepatol. 2018; 3(3): 203–212. PubMed Abstract \| Publisher Full Text\n\nMurphy DB, Sutton JA, Prescott LF, et al.: Opioid-induced delay in gastric emptying: a peripheral mechanism in humans. Anesthesiology. 1997; 87(4): 765–770. PubMed Abstract \| Publisher Full Text\n\nYuan CS, Foss JF, O’Connor M, et al.: Effects of enteric-coated methylnaltrexone in preventing opioid-induced delay in oral-cecal transit time. Clin Pharmacol Ther. 2000; 67(4): 398–404. PubMed Abstract \| Publisher Full Text\n\nWebster LR, Brenner DM, Barrett AC, et al.: Analysis of opioid-mediated analgesia in phase III studies of methylnaltrexone for opioid-induced constipation in patients with chronic noncancer pain. J Pain Res. 2015; 8: 771–780. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWebster LR, Israel RJ: Oral methylnaltrexone does not negatively impact analgesia in patients with opioid-induced constipation and chronic noncancer pain. J Pain Res. 2018; 11: 1503–1510. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRelistor [package insert]: Bridgewater, NJ: Salix Pharmaceuticals; 2018.\n\nMichna E, Blonsky ER, Schulman S, et al.: Subcutaneous methylnaltrexone for treatment of opioid-induced constipation in patients with chronic, nonmalignant pain: a randomized controlled study. J Pain. 2011; 12(5): 554–562. PubMed Abstract \| Publisher Full Text\n\nRauck R, Slatkin NE, Stambler N, et al.: Randomized, double-blind trial of oral methylnaltrexone for the treatment of opioid-induced constipation in patients with chronic noncancer pain. Pain Pract. 2017; 17(6): 820–828. PubMed Abstract \| Publisher Full Text\n\nWebster LR, Michna E, Khan A, et al.: Long-term safety and efficacy of subcutaneous methylnaltrexone in patients with opioid-induced constipation and chronic noncancer pain: a phase 3, open-label trial. Pain Med. 2017; 18(8): 1496–1504. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHandelsman L, Cochrane KJ, Aronson MJ, et al.: Two new rating scales for opiate withdrawal. Am J Drug Alcohol Abuse. 1987; 13(3): 293–308. PubMed Abstract \| Publisher Full Text\n\nSlatkin NE, Lynn R, Su C, et al.: Characterization of abdominal pain during methylnaltrexone treatment of opioid-induced constipation in advanced illness: a post hoc analysis of two clinical trials. J Pain Symptom Manage. 2011; 42(5): 754–760. PubMed Abstract \| Publisher Full Text\n\nCowan DT, Wilson-Barnett J, Griffiths P, et al.: A survey of chronic noncancer pain patients prescribed opioid analgesics. Pain Med. 2003; 4(4): 340–351. PubMed Abstract \| Publisher Full Text\n\nRedding SE, Liu S, Hung WW, et al.: Opioid interruptions, pain, and withdrawal symptoms in nursing home residents. Clin Ther. 2014; 36(11): 1555–1563. PubMed Abstract \| Publisher Full Text\n\nMehta N, et al.: Attrition of TEAEs: Post Hoc Pooled Analysis. Vivli [dataset]. 2021. Publisher Full Text" }	[ { "id": "94041", "date": "28 Sep 2021", "name": "Mayank Gupta", "expertise": [ "Reviewer Expertise Cancer pain", "palliative 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\nThank you for giving me the opportunity to review the manuscript.\nThis post hoc analysis study used data from two RCTs evaluating methylnaltrexone for opioid-induced constipation. The study aimed to find an association (if any) between the methylnaltrexone induced adverse effects (AEs) and its clinical effect i.e. Rescue free bowel movements. The results of the study demonstrate a statistically significant association between the AEs and the intended clinical effect i.e. laxation.\nHowever, the authors missed citing key recent work done by Chamberlain BH et al.1 and Nelson KK et al.2 who have evaluated the efficacy of methylnaltrexone for opioid-induced constipation. Rather than just citing package insert (reference number 16), it would be prudent to cite references like above when the authors mention the indications of Subcutaneous methylnaltrexone for opioid-induced constipation in advanced illnesses in the introduction part.\n\nOverall, a good article using a robust methodology for an outcome of clinical significance.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "9551", "date": "11 Jul 2023", "name": "Neel Mehta", "role": "Author Response", "response": "We have added these references to the introduction." } ] }, { "id": "94039", "date": "30 Sep 2021", "name": "Nebojsa Nick Knezevic", "expertise": [ "Reviewer Expertise chronic pain 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 post hoc analysis pools the results from two randomized, placebo-controlled clinical trials (n=1263) to examine the effect of subcutaneous or oral methylnaltrexone on adverse events in patients with opioid-induced constipation. All patients had chronic, non-cancer pain. The authors conclude that early-onset adverse events experienced in the methylnaltrexone group may be the result of laxation related to rescue-free bowel movements (RFBM).\nIn the title and several parts of the article (regarding Table 3 in particular), the authors use the term “treatment-emergent adverse events”, yet throughout most of the article they simply use “adverse events.” How was this distinction made?\n\nFew statistical analyses are presented in the paper. When describing the results of the Tables, the authors often use terms such as “generally well-balanced”, “comparable”, “modestly lower” and “slightly greater”. When describing discontinuation rates (Table 1), patient baseline characteristics (Table 2), and adverse events (Tables 3 and 4), it would be relevant to use statistical significance to characterize similarities and differences between groups.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "9552", "date": "11 Jul 2023", "name": "Neel Mehta", "role": "Author Response", "response": "There was no distinction in use of “treatment-emergent adverse events” and “adverse events”, this was more for ease of reading. We have revised all instances to “TEAE”. We have added more detail in the baseline demographics section that clarifies P>0.05 for methylnaltrexone vs placebo for all baseline parameters. We did not perform any other statistical analyses." } ] } ]	1	https://f1000research.com/articles/10-891
https://f1000research.com/articles/12-814/v1	11 Jul 23	{ "type": "Brief Report", "title": "Bioconversion of biowaste by black soldier fly larvae (Hermetia illucens L.) for dried larvae production: A life cycle assessment and environmental impact analysis", "authors": [ "Rudy Agung Nugroho", "Muhammad Nasir Rofiq", "Arif Dwi Santoso", "Ahmad Ismed Yanuar", "Rahmania Hanifa", "Nadirah Nadirah", "Muhammad Nasir Rofiq", "Arif Dwi Santoso", "Ahmad Ismed Yanuar", "Rahmania Hanifa", "Nadirah Nadirah" ], "abstract": "Background: Hermetia illucens L. have gained popularity in recent years as an environmentally friendly response to both the present and potential future food/feed crisis. The larvae of H. illucens L., or black soldier fly larvae (BSFL), is an alternative solution to tackle the issue of organic waste bioconversion. However, understanding the environmental loads associated with biowaste bioconversion using BSFL to produce dried BSFL is a pivotal point to keep the environment sustainable. This study reported a life cycle assessment (LCA) of the biowaste bioconversion process of BSFL and determined the environment impact analysis to make recommendations for modifications to lessen environmental consequences.\nMethods: The methodology used is life cycle assessment (LCA), which includes: (a) system boundary determination (gate-to-gate), starting from biowaste production, biowaste bioconversion, prepupae and BSFL frass production. The system boundary of the dried BSFL production is designed for both the processing and production of one cycle of BSFL; (b) life cycle inventory activities carried out at PT Biomagg Sinergi Internasional, Depok, West Java, Indonesia; (c) conducting life cycle impact assessment on five environmental impact categories namely global warming potential (GWP), acidification (AC), terrestrial eutrophication (TE), fossil fuel depletion (FFE), eco-toxicity (ET); and (d) interpretation of the assessment result. The LCA is conducted using openLCA 1.11 software and TRACI 2.1 impact assessment method.\nResults: The impact values of GWP, AC, TE, FFE, and ET, per 100 kg of BSFL dried production was 6.687 kg CO2 eq; 0.029 kg SO2-eq; 0.092 kg N-eq; 16.732 MJ surplus; 121.231 CTUe. Production of prepupa had the highest hotspots in these emissions, followed dried BSFL production.\nConclusions: Efforts to reduce environmental impacts that can be done are by implementing an integrated rearing system using substrate from a single type of known substrate for BSFL and using alternative drying methods for BSFL dried production.", "keywords": [ "Bioconversion", "Hermetia illucens", "LCA", "Sustainable" ], "content": "Introduction\n\nThe popularity of farmed insects as a future source of food, feed, and energy is growing.1–3 Insects have been identified as a viable answer to the worldwide difficulties connected with a shortage of protein sources for feed and food as the world population grows.4 In recent years, there has been considerable growth in the number of research and commercial advances related to the use of insect production in connection to recycling, reduce, and reuse of agri-food system side-streams and waste biomass.5–7 Insects have a higher feed conversion efficiency and fewer greenhouse gas emissions than traditional cattle, as well as a nutritional content that makes them potentially acceptable for food and animal feed.8\n\nFurther, the United Nations Food and Agriculture Organization has recognized the potential of edible insects to contribute to healthy and sustainable diets and has urged their inclusion in the diets of people all over the globe.9 The black soldier fly (BSF) or Hermetia illucens is a focus species among farmed insects owing to the ability of its larvae (BSFL) to rapidly thrive on various organic waste streams.10,11 The BSFL consumes a vast amount of organic waste and converts it into larval biomass, which may later be converted into animal feeds.12 As commonly employed bio-converter agents for diverse organic waste, the BSFL are often used as feed for poultry and fish because of their high protein content.13 The protein content of the BSFL range from 40–44%, and is rich in amino acid, which is better compared to soybean meal.14 Besides protein and amino acid, dietary BSFL oil is beneficial to enhance feed conversion ratio and increase the incorporation of medium-chain fatty acids into abdominal fat pad and serum antioxidant capacity specifically in broiler chickens.15\n\nDespite several literature sources on economic feasibility and societal acceptability, many unanswered topics remain for academics to investigate. Industrial activities (for example: PT Biomagg, Sinergi Internasional, a BSF farm located in Depok, West Java, Indonesia) will certainly have an impact on the environment, such as changes in the quality of water, soil, and air. To reduce pollution and environmental impacts that occur during the product life cycle, the appropriate method for analyzing is a life cycle assessment (LCA). LCA analysis aims to calculate the environmental load based on an inventory analysis of the use of resources, energy, air, fuel, and others so that the environmental burden can be identified and then analyzed using different alternatives to reduce the impact.16–18 The present study reported to identify and analyze input output based on inventory data from BSFL dried products and determine potential environmental impacts in the form of global warming potential (GWP), acidification (AC), terrestrial eutrophication (TE), fossil fuel depletion (FFE), and ecotoxicity (ET).\n\n\nMethods\n\nThe current report is a preliminary study of the life cycle assessment and environmental impact analysis of BSFL farming in producing dried BSFL by using biowaste as a substrate for BSFL. The biowaste was provided from the traditional market, Depok, West Java, Indonesia. The study was located at PT Biomagg Sinergi Internasional, located in Depok, West Java, Indonesia (6°22′48.4″S 106°52′51.7″E). The system boundary (gate-to-gate) is designed for the core process of both processing and production of the dried larva. The present study used the functional unit as 100 kg of dried BSFL, which is an amount of dried BSFL production per cycle. Further, five environmental impact categories, GWP, AC, TE, FFE, and ET were chosen (Figure 1-Left). The following processes were evaluated: 1) biowaste preparation for BSFL substrate, 2) egg hatching to produce baby larvae, 3) bioconversion of biowaste, 4) production of prepupa, and 5) production of the dried larva (Figure 1-Right). Respectively, 1) at biowaste preparation for BSFL substrate, the volume of biowaste (1000 kg) and diesel for crushing biowaste and operation time of chopper machine were recorded. The biowaste was crushed using the chopper machine to homogenize the waste to make it easy to digest for BSFL. Meanwhile, 2) the number of eggs that were hatched (100 g), which were provided from PT Biomagg Sinergi Internasional, and the energy of electricity consumed (0.264 kWh) during the hatching process were noted. The eggs were incubated in the plastic box with crushed biowaste as substrate after they hatched. The egg was incubated for 3 days to produce baby larvae. 3) In the bioconversion of biowaste, the volume of biowaste (1000 kg), mass of baby larvae of BSFL (100 kg) and the energy of electricity consumed (0.264 kWh) were also recorded. Further, 4) the volume of crushed biowaste (1000 kg), baby larva (100 g), and electricity (0.264 kWh) during the production of prepupa were obtained and noted. Finally, 5) the wet prepupa (1000 kg), electricity energy consumed, and hour of microwave used in production of dried prepupa per 100 kg, were kept. All data in step 1–5 was used as life cycle inventory data for measuring impact assessment, as described below, and operation time of chopper machine were recorded.\n\nThe data used was starting from biowaste production, biowaste bioconversion, prepupa and frass production, and BSFL dried production. This data was primary data (volume of biowaste and diesel, the number of eggs, mass of baby larvae of BSFL and the energy of electricity consumed) that were directly taken from the PT Biomagg Sinergi Internasional19 and was evaluated using the OpenLCA 1.11.0 (GreenDelta, Berlin), Ecoinvent database version 3.8 (Secondary data) and TRACI 2.1 method based on a gate-to-gate approach. Secondary data such as data biowaste, electricity, diesel, and chopper were obtained from the dataset of Ecoinvent 3.8 database. The Life Cycle Inventory (LCI) involved input waste (biowaste), emissions, and energy consumption of each subprocess, based on the principle of mass balance. The LCI involved input waste (biowaste), emissions, and energy consumption of each subprocess and were based on the principle of mass balance. Meanwhile, the impact environment that includes GWP, AC, TE, FFE, and, ET, were evaluated.\n\nAdditionally, all inventory data was obtained and calculated from this facility, except for CH4 and N2O emissions. The published values for CH4 and N2O emissions during BSFL bioconversion were used.20 It was anticipated that residue during bioconversion produced emissions equivalent to ordinary organic waste from home or kitchen garbage. Furthermore, the results of the LCI evaluation may be utilized to examine life cycle impacts such as environmental implications. As previously stated, the relevant inventory resulted in the identification of five environmental impact categories. All methods have been deposited on protocols.io at: https://dx.doi.org/10.17504/protocols.io.8epv5j54dl1b/v1.21\n\n\nResults and Discussion\n\nThe present report evaluated the LCA and environmental impact analysis of the dried BSFL production from biowaste bioconversion using BSFL in PT Biomagg Sinergi Internasional, Depok, West Java, Indonesia (Table 1).19\n\nThe GWP of the BSFL bioconversion system was calculated to be 6.687 kg CO2-eq. The specified amounts were 2.898 kg CO2-eq for dried BSLF production use, 3.239 kg CO2-eq for prepupa production, 0.452 CO2-eq for bioconversion of biowaste, 0.096 kg CO2-eq for eggs BSF hatching, and 0.680 kg CO2-eq for production crushed biowaste. A past study by Salomoneet al.,22 revealed that each 100 kg of food waste/biowaste emits 3.2 kg CO2 equivalent per global warming potential. Meanwhile, the greatest proportion (39.33%) of the overall energy usage was attributable to drying. Salomone, Saija22 also stated that substantial GWP effects were generated by electricity use during the prepupa drying and using the microwave was related with the greatest energy consumption in the dried BSFL production system (Figure 2A).\n\nMeanwhile, acidification (Figure 2B) was often associated with the pollutants which are resulted from N- compounds. The total effect of acidification was 0.029 kg SO2-eq. The present report stated that the emissions from the production of the prepupa process had the greatest influence on acidification. High NH3 emissions during the prepupa production caused a significant acidification burden. Further, the overall effect of NH3 emissions on terrestrial eutrophication was 0.092 kg N-equivalent. During the production of prepupa, emissions of NH3 accounted for most of the emissions, which was 0.0429 kg N-equivalent. In addition, the sum of the effect on fossil fuel depletion was 14.76 MJ surplus. The fossil fuel depletion produced by the production of crushed biowaste was 10.88 MJ surplus, which used a diesel-electric generating set in operating the chopper machine. Finally, the eco-toxicity for the system was 119.264 CTu. The eco-toxicity was related to electricity 66.017 CTu and 1.624 CTu in tap water used.\n\n\nConclusion\n\nThis brief report revealed the GWP, the effects of acidification, terrestrial eutrophication, and eco-toxicity, bridging a significant information gap regarding the environmental impact of the BSFL bioconversion system. Contribution analysis might assist in locating “hot spots” within the selected environmental impact categories. Electricity and tap water for prepupa production, and electricity consumption for crushing biowaste, were the top three processes in terms of the GWP. This study also reported the environmental impact of the production of 100 kg of dried BSFL using the life cycle assessment method. Environmental impact analyzed includes the potential for global warming potential, acidification, terrestrial eutrophication, fossil fuel depletion, and eco-toxicity with their respective values of 6.687 kg CO2 eq; 0.029 SO2- eq; 0.092 kg N-eq; 14.767 MJ surplus; 119.264 CTUe. The prepupa production is the biggest contributor to global warming potential, acidification, terrestrial eutrophication, and eco-toxicity of all stages in dried BSFL production. It is suggested to use alternative single raw materials for substrate BSFL and another drying method, so that the sustainable BSFL dried production process can be achieved. Another recommendation is optimizing the use of tap water, by tightening the implementation of the SOP for tap water in order to be more economical and efficient for usage in BSFL dried production.", "appendix": "Data availability\n\nFigshare: Life Cycle Assessment BSF, https://doi.org/10.6084/m9.figshare.22224034. 19\n\nThis project contains the following underlying data:\n\n• Impact anaylisis assessment.xlsx (Present data shows raw data from the life cycle inventory to assess the impacts of BSFL dried production. The impacts assessment are: Global warming Potential, Acidification, Terestrial Eutrophication, Fossil Fuel Depletion, and Ecotoxicity)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nProtocol.io: Life Cycle Assessment for Black Soldier Fly Larvae Dried Production, https://dx.doi.org/10.17504/protocols.io.8epv5j54dl1b/v1. 21\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 also like to thank Manajemen talenta Badan Riset dan Inovasi Nasional/National Research and Innovation Agency, especially The Research Center for Sustainable Production System and Life Cycle Assessment and Faculty of Mathematics and Natural Sciences, Mulawarman University for its support. Our sincere gratitude to all members of Research Centre for Sustainable Production System and Life Cycle Assessment, National Research and Innovation Agency, Indonesia.\n\n\nReferences\n\nLange KW, Nakamura Y: Edible insects as future food: chances and challenges. J. Future Foods. 2021; 1(1): 38–46. Publisher Full Text\n\nMoruzzo R, Mancini S, Guidi A: Edible insects and sustainable development goals. Insects. 2021; 12(6): 557. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNugroho R, Nur F: Insect-based protein: future promising protein source for fish cultured. IOP conference series: Earth and environmental Science. IOP Publishing; 2018; 144. : 012002. Publisher Full Text\n\nVan Huis A, Van Itterbeeck J, Klunder H, et al.: Edible insects: future prospects for food and feed security. 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Publisher Full Text\n\nAddo P, Oduro-Kwarteng S, Gyasi SF, et al.: Bioconversion of municipal organic solid waste in to compost using Black Soldier Fly (Hermetia illucens). International Journal of Recycling Organic Waste in Agriculture. 2022; 11(4): 515–526.\n\nTomberlin J, Van Huis A: Black soldier fly from pest to ‘crown jewel’of the insects as feed industry: an historical perspective. J. Insects Food Feed. 2020; 6(1): 1–4. Publisher Full Text\n\nLogan LA, Latty T, Roberts TH: Effective bioconversion of farmed chicken products by black soldier fly larvae at commercially relevant growth temperatures. J. Appl. Entomol. 2021; 145(6): 621–628. Publisher Full Text\n\nPermana AD, Rohmatillah DDF, Putra RE, et al.: Bioconversion of Fermented Barley Waste by Black Soldier Fly Hermetia illucens L.(Diptera; Stratiomyidae). Jurnal Biodjati. 2021; 6(2): 235–245. Publisher Full Text\n\nLee J, Kim Y-M, Park Y-K, et al.: Black soldier fly (Hermetia illucens) larvae enhances immune activities and increases survivability of broiler chicks against experimental infection of Salmonella gallinarum. J. Vet. Med. Sci. 2018; 80(5): 736–740. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim YB, Kim D-H, Jeong S-B, et al.: Black soldier fly larvae oil as an alternative fat source in broiler nutrition. Poult. Sci. 2020; 99(6): 3133–3143. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChopra J, Tiwari BR, Dubey BK, et al.: Environmental impact analysis of oleaginous yeast based biodiesel and bio-crude production by life cycle assessment. J. Clean. Prod. 2020; 271: 122349. Publisher Full Text\n\nEspada JJ, Rodríguez R, de la Peña A , et al.: Environmental impact analysis of surface printing and 3D inkjet printing applications using an imine based covalent organic framework: A life cycle assessment study. J. Clean. Prod. 2023; 395: 136381. Publisher Full Text\n\nKamari A, Kotula BM, Schultz CPL: A BIM-based LCA tool for sustainable building design during the early design stage. Smart and Sustainable. Built. Environ. 2022; 11: 217–244. Publisher Full Text\n\nNugroho RA, Rofiq MN, Santoso AD, et al.: Bioconversion of biowaste by black soldier fly larvae (Hermetia illucens L.) for dried larvae production: A life cycle assessment and environmental impact analysis. Figshare: Raw data of LCA BSF.2023. Publisher Full Text\n\nMertenat A, Diener S, Zurbrügg C: Black Soldier Fly biowaste treatment–Assessment of global warming potential. Waste Manag. 2019; 84: 173–181. PubMed Abstract \| Publisher Full Text\n\nNugroho RA, Rofiq MN, Santoso AD, et al.: Bioconversion of biowaste by black soldier fly larvae (Hermetia illucens L.) for dried larvae production: A life cycle assessment and environmental impact analysis. Protocol.io: Life Cycle Assessment for Black Soldier Fly Larvae Dried Production.2023. Publisher Full Text\n\nSalomone R, Saija G, Mondello G, et al.: Environmental impact of food waste bioconversion by insects: application of life cycle assessment to process using Hermetia illucens. J. Clean. Prod. 2017; 140: 890–905. Publisher Full Text" }	[ { "id": "186279", "date": "18 Jul 2023", "name": "Dino Rimantho", "expertise": [ "Reviewer Expertise Environmental management", "Waste Management", "Environmental Engineering" ], "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 presents the bioconversion of biowaste by black soldier fly (Hermetia illucens L.) larvae for dry larvae production: Life cycle study and environmental impact analysis. This article uses LCA as a research methodology. This research uses open-source LCA, which is easy to apply. Furthermore, life cycle assessment (LCA) techniques are used and include (a) system boundary determination (gate-to-gate), starting with biowaste production, biowaste bioconversion, prepupae, and BSFL frass. This methodology adds to the literature on using BSFL Bioconversion through BSFL cultivation. It has the ability to decompose organic waste so that it can be an alternative solution in urban solid waste management. Some interesting points include:\nThis article does not need to present statistical analysts because the method calculates life cycle analysis from Maggot BSF production. In addition, the authors have used LCA Open Source software as their analysis tools.\nIn the introductory section, it is necessary to add BSFL application literature in other fields, such as health, renewable energy, animal feed, etc, so that the presence of this article can show the environmental impact of BSFL cultivation.\nIn the results and discussion section, it is necessary to develop related to the weaknesses of this article so that it can become a recommendation for further research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Not applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "198614", "date": "04 Sep 2023", "name": "Pande Gde Sasmita Julyantoro", "expertise": [ "Reviewer Expertise Aquatic microbiology", "aquaculture" ], "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 reported a life cycle assessment (LCA) of the biowaste bioconversion process of BSFL and determined the environmental impact categories namely global warming potential (GWP), acidification (AC), terrestrial eutrophication (TE), fossil fuel depletion (FFE), eco-toxicity (ET). Interesting results showed that Electricity and tap water for prepupa production, and electricity consumption for crushing biowaste, were the top three processes in terms of the GWP and that prepupa production is the biggest contributor to global warming potential, acidification, terrestrial eutrophication, and eco-toxicity of all stages in dried BSFL production.\nThe recommendation/suggestion of this study might be not only using alternative single raw materials for substrate BSFL, using another drying method, and optimizing the use of tap water but might also provide information on the optimum dried BSFL production when using a high-efficiency bioconversion process.\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? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-814
https://f1000research.com/articles/12-813/v1	11 Jul 23	{ "type": "Study Protocol", "title": "Effectiveness of pelvis and trunk stabilization exercises over conventional physiotherapy to improve dynamic trunk balance in cerebellar ataxia: a randomized controlled trial", "authors": [ "Anam Sasun", "Mohammad Irshad Qureshi", "Raghumahanti Raghuveer", "Pallavi Harjpal", "Mohammad Irshad Qureshi", "Raghumahanti Raghuveer", "Pallavi Harjpal" ], "abstract": "Cerebellar ataxia is caused by several hereditary or acquired aetiologies that eventually lead to abnormalities in the cerebellum. Patients with cerebellar ataxia may experience balance issues, eye movement abnormalities, limb incoordination, gait instability, and speech impairment as a result. The available treatment options for cerebellar ataxia are rather limited, causing many patients to struggle with daily activities. Although the success rate of a range of therapeutic interventions has been determined, evidence-based exercise guidelines for the treatment of balance disorders and associated problems in people with cerebellar ataxia are currently unavailable. Thus, physiotherapists must explore novel approaches to successfully manage the symptoms of ataxia and further improve the quality of life of patients. The current study protocol will provide new insight as no article available to date has looked at trunk and pelvis stabilization exercise programme as an intervention for treating cerebellar ataxia. We hereby propose a study, which aims to investigate the impact of conventional exercises and trunk and pelvis stabilization exercises along with conventional exercises on subjects with Cerebellar ataxia in a two-arm randomized controlled trial on improving SARA, TIS, BBS, Barthel Index, WHOQOL The total participants will be divided into two-arm parallel groups and the intervention will be given for complete 6 weeks, 5 days in a week. The outcome measure will be evaluated at baseline and the end of 6 weeks. The results will be evaluated after 6 weeks. If the hypothesis of our study proves to be effective, then this physiotherapy intervention could be included in the management of cerebellar ataxia", "keywords": [ "Cerebellar ataxia", "Proprioceptive Neuromuscular Facilitation", "Balance", "Physiotherapy interventions", "randomized controlled trial", "Quality of life.", "Trunk impairment scale", "Severity of Ataxia Scale" ], "content": "Introduction\n\nCerebellar ataxia refers to a cluster of movement disorders caused by the vandalization of the cerebellum or its connections. The cerebellum oversees ensuring the precision and uniformity of actions required for centered motor action. The vestibular component of the cerebellum is crucial for coordinated movements. Cerebellar dysfunction is characterized by ataxia, hypotonia, asynergy, dysmetria, nystagmus, dysdiadochokinesia, tremor, and cognitive inability.1 Hemorrhagic stroke, cerebellar stroke, medications (phenytoin, carbamazepine, lithium), meningitis, and abscesses are examples of acute causes of ataxia. Brain tumors, genetic ataxia, degenerative diseases, cerebellar atrophy, and cerebellar degeneration are examples of subacute and chronic causes. Patients report a significant loss of quality of life and a subsequent decrease in daily living activity performance. Varieties of ataxia are linked to decreased balance. Tumbles caused by impaired balance are common in people with cerebellar ataxia, with more than 70% experiencing at least one fall in the next 12 months.\n\nTo date, no effective pharmacological treatments have been available that have worked efficiently in decreasing or slowing the progression of pathology. Physiotherapy-centred rehabilitation exercises play a crucial role in controlling ataxia progression and improving patients’ functions. Rehabilitation strategies can aid in the abolition of balance and gait disorders, the decrease of fear of falling, and the increase of social participation, and independence in daily life activities.2 Moreover, to prevent secondary complications and promote the independence of the patient, exercises play a very vital role. Static cycling, biofeedback, treadmill training, gaze stimulation exercises and Opto-kinetic stimuli are known to improve balance and functional independence. Growing gait ataxia frequently results in decreased mobility and the ability to engage in everyday activities, thus negatively impacting the quality of life.\n\nDespite the fact that the trunk is recognized as a significant variable in activity and is frequently affected in dysfunction of cerebellum, it is neglected routinely in rehabilitation. Pelvis is marked as a key structure that works to join the trunk to the lower limbs. The function it performs is to connect the trunk to the lower extremities, support the body’s weight, transferring its load onto the lower limbs, and bears the body’s weight and shifts its load to the lower limbs. Pelvic stability is defined as the ability of the lower trunk and proximal hip muscles to coordinate with their own activity while performing balance and mobility activities in which the pelvis supports dynamic balance in order to allow for effective lower limb mobility.3 A strong trunk allows for more regular movement in the rest of the body. Trunk stabilisation is required to support upper and lower extremity movements, meet loads, and protect the spinal cord. During kinetic chain activities, the trunk muscles act as a corset to provide both a stabilising and a mobilising function.\n\nTrunk stabilization training intends to enhance the control of the muscles required to brace the trunk against internal as well as external forces. Although all abdominal muscles contribute to vertebral stability, rehabilitation programs have focused on the transversus abdominis muscle, for evaluation and training.4 Pelvic proprioceptive neuromuscular facilitation boosts joint proprioception, which enhances pelvic control, which is further important for maintaining control of the trunk, and balance. Techniques such as rhythmic initiation aid in the movement of the limb or body through the desired range of motion, beginning with passive motion and progressing to active resisted movement.5 There is a dearth of literature stating the impact of pelvis stabilization exercises and trunk stabilization exercises on achieving dynamic trunk control in patients with cerebral ataxia. Thus, there is a need to conduct a study on the independent effects of the pelvis and trunk stabilization exercises to achieve dynamic trunk balance in patients with cerebral ataxia.\n\nThe designed intervention aims to see the impact of the pelvis and trunk stabilization exercises over conventional physiotherapy exercises on dynamic trunk balance in patients with cerebellar ataxia in two-arm parallel/open-label equivalence randomized controlled trial in improving TIS, SARA, BBS, Barthel index, and WHOQOL on marginal difference.\n\nPrimary objective:\n\n1. To study the effect of pelvis and trunk stabilization over conventional physiotherapy in improving severity of ataxia using the Severity of Ataxia Scale (SARA).\n\n2. To study the effect of pelvis and trunk stabilization over conventional physiotherapy in improving Trunk balance using the Trunk Impairment Scale (TIS).\n\n3. To compare the effects of Pelvis and Trunk stabilization exercises over Conventional Physiotherapy exercises to improve Severity of ataxia, and trunk balance using Severity of ataxia scale and, Trunk impairment scale.\n\nSecondary objective:\n\n1. To study the effect of pelvis and trunk stabilization over conventional physiotherapy in improving balance using Berg Balance Scale.\n\n2. To study the effect of pelvis and trunk stabilization over conventional physiotherapy in improving activity of daily living using the Barthel index.\n\n3. To study the effect of pelvis and trunk stabilization over conventional physiotherapy in improving quality of life using the World health related quality of life.\n\n4. To compare the effects of Pelvis and Trunk stabilization exercises over Conventional Physiotherapy exercises to improve balance, activities of daily living and quality of life using Berg balance scale, Barthel index and World health related quality of life.\n\nSingle-centric, two arm parallel open label equivalence, randomized controlled trial.\n\nEthical considerations – Approval was obtained from the Datta Meghe Institute of Higher Education and Research. IEC no. – DMIHER (DU)/IEC/2023/812 IEC approval date – 21/03/2023.\n\nPatients will be explained about the study procedure in their native language. Informed written consent will be obtained from all study participants.\n\n\nMethods\n\nThis is an interventional study, where participants will be recruited from Physiotherapy OPD of Acharya Vinoba Bhave Rural Hospital Sawangi, Meghe, Wardha, Maharashtra. After receiving an approval from institutional ethics committee of Datta Meghe Institute of Higher Education and Research. Study participants will be divided into Arm-A (Control group) and Arm-B (Interventional-group) with an intent to treat cerebellar ataxic population. A written consent form will be obtained from each patient. Participants will be assessed and screened using inclusion and exclusion criteria of the study.1:1 allocation will be done with an intent to treat the cause. Randomization will be done using computer-generated system. The study is a parallel group-RCT with two arms for subject allocation. Arm-A will receive Conventional Physiotherapy exercises whereas, Arm-B will receive Trunk and pelvis stabilization exercises along-with physiotherapy exercises. The primary and secondary outcome measures used in the study will be quantafied at baseline and at the end of the six-week treatment by a postgraduate resident in neuro-physiotherapy with similar expertise who is aware of the study but blind to the intervention. The design of study is visualized in (Figure 1). The study will be monitored PG guide, HOD, principal and chief advisor of research cell. The final dataset will be uploaded to institutional research website and will be accessible to concerned authorities.\n\nCriteria for inclusion of subjects\n\n1. Patient diagnosed as Cerebellar Ataxia by Medical Doctor.\n\n2. Both Male and Female gender.\n\n3. Above 30-60 years of age.\n\n4. Berg Balance Score <20.\n\n5. Those willing to participate in the study.\n\n6. Those having ability to understand and follow instructions.\n\nCriteria for exclusion of subjects\n\n1. Patients having musculoskeletal injury limiting ability to bear weight.\n\n2. Conditions that impact lower limb mobility.\n\n3. Subjects with unstable cardiovascular condition, as determined by the physician.\n\n4. Patients having significant cognitive impairments, limiting ability to give informed consent.\n\n5. Participants enrolled in another clinical trial.\n\nGroup A (Conventional group): Participants in this group will undergo 60 minutes of conventional therapy. It will include strengthening, sensory stimulation, stretching, mobilising, and teaching functional mobility for the upper and lower limbs. It will be performed for six weeks, five days per week. Identification of weakened muscles will be done. Strengthening exercises for weakened trunk and lower limb at standing, sitting and supine position will be performed. Sensory stimulation will be provided through active ankle mobilisation. Active and functional training will be supplemented with passive mobilisation and stretching. Stretching for lower limb muscles will be done. The hold time for stretching will be 30 seconds with a rest duration of ten seconds. For functional ability, common mat activities will be incorporated.6\n\nGroup B (Interventional-group): Participants in this group will undergo trunk and pelvic stabilization exercises along-with Conventional physiotherapy exercises. Trunk stabilization exercise will include Trunk Proprioceptive neuromuscular Facilitation (PNF). Trunk PNF will include patterns like, Chopping, Lifting, Bilateral lower extremity flexion with knee flexion for lower trunk flexion, Bilateral lower extremity flexion with knee flexion for lower trunk extension, Trunk Lateral flexion, right lateral flexion with extension. Each exercise will be performed in ten repetition ×1 set with hold time being five to ten seconds and relaxation time being five seconds.7 Pelvis Stabilization exercise will include Pelvic Proprioceptive neuromuscular Facilitation (PNF).8 Pelvic motions like anterior elevation, posterior depression, posterior elevation, and anterior depression will be performed. Rhythmic initiation technique of PNF will be used to perform patterns with further progression into combinations of isotonics, dynamic reversal, stabilizing reversal followed by contract relax and hold relax technique. Each exercise will be performed for five repetitions, Sessions/Day three times, with a hold time of five seconds, rest time of two seconds.\n\nPrimary outcome measures\n\n1. Change in Trunk impairment scale (TIS) Score9\n\nThe trunk impairment scale totals the scores for static and dynamic sitting balance, as well as coordination. It is a 17-point scale. Its continued use in clinical practice and research is supported. To rate the quality of trunk movement, the scale can be used as a treatment guideline. The highest score is 23, the lowest is 0, and the total inter-observer reliability is 0.99.\n\n2. Severity of Ataxia Scale (SARA) Score10\n\nSchmitz-Hibusch developed this scale as a clinical assessment tool for calculating the severity of ataxia. It evaluates upper and lower limb ataxia, gait, and balance. It is divided into 8 categories, with a score ranging from 0 (no ataxia) to 40 (the most severe ataxia).\n\nSecondary outcome measures\n\n1. Change in Berg Balance Scale Score11\n\nIt is a performance tool that is based on balance. It is a 5-point scale, with each task scored between 0 and 4. The highest possible score is 56. It includes 14 tasks that are scored between 0 and 4. A participant’s maximum total score is 56.\n\n2. Change in Barthel Index Score\n\nIt is a 10-item assessment scale used to measure the performance of daily living activities. A lower score denotes more dependency.\n\n3. Change in World health-related quality of Life (WHO-QOL) score\n\nIt is a self-reported questionnaire consisting of 26 questions on patients’ health and well-being.\n\nThis study protocol will be an independent two-group study investigating the efficacy of trunk and pelvis stabilization exercises over conventional physiotherapy exercises to improve dynamic trunk balance in cerebellar ataxia. G. Power 3.15 software was used to determine the total participants.\n\nFormula using mean difference\n\nMean ± SD. (Pre) result on Trunk Impairment Scale for experimental group = 5.17 (1.26)\n\nMean ± SD. (Post) result on Trunk impairment Scale for experimental group = 9.13 (1.72)\n\nDifference = 3.96 (3.27 to 5.05). (As per reference Article)\n\nPooled standard deviation. = (1.26 + 1.72)/2 = 1.49\n\nClinically relevant superiority = 30% = (3.96 30)/100 = 1.188\n\nAs per reference articles.\n\nTotal samples required = 20 per Group.\n\nConsidering 10% dropout = 2\n\nTotal samples required (n1 = n2 = 20 per group)\n\nThe total sample size required (N) = 220 = 40\n\nNotations:\n\nReference Article: Effects of Pelvic Stability Training on Movement, Control, Hip Muscles Strength, Walking Speed, and Daily Activities after Stroke: A Randomized Controlled Trial.3\n\n\nDiscussion\n\nPeople suffering from ataxia might regard physiotherapy as their “sole faith”. We intended to investigate the impact of the pelvis and trunk-stabilization exercises over conventional physiotherapy exercises on dynamic trunk balance in individuals suffering from cerebellar ataxia. Further, the study’s objective is to study the effect of pelvis and trunk stabilization over conventional physiotherapy in improving balance using the SARA, BBS, TIS, Barthel Index, and WHOQOL as outcome measures. The results of the study will be assessed at baseline and after 6 weeks of study. Mohammad Elshafey et al. (2022), carried out a study, to determine the impact of a core stability exercise program on coordination and balance in children with cerebellar ataxia.12 Winser et al. (2022), published a systematic review – meta-analysis to study the implications of therapeutic exercise on the severity of disease, balance, and functional independence in cerebellar ataxia patients.13\n\nFurther, Dubey et al. (2018), published an RCT concluding the positive impact of pelvis exercise on movement, and muscle strength of walking in stroke patients. Patients with cerebellar ataxia show greater trunk movements which reflect a lack of coordination between the segments of the body which impacts the spatiotemporal variables of gait local stability.14 According to Marimuthu et al (2022), trunk and neck-specific PNF exercises proved to be a useful intervention in improving balance and trunk control among patients.15 Cerebellar ataxia is associated with cerebellar dysfunction and various balance disorders.16 Further, Poor predictive control has been known to negatively impact the feed-forward part of the movement, which has been associated with the motor symptoms of cerebellar damage.17\n\nThe current study protocol will provide new insight as no article available to date has looked at trunk and pelvis stabilization exercise programs as an intervention for treating cerebellar ataxia.\n\nR studio software 4.3 version will be used to calculate the results. Descriptive statistics will be calculated on the quantitative assessment over the parameters for mean, standard deviation, maximum, minimum, and median for the variables (age, gender, hand dominance). For qualitative assessment frequency and percentage will be calculated over the variables (gender, hand dominance). All the results for the inferential statistics will be tabulated and tested for significance at a 5% level of significance (P= <0.05). The outcome variables (Primary variables: Trunk impairment scale for dynamic trunk balance, Severity of ataxia scale for calculating ataxia severity, and, Secondary variables: Berg balance scale for calculating balance, Barthel index for evaluating independence in activities of daily living and World health-related quality of life for evaluating the quality of life) will be evaluated for testing pre and post result using paired t-test. The outcome variables will be initially tested for normality using Kolmogorov-Smirnov Test for data testing. If data fails to follow normality will be attempted to transform in normal distribution using mathematical algorithm tests like Log Function, Inverse Function, Exponential function, or Boxcox transformation. If data persists with non-normal distribution then, Alternative non-parametric test will be used for the parametric test result. For the paired-t test, an alternative Wilcoxon sign t-test will be used. An unpaired t-test will be used to find significant differences over the mean for both primary and secondary variables between the control and interventional group. Alternate non-parametric Mann-Whitney will be used. Association analysis for finding sig for the unpaired t-test. The significance of cofounding parameters will be evaluated by using the Chi-squared test or Fisher’s exact test or by using multi-variant analysis.\n\nNot started.\n\nPlanning to present my study protocol at the conference preceding.", "appendix": "Data availability\n\nNot applicable as it’s a study protocol.\n\nZenodo: SPIRIT_checklist.docx. DOI: https://doi.org/10.5281/zenodo.8013885\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nMukhtar T, Afzal Pt A, Hussain S, et al.: Effects of Gaze Stability Exercises with Proprioception Training to Improve Gait and Functional Independence in Cerebellar Ataxic Patients. Pak. J. Med. Health Sci. 2021; 15: 3467–3469. Publisher Full Text\n\nZesiewicz TA, Wilmot G, Kuo S-H, et al.: Comprehensive systematic review summary: Treatment of cerebellar motor dysfunction and ataxia. Neurology. 2018; 90: 464–471. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDubey L, Karthikbabu S, Mohan D: Effects of pelvic stability training on movement control, hip muscles strength, walking speed, and daily activities after stroke: a randomized controlled trial. Ann. Neurosci. 2018; 25: 80–89. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFreund JE, Stetts DM: Use of trunk stabilization and locomotor training in an adult with cerebellar ataxia: A single system design. Physiother. Theory Pract. 2010; 26: 447–458. PubMed Abstract \| Publisher Full Text\n\nBeckers D, Buck M: PNF in Practice: An Illustrated Guide. Berlin, Heidelberg: Springer Berlin Heidelberg; 2021. Publisher Full Text\n\nMilne SC, Corben LA, Roberts M, et al.: Rehabilitation for ataxia study: protocol for a randorandomizedrolled trial of an outpatient and supported home-based physiotherapy programme for people with hereditary cerebellar ataxia. BMJ Open. 2020; 10: e040230. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBae SH, Lee HG, Kim YE, et al.: Effects of Trunk Stabilization Exercises on Different Support Surfaces on the Cross-sectional Area of the Trunk Muscles and Balance Ability. J. Phys. Ther. Sci. 2013; 25: 741–745. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoob MA, Kovela RK Jr MAB, Sr RKK: Effectiveness of Pelvic Proprioceptive Neuromuscular Facilitation Techniques on Balance and Gait Parameters in Chronic Stroke Patients: A Randomized Clinical Trial. Cureus. 2022; 14: e30630. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSamal SN, Samal SS: Neha Ingale Chaudhary, Sachin Chaudhary, Vasant Gawande: Efficacy Of Core Strengthening Exercises On Swissball Versus Conventional Exercises For Improving Trunk Balance In Hemiplegic Patients Following Stroke. Int. J. Res. Pharm. Sci. 2021; 12: 889–893. Publisher Full Text\n\nSchmitz-Hübsch T, du Montcel ST , Baliko L, et al.: Scale for the assessment and rating of ataxia: development of a new clinical scale. Neurology. 2006; 66: 1717–1720. PubMed Abstract \| Publisher Full Text\n\nWinser SJ, Smith CM, Hale LA, et al.: Clinical assessment of balance using BBS and SARAbal in cerebellar ataxia: Synthesis of findings of a psychometric property analysis. Hong Kong Physiother. J. 2018; 38: 53–61. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nElshafey MA, Abdrabo MS, Elnaggar RK: Effects of a core stability exercise program on balance and coordination in children with cerebellar ataxic cerebral palsy. J. Musculoskelet. Neuronal Interact. 2022; 22: 172–178. PubMed Abstract\n\nWinser S, Chan HK, Chen WK, et al.: Effects of therapeutic exercise on disease severity, balance, and functional Independence among individuals with cerebellar ataxia: A systematic review with meta-analysis. Physiother. Theory Pract. 2022; 39: 1355–1375. PubMed Abstract \| Publisher Full Text\n\nChini G, Ranavolo A, Draicchio F, et al.: Local Stability of the Trunk in Patients with Degenerative Cerebellar Ataxia During Walking. Cerebellum. 2017; 16: 26–33. PubMed Abstract \| Publisher Full Text\n\nDinesh M, Thenmozhi P, KalaBarathi S: Proprioceptive Neuromuscular Facilitation Neck Pattern and Trunk Specific Exercise on Trunk Control and Balance—an Experimental Study. Int. J. Ther. Massage Bodyw. 2022; 15: 9–17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPathan A, Telang P: A Review Article on Assistive and Rehabilitation Technology in Cerebellar Ataxia. J. Pharm. Negat. Results. 2022; 3012–3016. Publisher Full Text\n\nNawkhare AV, Shamal S, Udhoji SP, et al.: Convalescence after physiotherapy intervention in a classic rare case of cerebellar bleed: A case report. Med. Sci. 2023; 27. Publisher Full Text" }	[ { "id": "195453", "date": "25 Sep 2023", "name": "Ragab Elnaggar", "expertise": [ "Reviewer Expertise Physical Therapy and Health Rehabilitation" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a protocol for a prospective, open-label clinical trial that will study the effectiveness of trunk and pelvic stabilization exercises on dynamic trunk balance in patients with cerebellar ataxia. I have some major/minor concerns that the authors need to address before considering the study appropriate. These are as follows:\nAbstract\nAbbreviations should be spoked out the first time they are mentioned (SARA, TIS, BBS, and WHOQOL)\n\nThe data analysis plan as has been stated in the abstract is not clear. Revise for clarity.\n\nA synopsis of the potential clinical implications should be provided in the conclusion subsection of the abstract.\nIntroduction\nThe authors used the term “trunk and pelvic stabilization” exercise. What is the difference between your intended study approach and the commonly known “Core stability” exercise? This is critical to clarify.\n\nI have a major concern regarding the novelty of the intended study. There exist plenty of published articles that explore the role of “trunk and pelvic stabilization” for different postural control outcomes. However, I am open to changing my point of view if the authors pinpointed the research gap appropriately (in light of the related literature) and made it clear what drove them to conduct the study\n\nThe introduction does not provide the proper context about the topic. The logical flow of the idea is lacking. Authors need to provide further context and background information about the role of trunk and pelvic stabilization exercises in patients with cerebellar ataxia or other conditions sharing similar symptoms.\n\nThe significance of the study is not clear. Please, provide a justification of the importance of the intended study, highlight the impact it would have on the research field, define its contribution to new knowledge, and explain how others will benefit from it.\n\nIn other words, the connection between the background and the research question should be made clear.\n\nWhy did you split the study's primary/secondary objectives into several statements? They are redundant and could be compiled in two statements (one primary and one secondary objective).\nMethods\nThere is a potential risk of open-label design. I think this could be partially addressed if the authors considered blinding the outcome assessor.\n\nA detailed description of the study design is needed. This should include information about recruitment, blinding, and randomization procedures.\n\nYou conducted a priori power analysis to determine the appropriate sample size. Please, provide proper credit to the source of the information you employed for the analysis.\n\nThe intended treatment (i.e., the core stability training) needs a clear description. As I attempted to envision how exercises would be done, I couldn't quite get it. So, a detailed description of the exercise program (exercise description, instruction for performance, volume, intensity,….. etc.) is imperatively needed to help other researchers replicate it.\n\nAlso, a further description of the outcome measures (i.e., measurement procedures) should be provided.\n\nThe training volume and frequency as proposed are different. This could affect the study results. Training should be equated for both groups.\n\nHave you registered the protocol in any of the WHO clinical trial registration repositories? If yes, give the registration details.\nData analysis\nGiven the many outcome measures in the study, I would not recommend a t-test or the non-parametric equivalent for the data analysis. I would suggest mixed-model ANOVA to calculate the pre-to-post change differences.\n\nDiscussion\nThe discussion requires additional development. Authors should discuss in-depth focusing on the relevance of the study, and outlining the potential implications for practice\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "219289", "date": "14 Nov 2023", "name": "Helen Hartley", "expertise": [ "Reviewer Expertise Neuro Oncology", "Rehabilitation", "Ataxia" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors are presenting a protocol for a RCT examining the effectiveness of pelvis and trunk stabilization compared with conventional physiotherapy in cerebellar ataxia. There is a place for further research in this area as interventions specific to cerebellar ataxia are not well described however, there are a number of areas where the rationale for this study could be enhanced.\nComments as below;\nAbstract Add sentence on data analysis\nIntroduction Generally this section is under referenced.\nWould suggest rewording in the first paragraph where 'vandalization' is used.\nPlease reference the comments on falls (end of first paragraph) and the comments on types of interventions that improve balance (end of second paragraph).\nThere is further scope to refer to the systematic reviews that have been published on ataxia interventions in adults - and draw from this the need for further research.\nTrunk stabilisation training should be clearly defined and differences between this and core control or (proximal control exercises) should be clearly stated\nPlease add in full the outcome measures prior to abbreviating e.g, TIS, SARA\nNot clear why the primary objectives have been chosen i.e. over the secondary objectives - can you clarify why SARA and TIS have been chosen as primary. Not sure what no 3 primary objective is? - is it 1 and 2 repeated (similarly number 4 in the secondary objective)\nMethods Can you confirm will the participants potentially have cerebellar ataxia from an acute or genetic origin?\nSample size calculation - please reference this section\nDo Group B receive the trunk stabilisation exercises in addition to the conventional therapy? I.e., is the amount of intervention therefore different between the two groups? If so, need to clearly state this and justify this design and acknowledge this may impact on outcome\n\nDiscussion This section doesn't flow well as it is before the analysis. Some elements of the discussion could be used in the introduction to increase the rationale for the study. I am not sure of the purpose of the discussion here?\nData analysis Please can you provide information as to why you will try and transform the data into normal distribution and the rationale for this And reference choice of statistical testing\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "219285", "date": "16 Nov 2023", "name": "Sarah Milne", "expertise": [ "Reviewer Expertise Rehabilitation", "physiotherapy", "cerebellar ataxia", "neurological rehabilitation" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a randomised controlled trial protocol examining the efficacy of additional trunk and pelvic stabilisation exercises compared to a conventional rehabilitation program in individuals with cerebellar ataxia. This is an appropriate intervention targeting the postural instability in individuals with ataxia, that has yet to be explored. I have a few comments and suggestions for strengthening the protocol.\n\nAbstract:\n“Evidence-guidelines for treatment of balance disorders… are currently unavailable” – this is an incorrect statement. Refer to Friedreich's Ataxia Research Alliance - Clinical Care Guidelines (curefa.org) and Medical Guidelines - Ataxia UK\n“No article available to date has looked at trunk and pelvis stabilization exercise program” – is incorrect also. Please refer to: Tabbassum, KN et al. (2013) Core Stability Training with Conventional Balance Training Improves Dynamic Balance in Progressive Degenerative Cerebellar Ataxia. Indian Journal of Physiotherapy and Occupational Therapy 7(1): 136-140.\nPlease spell out outcome measures in full first time used in the abstract.\nIntroduction:\nParagraph 2: Please find references for the following sentence: “Static cycling, biofeedback, treadmill training, gaze stimulation exercises and Opto-kinetic stimuli are known to improve balance and functional independence.”\nMethod:\nCould you please provide further detail on how you are going to recruit participants? Are they inpatients or outpatients? Where will you ask them to participate?\nPlease indicate if allocation will be concealed from the enrolling investigator.\nGroup B – Intervnetional group – could you please clarify if participants will receive 60 minutes of conventional physiotherapy as well as the stabilisation exercises and therefore how long they will receive each day. This will give an indication of dosage to allow comparison across both groups.\nCould you consider using the TIDieR checklist to describe your intervention in more detail. This will be important if your results demonstrate significant improvement with the additional trunk and pelvis exercises.\nCould you please confirm your primary outcome measure. Is it the TIS? Or the SARA?\nCould you please clarify your sample size estimation – it appears to state that you need 20 participants per group and to factor in a 10% drop out (n=2). Does this mean your sample size should be 22 per group?\nAre you going to record any adverse events?\nPlease indicate what demographic and disease characteristics you are going to collect. This will be very important as it appears you will include both progressive and non-progressive ataxia diagnoses, which may influence your results.\nDiscussion\nYou mention three prior studies in the discussion but don’t explain further about how the findings from this study will build on these studies.\nAnalysis\n“For qualitative assessment frequency and percentage will be calculated over the variables (gender, hand dominance).” I am not sure you mean ‘qualitative’ here as gender and hand dominance are quantitative data. You have repeated hand dominance after both assessments.\nWith the between group analysis chosen, how will you account for any differences at baseline?\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/12-813
https://f1000research.com/articles/12-812/v1	11 Jul 23	{ "type": "Research Article", "title": "Clinical characteristics, risk factors and complications of COVID-19 among critically ill older adults - A case control study", "authors": [ "Arfath Ahmed", "Sheetal Raj Moolambally", "Archith Boloor", "Animesh Jain", "Nandish Kumar S", "Sharath Babu S", "Arfath Ahmed", "Archith Boloor", "Animesh Jain", "Nandish Kumar S", "Sharath Babu S" ], "abstract": "Background: The older population is often disproportionately and adversely affected during humanitarian emergencies, as has also been seen during the COVID-19 pandemic. Data regarding COVID-19 in older adults is usually over-generalized and does not delve into details of the clinical characteristics in them. This study was conducted to analyze clinical and laboratory characteristics, risk factors, and complications of COVID-19 between older adults who survived and those who did not.\nMethods: We conducted a case-control study among older adults(age> 60 years) admitted to the Intensive Care Unit(ICU) during the COVID-19 pandemic. The non-survivors(cases) were matched with age and sex-matched survivors (control) in a ratio of 1: 3. The data regarding socio-demographics, clinical characteristics, complications, treatment, laboratory data, and outcomes were analyzed.\nResults: The most common signs and symptoms observed were fever (cases vs controls)(68.92 vs. 68.8%), followed by shortness of breath (62.2% Vs. 52.2%), and cough(47.3% Vs. 60.2%). Our analysis found no association between the presence of any of the comorbidities and mortality. At admission, laboratory markers such as LDH(Lactate Dehydrogenase), WBC(White Blood Count), creatinine, CRP(C-Reactive Protein), D-dimer, ferritin, and IL-6 were found to be significantly higher among the cases than among the controls. Complications such as the development of seizure, bacteremia, acute renal injury, respiratory failure, and septic shock were seen to have a significant association with non-survivors.\nConclusions: Hypoxia, tachycardia, and tachypnoea at presentation were associated with higher mortality. The older adults in this study mostly presented with the typical clinical features of COVID-19 pneumonia. The presence of comorbid-illnesses among them did not affect mortality. Higher death was seen among those with higher levels of CRP, LDH, D-dimer, and ferritin; and with lower lymphocyte counts.", "keywords": [ "COVID-19 pandemic", "Older adults", "Elderly", "Intensive care", "critically ill older adults", "risk factors for COVID-19", "atypical presentation of COVID-19" ], "content": "", "appendix": "" }	[ { "id": "220481", "date": "04 Dec 2023", "name": "Upinder Kaur", "expertise": [ "Reviewer Expertise Vaccine safety", "Pharmacovigilance", "Elderly drug safety" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nReduce the number of references in the Introduction section.\nSpecify, what percentage or proportion of COVID-positive cases was taken for the sample size calculation?\nThis being a case control study, more likely to be of retrospective nature, how was written informed consent obtained? More so from patients - non-survivors?\nResults: Authors mention systolic and diastolic blood pressure were higher in case group. The same should be deleted as it neither seems clinically significant nor statistically significant.\nWhich diseases were included in chronic neurologic disorders?\nThough not statistically significant, presence of co-morbdities such as lung disease (COPD and asthma) and cardiac disease were higher in case group. This should be mentioned in Results and briefly highlighted in Discussion.\nLikewise in symptoms, mention the common symptoms followed by symptoms which were noticed in higher percentage in case or control group. For example cough, anosmia, loss of taste, muscle aches and seizures.\nTable 5, mention the units of cell count in cells/µL. Mention the units of HbA1c.\nProvide platelet count in the two groups. Comment upon the thyroid function status of the two groups.\nMention about stroke rates in the two groups in Results section.\nDiscussion: Needs major revision. Avoid mentioning the sample size and exact rates. Avoid describing co-morbidities, age distribution again. This is mentioned in Results section. Write in terms of majority or most common observations. Discussion should be limited to important findings of the paper.\nThe present study did not find gender to be associated with severe COVID-19. The percentage of individuals with lung disease was higher (though not statistically significant) in cases. Likewise, wheezing was statistically more common in non-survivors. In this context, a larger study from North India by Kaur et al. (20221) should be discussed. The study highlighted male gender and presence of lung disease to be significant determinants of severe COVID-19.\nAuthors should briefly describe the common symptoms observed in their study with the ones reported in other studies. This should be followed by signs and laboratory findings or complications. Only the atypical ones need to be discussed.\nA better way is to include the atypical findings of the present study and those of other studies in a separate Table. Seizure rates, anosmia, wheeze and complications need to be emphasized rather than the typical clinical features observed in other studies. Varying seizure rates in the two groups might be because of a higher percentage of neurological disorder in the Case group.\nA larger section is attributed to co-morbidities, which is not necessary. The part needs to be shortened.\nAuthors should provide a Limitation section. A major limitation is the retrospective analysis of the present study. Failure to consider the Vaccination history. Authors have collected the data until September 2022 by which time a greater percentage of elderly, being the priority groups would have received the vaccine. Also no history of previous COVID-19 has been mentioned, which is another big limitation. If thyroid function status was not included, this is another limitation. Any vaccine received after recovery from COVID-19 and presence of thyroid abnormality have been proposed as major determinants of complications such as persistent health issues and long term adverse events which can be independent determinants of mortality in COVID-19 patients. Such studies need to be discussed in the Limitation section of the present paper (Kaur et al., 20222).\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/12-812
https://f1000research.com/articles/12-806/v1	10 Jul 23	{ "type": "Systematic Review", "title": "Re-starting anticoagulation and antiplatelets after gastrointestinal bleeding: A systematic review", "authors": [ "Ethan Slouha", "Haley Jensen", "Hope Fozo", "Rhea Raj", "Sneha Thomas", "Vasavi Gorantla", "Ethan Slouha", "Haley Jensen", "Hope Fozo", "Rhea Raj", "Vasavi Gorantla" ], "abstract": "Background: Gastrointestinal bleeds (GIB) are associated with high morbidity and mortality, with upper GIB accounting for 20,000 deaths annually in the United States of America. Accurate risk stratification is essential in determining and differentiating high-risk versus low-risk patients, as low-risk patients have an overall better prognosis. Patients taking antithrombotics to reduce the risk of thromboembolic events have a 4% chance of developing a GIB. This then places physicians in a difficult position as they must perform a risk-and-benefit analysis of whether to reinstate antithrombotics after a major GIB. This systematic review aims to assess the general trends in time for resuming anticoagulation in the setting of upper GI bleed.\nMethods: A literary search of three different databases was performed by three independent reviewers. The research databases included PubMed, ScienceDirect, and ProQuest. Specific keywords were used to narrow the search and articles were screened based on inclusion and exclusion criteria.\nResults: Our initial search generated 11,769 potential articles and 22 articles were ultimately used for this review using specific inclusion and exclusion criteria. There is an increase in thrombotic events following a GIB if anticoagulants are not resumed. We also found that the best time to resume therapy was 15-30 days post-GIB.\nConclusions: Therefore, the decision to resume anticoagulation therapy should consider the patients’ medical history and should fall within 15-30 days post-GIB.", "keywords": [ "Anticoagulants", "Restarting Anticoagulants", "GI bleeds", "GI bleeding", "Resuming Anticoagulants", "Pharmacology", "Post-GI bleed", "Anticoagulant bleeding" ], "content": "Introduction\n\nGastrointestinal bleeding (GIB) is any bleeding that originates within the GI tract from the esophagus to the anus. This bleeding can be microscopic and only detected by lab testing or visible as blood in the stool or emesis.1 In most cases, GIBs are classified into two broad categories: upper and lower GIBs.2 Upper GIBs refers to bleeding originating from a source proximal to the Ligament of Trietz3 and is usually associated with hematemesis (vomiting of blood) and melena (black, tarry stool). According to El-Tawil et al., Upper GI bleeds affect 50-100 out of every 100,000 Americans per year and accounts for 20,000 deaths.4 Lower GIBs are classified as originating from a source distal to the Ligament of Treitz and are commonly associated with hematochezia (bright red blood in stool).5 Lower GIBs are less common, accounting for approximately 20-30% of all GIBs.6\n\nEach year, there is an increasing number of patients being prescribed anti-thrombotic and anticoagulant therapies. Unfortunately, these therapies tend to place patients at an increased risk of developing GIBs. Current research indicates that 4% of individuals on anticoagulants experience GIBs at some point during treatment.7 The decision to restart anticoagulation and antithrombotic therapy in patients post-GIB is a challenging task for many physicians; this makes risk stratification and shared decision making essential in the judgement to restart therapy.8\n\nAnticoagulants mechanism\n\nAnticoagulants act as blood thinners by preventing the synthesis of clotting factors or by directly blocking them. Warfarin works via competitive inhibition of the enzyme vitamin K epoxide reductase to decrease the synthesis of vitamin K-dependent clotting factors II, VII, IX, X, and proteins C and S that aid in coagulation.9 Prescribing warfarin to patients requires careful monitoring and assessment by physicians due to various factors, such as the patient’s genes, laboratory values, and a diet rich in vitamin K. These factors may affect the proper dosage of warfarin.9 Warfarin is administered orally and inhibits multiple clotting factors, whereas direct oral anticoagulants (DOACs) work by blocking one specific clotting factor. Examples of DOACs are dabigatran, rivaroxaban, apixaban, and edoxaban.10\n\nAntithrombotic mechanism\n\nAntithrombotics, such as aspirin, prohibits the aggregation of platelets in the vasculature and reduce the risk of thrombosis.11 Aspirin works by permanently inhibiting COX-1 and COX-2. Aspirin as an antithrombotic drug, rather than an anti-inflammatory drug, requires a much smaller dosage to inhibit COX-1; aspirin at higher doses inhibits COX-2 and acts as an anti-inflammatory agent.11 By inhibiting COX-1, arachidonic acid cannot be converted to thromboxane A2, a prostanoid that works to stimulate platelet aggregation. Aspirin is therefore a powerful antithrombotic drug that works to inhibit the synthesis of platelet modulators.11 Other known antithrombotics work in similarly to inhibit platelet aggregation. Therefore, antithrombotics work as blood thinners and reduce the risk of thromboembolic events and ischemic stroke.\n\nPhysicians who decide to restart patients on anticoagulants must also decide the best time to do so. We sought to determine if there was a timeframe in which restarting anticoagulants and anti-thrombolytics best reduced the risk of rebleed while also protecting patients from a thrombotic event.\n\n\nMethods\n\nA comprehensive literature search was performed using ProQuest, Science Direct, and PubMed databases from the 1 December 1992 to the 31 of December 2022. Keywords included ‘resuming anticoagulation and gastrointestinal bleeding’, ‘re-starting anticoagulation after gastrointestinal bleeding’, and ‘resuming antithrombotic after gastrointestinal bleeding’. The electronic search focused on peer-reviewed journals deemed to be in line with the goal of this paper. Articles not written in English, articles published before 1992, and duplicate articles were excluded during the screening process. Once the search was complete, three co-authors reviewed the results independently. Articles gathered from the investigation were analyzed based on their titles, study type, abstract, and full-text accessibility. Our initial search in the previously mentioned databases resulted in 11,764 articles. These selected articles were further narrowed down according to keyword specifics and preview of abstracts according to the inclusion and exclusion criteria; a total of 22 articles were deemed to be within our interest.\n\nThe following inclusion criteria were used: articles written in English, articles conducted on humans, articles published between 1992 and 2022, articles relevant to our interest, articles that are full-text, peer-reviewed, and include case-control, meta-analysis, observational, and cohort studies.\n\nExclusion criteria used were articles not written in English, articles published before 1992, systematic reviews, case reports, or review articles. All duplicates and non-full-text articles were also excluded. The process of inclusion and exclusion of articles is illustrated in Figure 1.\n\nThe studies were assessed for bias. It was determined that there was a medium risk for bias as the studies were primarily conducted based on medical reports and insurance claims. The risk of bias of the individual studies were assessed using the Grading of Recommendations, Assessments, Development and Evaluation (GRADE). GRADE is a tool that evaluates flaws like imprecision, indirectness, and publications.\n\n\nResults\n\nA total of 11,764 articles were found; 92 were from PubMed, 6419 from ScienceDirect, 5253 from ProQuest, and four were found from citations of included articles. Among the exclusions were 12 duplicate articles and 102 articles published before 1992. This resulted in 114 articles being excluded from the automatic screening process, leaving 11,657 articles for manual screening. Articles were manually screen based on the title, study type, abstract, and availability, resulting in 435 articles to be checked for eligibility. Ultimately, 22 articles were used (Table 1).\n\nOverall, 18 articles focused on resuming anticoagulant therapy post-GIB and the major findings presented indicated that those who resumed therapy had a reduced risk of a thrombotic event. There were some patients who did have a rebleed but the overall outcomes showed that the benefits from resuming anticoagulant therapy outweighed the risk. With respect to the four antithrombotic/antiplatelet therapy articles, there were similar results; however there was a great risk in rebleed as most of these therapies are given in conjunction with anticoagulants.\n\n\nDiscussion\n\nThe decision to resume anticoagulants and antithrombotic post-GIB is crucial when confronted with patients with a history of thrombotic events, mechanical heart valves, and atrial fibrillation, despite the associated risk of recurrent bleeding.12 The clinical impacts of thromboembolism and recurrent GIB are not equivalent and need to be accounted for when determining whether to resume anticoagulant and antithrombotic therapy. Little et al. reports that the case-fatality rate and institutionalization due to a thromboembolic event at three months post-GIB was 41% (Europe) and 57% (U.S.).12 In contrast, the case-fatality rate of oral anticoagulants (OAC)-caused recurrent GIB was between 8-13%.12 Research has shown that while there is an increase in the risk of recurrent bleeding, there is a decreased risk of thrombolytic events and all-cause mortality.\n\nAccording to multiple studies, an average of 60% of patients who suffered a GIB were resumed on OACs as a preventive measure.12,13 Up to half of the patients resuming OACs post-GIB were restarted on the same drug and dosage, and around 40% of patients were switched to a drug that was not an OAC.14 Restarting OACs in patients who suffered atrial fibrillation and bleeding events were associated with a significant decrease in thromboembolism and did not significantly increase the risk of recurrent bleeding. This then contributed to a reduction of all-cause mortality in patients.13,15–18 Proietti et al., found a decreased risk of thromboembolic events in patients who restarted OACs versus. those who did not, with a relative risk reduction of 44%.19 There was also a significant reduction in all-cause mortality and thromboembolic event (hazard ratio (HR) 0.35; 95% confidence interval (CI); HR 0.76; 95% CI) in patients who were restarted on OACs.19\n\nSostres et al., compared patients who resumed OACs versus those who did not after a GIB, they found that of the 811 patients that stopped therapy, 17.8% of patients experienced a thromboembolic event during the follow-up period, while 24.9% had a recurrent GIB.20 There was a significant difference in those that resumed therapy versus those who did not, with patients who resumed having a lower risk of an ischemic event (HR 0.626; 95% CI) and a decreased mortality (HR.0606), although they did have a higher risk of rebleeding (HR 2.184; 95% CI).20 Rebleeding during the time following the initial GIB is a likely event. Candeloro et al. explored the status of recurrent GIB in patients who restarted and discontinued OACs post GIB and found that the rebleeds tend to occur where the original bleed stemmed from Ref. 18. Proietti et al., found that recurrent GIBs occurred in 10.2% of patients who resumed OACs compared to 5% of patients who did not restart.19 Similarly, Tapaskar et al., found that 10.1% of patients who resumed OACs post-GIB had recurrent GIB compared to 5.3% of patients who discontinued OACs.21 Across those studies, there was an average of a 5% increase in risk for GI bleed; both studies found these results insignificant.\n\nSeveral studies have been conducted to assess the resumption of warfarin post-GIB, as it is infamously known for its unpredictability. Witt et al., found that at least 35% of patients resumed warfarin after a GIB.22 Smit and Gelder showed that after significant bleeding, 47% of warfarin users were restarted on their therapy, and there was a decrease in thromboembolic events and all-cause mortality. In a study population of 1825, Chai-Adisaksopha et al. reported a significant reduction in thromboembolic events in patients who resumed warfarin therapy post-GIB.23 Across multiple studies, there was an average of 6% decrease in thrombolytic events for those who resumed warfarin therapy.12,22–24 Resumption of warfarin was associated with a significant reduction in all-cause mortality in patients.22–26 Chai-Adisaksopha et al. reported that death occurred in 24.6% of patients who resumed warfarin, whereas, in patients who did not resume warfarin, death occurred in 39.2% of patients.23 Similarly, Little et al. observed that the all-cause mortality rate was 21.5% in patients who resumed warfarin compared to 31.6% who did not.12\n\nAcross all studies, only one patient death was reported which was associated with a massive gastrointestinal bleed in a patient who resumed warfarin.25 On average, rebleeding occurred in 11.6% of patients restarted on warfarin and 5.7% of patients who were not restarted; however, the studies found that these differences were not statistically significant.17,19,22–24,26,27 Although it is assumed that patients who do not resume anticoagulants are at a lower risk of rebleeding and bleeding-related complications, Majeed et al. demonstrated that these patients would require closer monitoring and shorter follow-up (92 weeks) as compared to those who were restarted on VKAs (142 weeks, p < 0.001).26 The rate of recurrent bleed is high whether the patient is resumed on anticoagulants or not, with bleeding occurring at a median of 24 weeks in those that were resumed on anticoagulants and 23 weeks in patients that were not.26\n\nSome physicians decide to switch treatment plans, such as changing from warfarin to DOAC post-GIB.18,28 Little et al. found that apixaban was the DOAC of choice in most cases.12 There was a 3% increase in patients who experienced a recurrent GIB after the resumption of DOACs.12,27 Proietti et al. focused on dabigatran and found that patients who were started on dabigatran had a reduced risk for recurrent GIB compared to those who started on warfarin.18 Smit and Gelder reported that 49% of dabigatran users restarted anticoagulation after significant bleeding, and the risk of ischemic stroke and all-cause mortality decreased.29 There was some conflict on the overall effectiveness of DOAC’s competence post-GIBs. Sengupta et al. found that patients with a history of venous thromboembolism who were restarted on DOAC had a risk of 2.7% for a thromboembolic event compared to 2.2% in patients whose DOAC was held 90 days post-GIB.30 In that same year, however, Proietti et al. found a reduced risk of thromboembolic events and all-cause mortality in patients who restarted on DOACs after a GIB.19\n\nPatients who restarted on DOACs within 30 days of the index bleed were not associated with a recurrent bleed.30 Sengupta et al. reported no difference in readmission for a recurrent GIB in patients started on DOACs compared to those who were not restarted on DOACs.30 Other studies, however, have reported recurrent GIB issues associated with rivaroxaban.17,27,30 Valanejad et al. demonstrated that rivaroxaban was the only DOAC that increased the risk of recurrent GIB.27 Overall, most research reports that the resumption of DOACs reduces the risk of thromboembolism and all-cause mortality with a selective increase in recurrent GIBs.12,17,19,28 The results were relatively similar when comparing DOACs with warfarin use, but a benefit of the DOACs with resuming treatment post-GIB is the predictability and reduced monitoring that is typically associated with DOACs as compared to warfarin.\n\nHeparin is a low molecular weight anti-coagulant typically used as a bridging therapy. Individuals with a history of thrombolytic events, cancer, and who were younger tended to be restarted on heparin post-GIB by the first outpatient hemodialysis session.31 Heparin doses tend to be decreased post-GIB, and Shen et. al found no significant association between recurrent GIB (HR.78, 95% CI) and death (HR 1.01, 95%) compared to those who did not resume heparin therapy [39]. Resumption of heparin in both studies reduced thrombolytic events while non-significantly contributing to recurrent GIB.18,31\n\nAntithrombotic therapy resumption post-GIB was also a point of interest. Studies showed that antithrombotic were paired with anti-coagulants and proton-pump inhibitors and were typically not given alone.16,18,20,21,30,32 Of the patients on antithrombotics, 8.5% were discontinued to reduce rebleeding risk, while 6.8% of patients were switched to a different antithrombotic.18 Patients restarted on antithrombotics with anticoagulants, and a small few alone, had a higher risk of rebleed than those just resuming OAC.16 Patients on dual antithrombotic therapy were also associated with lower mortality (15.9%) than those that were not (29.3%; p = 0.009).20 Sostres et al., also reported that patients who did not resume anticoagulant and/or antithrombotic therapy within 90 days after the initial bleed had higher all-cause mortality and higher risk of thromboembolism.20 Tapaskar et al., however, reported that they were unable to identify the significance of resuming or discontinuing antithrombotic in patients post-GIB.21 Sengupta et al. did discover that patients who were taking thienopyridines were more likely to have a recurrent GIB.30 Ultimately, anticoagulants were better than antithrombotic in terms of thromboembolic and mortality outcomes with less incidences of recurrent bleeds.\n\nStudies have noted that resuming anticoagulation is optimal around 90 days. However, other studies have indicated that thrombotic events occur within these days, leaving with a greater increase in mortality.16,20,27,33 Narrowing down this time frame is optimal. The type and severity of the GIB plays a role in the clinician’s decision on when to resume anticoagulants.33 Hafiz et al. suggested a prophylactic dose of anticoagulants be administered before graduating to a full dose to balance the risk of a thromboembolic event.33 They also indicated that resuming antithrombotic therapy within seven days of the initial bleeding event has an overall beneficial effect.33 Sostres et al. found that 98.5% of patients reinstated therapy within the first 30 days (median of 6 and mean of 7.6 ± 6.4 days), suggesting that the first week might be the optimal time for resuming anticoagulant or antithrombotic therapy.20 However, they also stress that clinicians should use risk stratification tools and make decisions case-by-case.20\n\nOther studies have shown that as compared to patients that were resumed on therapy at least seven days after the index bleed, patients that were resumed on therapy within the first seven days were associated with a higher rate of rebleeding (30.6% p = 0.044) and a lower rate of ischemic events (13.6%; p = 0.025).20,22,25 Patients who resumed after day 7 had a lower rebleeding rate than those who restarted anticoagulants within the first seven days.25 Mortality during follow-up of patients was lowest when warfarin was restarted between 15-90 days post-GIB.22 Lee et al. suggests the optimal timing for resumption of warfarin lies between 14-20 days after the initial bleeding event after a SEE has been performed to ensure that the patient is hemodynamically stable.24 Majed et al. however, suggested that the risk of rebleeding within the first three weeks after the index bleed is very high and that risk reduces significantly by the sixth week. Hence, the optimal time for resumption lies between the third and sixth week after the initial bleed.26 The time frame varies greatly between <7 days up to 90 days, ultimately showing a decrease in thrombolytic events. Most research points toward 15-30 days post GIB as an optimal window as to when to resume therapy, but it is still clear that this needs to be assessed based on the patient’s presentation and medical history.\n\nWhile we found a greater benefit in resuming anticoagulant and antithrombotic therapies post-GIB, there are still factors to consider as to why physicians wouldn’t resume these therapies. Physicians tend to hesitate resumption in patients with upper, lower, and unknown-source GIB, diabetes, renal disease, coronary artery disease, and history of falls, specifically for warfarin due to either medication adherence or increase chance in rebleeds and other adverse events.27,34 Older patients or patients with dementia and living in a long-term care facility were also less likely to be placed on OACs post GIB.24 Patients who underwent blood transfusion during hospitalization and required monitoring in intensive care units and previous GIB bleeds, were usually given alternate medication to prevent thromboembolism.19,30 Quershi et al. reported that on top of the previously mentioned factors, 19% of patients could not follow-up treatment with an anticoagulant clinic and had insurance issues.25 The physician’s preference was also indicated in 18% of the cases not to restart anticoagulation.25 While this paper addresses some of the reasons for resuming anticoagulant and antithrombotic therapy, specific reasons should be addressed in further research.\n\nThe studies did present with some limitations in that they were largely retrospective investigations using health insurance claims. Retrieving reports from health insurance claims do run the risk of being inaccurate. This also limits the study population, depending on the origin of the study, due to patient who are not covered under insurance, as their population could be an important factor to consider in rates of rebleeds or thrombolytic events.\n\n\nConclusions\n\nOACs significantly reduced thromboembolic and all-cause mortality rates while also increasing the risk for a recurrent GIB. Warfarin is associated with a slightly higher risk of GIB when compared to DOACs and has a less predictable outcome as a vitamin K antagonist. DOACs tend to provide the same benefits in reducing thromboembolic events and all-cause mortality as warfarin but have a lower increased risk of recurrent bleeding. Heparin resumption has also been analyzed as it is typically used for bridging therapy and for hemodialysis patients, also showing similar beneficial effects as warfarin and DOACs, with few side effects following the first outpatient session of hemodialysis as another form of anti-coagulants used to resume other treatment plans for specific conditions.\n\nAntithrombotic also needs to be addressed following a GIB. Studies we have found showed that, while usually paired with anticoagulants, certain antithrombotic further increases the risk for recurrent bleeds. We also attempted to address the timing of when to resume anticoagulant and antithrombotic therapy, and while the research varied in resumption time, the studies indicated that an average of 15-30 days post-GIB would be the most beneficial time. The most critical factor to consider when resuming anticoagulation and antithrombotic therapy, however, is the patient’s medical history such as atrial fibrillation, dementia, renal disease, among others. Some patients are unable to safely resume therapy due to deteriorating cognition or inability to receive the appropriate care. However, physicians’ future decisions should consider that the benefits outlined here may be greater than the risk of recurrent GIB, especially when timed appropriately.\n\nUltimately through our search, we found there is a benefit from using antithrombotics post-GIB. Most of these benefits occur through reducing the possibility of thrombolytic events such as pulmonary embolism or stroke. There are more positive results using a single anticoagulant with slight differences between warfarin of DOACs, both reducing the risk of a thrombolytic event. Differences between each is the risk in recurrence of a rebleed; however, when compared to a clot, the rebleed is not enough to outweigh the benefits of preventing this sort of events. Antithrombotics have also be reviewed, and while they’re usually taken with an OAC, there is a greater risk of rebleed compared to with OACs alone.", "appendix": "Data availability\n\nAll underlying data are included as part of the article and no additional data are required.\n\nSlouha, E., Jensen, H., Fozo, H., Raj, R., Thomas, S., & Gorantla, V. (2023). Re-starting Anticoagulation and Antiplatelets after Gastrointestinal bleeding: A Systematic Review (Version 1). Figshare: PRISMA checklist for “Re-starting Anticoagulation and Antiplatelets after Gastrointestinal bleeding: A Systematic Review”, https://doi.org/10.6084/m9.figshare.22722526.v1 . 35\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\nZhao Y, Encinosa W: Hospitalizations for Gastrointestinal Bleeding in 1998 and 2006. HCUP Statistical Brief #65. Rockville, MD: Agency for Healthcare Research and Quality; December, 2008. Reference Source\n\nGastrointestinal bleeding. UCLA Health System.n.d. Retrieved October 25, 2022. Reference Source\n\nAntunes C, Copelin EL II: Upper Gastrointestinal Bleeding. [Updated 2021 Jul 21]. StatPearls. Treasure Island (FL): StatPearls Publishing; 2022 Jan. Reference Source\n\nEl-Tawil AM: Trends on gastrointestinal bleeding and mortality: where are we standing? World J. Gastroenterol. 2012; 18(11): 1154–1158. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGhassemi KA, Jensen DM: Lower GI bleeding: epidemiology and management. Curr. Gastroenterol. Rep. 2013; 15(7): 333. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmin SK, Antunes C: Lower Gastrointestinal Bleeding. [Updated 2021 Jul 19]. StatPearls. Treasure Island (FL): StatPearls Publishing; 2022 Jan. Reference Source\n\nTesta S, Ageno W, Antonucci E, et al.: Management of major bleeding and outcomes in patients treated with direct oral anticoagulants: results from the START-Event registry. Intern. Emerg. Med. 2018; 13(7): 1051–1058. PubMed Abstract \| Publisher Full Text\n\nSmit MD, Van Gelder IC: Resumption of anticoagulation after major bleeding decreases the risk of stroke in patients with atrial fibrillation. Evid. Based Med. 2017; 22(3): 107–108. PubMed Abstract \| Publisher Full Text\n\nPatel S, Singh R, Preuss CV, et al.: Warfarin. [Updated 2022 Jan 19]. StatPearls. Treasure Island (FL): StatPearls Publishing; 2022 Jan. Reference Source\n\nVazquez S, Rondina MT: Direct oral anticoagulants (DOACs). Vasc. Med (London, England). 2015; 20(6): 575–577. Publisher Full Text\n\nEikelboom JW, Hirsh J, Spencer FA, et al.: Antiplatelet drugs: Antithrombotic Therapy and Prevention of Thrombosis, 9th ed: American College of Chest Physicians Evidence-Based Clinical Practice Guidelines. Chest. 2012; 141(2 Suppl): e89S–e119S. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLittle D, Chai-Adisaksopha C, Hillis C, et al.: Resumption of anticoagulant therapy after anticoagulant-related gastrointestinal bleeding: A systematic review and meta-analysis. Thromb. Res. 2019; 175: 102–109. PubMed Abstract \| Publisher Full Text\n\nWang CL, Wu VC, Huang YT, et al.: Incidence and consequences of resuming oral anticoagulant therapy following hematuria and risks of ischemic stroke and major bleeding in patients with atrial fibrillation. J. Thromb. Thrombolysis. 2021; 51(1): 58–66. PubMed Abstract \| Publisher Full Text\n\nYanagisawa D, Abe K, Amano H, et al.: Thrombotic events and rebleeding after hemorrhage in patients taking direct oral anticoagulants for non-valvular atrial fibrillation. PLoS One. 2021; 16(11): e0260585. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhou Y, Guo Y, Liu D, et al.: Restarting of anticoagulation in patients with atrial fibrillation after major bleeding: A meta-analysis. J. Clin. Pharm. Ther. 2020; 45(4): 591–601. PubMed Abstract \| Publisher Full Text\n\nStaerk L, Lip GY, Olesen JB, et al.: Stroke and recurrent haemorrhage associated with antithrombotic treatment after gastrointestinal bleeding in patients with atrial fibrillation: nationwide cohort study. BMJ (Clinical Research ed.). 2015; 351: h5876. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTapaskar N, Pang A, Werner DA, et al.: Resuming Anticoagulation Following Hospitalization for Gastrointestinal Bleeding Is Associated with Reduced Thromboembolic Events and Improved Mortality: Results from a Systematic Review and Meta-Analysis. Dig. Dis. Sci. 2021; 66(2): 554–566. PubMed Abstract \| Publisher Full Text\n\nCandeloro M, van Es N , Cantor N, et al.: Recurrent bleeding and thrombotic events after resumption of oral anticoagulants following gastrointestinal bleeding: Communication from the ISTH SSC Subcommittee on Control of Anticoagulation. J. Thromb. Haemost. 2021; 19(10): 2618–2628. PubMed Abstract \| Publisher Full Text\n\nProietti M, Romiti GF, Romanazzi I, et al.: Restarting oral anticoagulant therapy after major bleeding in atrial fibrillation: A systematic review and meta-analysis. Int. J. Cardiol. 2018; 261: 84–91. PubMed Abstract \| Publisher Full Text\n\nSostres C, Marcén B, Laredo V, et al.: Risk of rebleeding, vascular events and death after gastrointestinal bleeding in anticoagulant and/or antiplatelet users. Aliment. Pharmacol. Ther. 2019; 50(8): 919–929. Publisher Full Text\n\nTapaskar N, Ham SA, Micic D, et al.: Restarting Warfarin versus Direct Oral Anticoagulants After Major Gastrointestinal Bleeding and Associated Outcomes in Atrial Fibrillation: A Cohort Study. Clin. Gastroenterol. Hepatol. 2022; 20(2): 381–389.e9. PubMed Abstract \| Publisher Full Text\n\nWitt DM, Delate T, Garcia DA, et al.: Risk of thromboembolism, recurrent hemorrhage, and death after warfarin therapy interruption for gastrointestinal tract bleeding. Arch. Intern. Med. 2012; 172(19): 1484–1491. PubMed Abstract \| Publisher Full Text\n\nChai-Adisaksopha C, Hillis C, Monreal M, et al.: Thromboembolic events, recurrent bleeding and mortality after resuming anticoagulant following gastrointestinal bleeding. A meta-analysis. Thromb. Haemost. 2015; 114(4): 819–825. PubMed Abstract \| Publisher Full Text\n\nLee JK, Kang HW, Kim SG, et al.: Risks related with withholding and resuming anticoagulation in patients with non-variceal upper gastrointestinal bleeding while on warfarin therapy. Int. J. Clin. Pract. 2012; 66(1): 64–68. PubMed Abstract \| Publisher Full Text\n\nQureshi W, Mittal C, Patsias I, et al.: Restarting anticoagulation and outcomes after major gastrointestinal bleeding in atrial fibrillation. Am. J. Cardiol. 2014; 113(4): 662–668. PubMed Abstract \| Publisher Full Text\n\nMajeed A, Wallvik N, Eriksson J, et al.: Optimal timing of vitamin K antagonist resumption after upper gastrointestinal bleeding. A risk modelling analysis. Thromb. Haemost. 2017; 117(3): 491–499. PubMed Abstract \| Publisher Full Text\n\nValanejad SM, Davis KA, Nisly SA: Outcomes Associated With Resuming Direct Oral Anticoagulant Therapy Following Admission for a Gastrointestinal Bleed. Ann. Pharmacother. 2020; 54(10): 975–980. PubMed Abstract \| Publisher Full Text\n\nLittle D, Sutradhar R, Cerasuolo JO, et al.: Rates of rebleeding, thrombosis and mortality associated with resumption of anticoagulant therapy after anticoagulant-related bleeding. CMAJ. 2021; 193(9): E304–E309. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSmit MD, Van Gelder IC: Resumption of anticoagulation after major bleeding decreases the risk of stroke in patients with atrial fibrillation. Evid. Based Med. 2017; 22(3): 107–108. PubMed Abstract \| Publisher Full Text\n\nSengupta N, Marshall AL, Jones BA, et al.: Rebleeding versus Thromboembolism After Hospitalization for Gastrointestinal Bleeding in Patients on Direct Oral Anticoagulants. Clin. Gastroenterol. Hepatol. 2018; 16(12): 1893–1900.e2. PubMed Abstract \| Publisher Full Text\n\nShen JI, Mitani AA, Winkelmayer WC: Heparin use in hemodialysis patients following gastrointestinal bleeding. Am. J. Nephrol. 2014; 40(4): 300–307. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nQureshi WT, Nasir U: Restarting oral anticoagulation among patients with atrial fibrillation with gastrointestinal bleeding was associated with lower risk of all-cause mortality and thromboembolism. Evid. Based Med. 2016; 21(4): 152. Publisher Full Text\n\nHafiz A, Abdulrahman IA, Sylvester KW, et al.: Evaluation of anticoagulation re-initiation practices following reversal of factor Xa inhibitors with andexanet alfa or 4F-PCC in patients with major bleeding events. Thrombosis Update. 2021; 5: 100076. Publisher Full Text\n\nQureshi WT, Nasir U: Restarting oral anticoagulation among patients with atrial fibrillation with gastrointestinal bleeding was associated with lower risk of all-cause mortality and thromboembolism. Evid. Based Med. 2016; 21(4): 152. PubMed Abstract \| Publisher Full Text\n\nSlouha E, Jensen H, Fozo H, et al.: Re-starting Anticoagulation and Antiplatelets after Gastrointestinal bleeding: A Systematic Review. figshare. Journal Contribution. 2023. Publisher Full Text" }	[ { "id": "226018", "date": "20 Dec 2023", "name": "Xue Xiao", "expertise": [ "Reviewer Expertise This article provides guidance and suggestions for restarting anticoagulation plans in the future. However", "as gynecological oncologists", "we hope that more articles related to postoperative restart of anticoagulation in gynecological malignant tumor patients will be included in this study in the future." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. Section of Introduction: GI appears for the first time, abbreviations should not be used, so please ask the author to modify it. 2. Section of Introduction: May I ask if the author agrees to change\"Upper GI bleeds affect 50-100 out of every 100,000 Americans per year and accounts for 20,000 deaths\" to \"Upper GI bleeds affect 50-100 out of every 100,000 Americans and accounts for 20,000 deaths per year\"? 3. Ask the author if they use \"re-starting anticoagulation after gastrointestinal bleeding\" as a keyword for search? 4.Section of Inclusion criteria: May I ask if the author agrees to change\"articles that are full-text\" to \"articles that are with full-text\"? 5. Section of Heparin:Ask the author if there are some articles about used Low molecular weight heparin in such patients?If so, please add. 6. As the author's opinion:there was a great risk in rebleed as most of these therapies are given in conjunction with anticoagulants, but there is on discussion about this in Section of Discussion,If there is any relevant content, please ask the author to supplement it.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [] }, { "id": "292646", "date": "03 Jul 2024", "name": "Sudhakar Pemminati", "expertise": [ "Reviewer Expertise Endocrine disorders" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI strongly recommend this article for indexing. The authors made special effort to review the re-starting anti-coagulation and anti-platelets after gastrointestinal bleeding. Gastrointestinal bleeding is one of the most important factor for morbidity and mortality in various patient population. I would like to ask authors to elaborate materials and methods. 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? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-806
https://f1000research.com/articles/12-801/v1	10 Jul 23	{ "type": "Study Protocol", "title": "Measurement properties of physical activity in adults with bronchiectasis: A systematic review protocol", "authors": [ "Anup Bhat", "Annemarie L Lee", "G Arun Maiya", "K. Vaishali", "Anup Bhat", "Annemarie L Lee", "G Arun Maiya" ], "abstract": "Abstract: People with bronchiectasis reduce their physical activity (PA) due to muscle weakness, dyspnea, fatigue, reduced exercise capacity and frequent cough with expectoration. Patient-reported and objective physical assessment methods have been used to evaluate PA in people with bronchiectasis. In the literature, significant differences in the PA measured using patient-reported outcome measures when compared with the objective methods. Given the availability of many PA assessment tools, it is tedious for the clinician or researcher to choose an outcome measure for clinical practice or research. The evidence on validity and reliability in bronchiectasis are unclear. Objectives: To identify the PA assessment tools, describe and evaluate the literature on psychometric properties of instruments measuring and analyzing PA. Methods: The search will be conducted in PubMed/Medline, Cochrane Central Register of Controlled Studies, Scopus and EMBASE databases. The keywords, index terms and synonyms of the following words will be used: bronchiectasis, physical activity, and outcome measures. Published studies of adult with clinical and/ or radiologically diagnosed bronchiectasis, aged >18 years, any gender and studies that assessed PA and/or if there are reports on measurement properties of PA will be included in the review. Studies using qualitative research methods, narrative reviews, letters to editors and editorials will be excluded. The quality of the study will be assessed and data will be extracted. Any disagreement will be resolved in the presence of an author not involved in the screening or selecting studies. Discussion: By assessing the quality of studies on measurement properties, this review will help researchers choose the outcome measure to evaluate the effects of interventions on PA. This review will identify the suite of outcome measures of PA for people with bronchiectasis that can be used for research and clinical purpose.", "keywords": [ "Bronchiectasis", "exercise", "movement", "outcome assessment", "physical exertion" ], "content": "Introduction\n\nBronchiectasis is a chronic airway disease which is marked by chronic cough with expectoration, and recurrent exacerbations.1,2 Clinical presentations may differ based on the underlying cause of bronchiectasis.2 Muscular weakness, loss of muscular endurance, dyspnea, fatigue and poor quality of life are major clinical features experienced by people with bronchiectasis.3 These factors collectively contribute to reduced exercise capacity and limited participation in physical activity (PA).3–5 Physical activity is any movement caused by muscular contraction resulting in energy consumption.6 To reduce symptoms of dyspnea, those with bronchiectasis often avoid activities of daily living, which result in further deconditioning.7,8 In addition, the frequency of coughing and sputum expectoration in people with bronchiectasis may increase with PA.9 As a consequence, the social stigma associated with chronic cough and sputum expectoration in public is associated with frustration and embarrassment to people with bronchiectasis.10 To avoid social embarrassment associated with coughing bouts, people with bronchiectasis often reduce their PA.9–11 José et al., assessed PA in the stable adult bronchiectasis population using pedometers and showed significant reduction in step counts compared to healthy age-matched peers.6 Similarly, Cakmak et al., demonstrated that both objectively measured PA using multisensorial PA monitor and through self-reported questionnaire in the stable adult bronchiectasis population was lower than age-matched healthy individuals.12 Furthermore, the study highlighted the significant difference between objective and subjective methods of PA assessment. Duration of PA measured through objective method was higher than those obtained from subjective method.12 O’Neil et al., compared pedometer and a questionnaire with the criterion assessment tool accelerometer in people with stable bronchiectasis. The physical activity in terms of step counts between pedometer and accelerometer were comparable; however, the questionnaire over-reported the moderate-vigorous physical activity (MVPA) compared with the accelerometer.13 Considering the lower level of PA in people with bronchiectasis compared to aged-matched peers, it is important for the PA assessment tool to be sensitive enough to appreciate small changes.12 Physical activity has an impact on the prognosis of bronchiectasis14; those with lower PA levels had higher risk of hospitalization.14 Increased rate of exacerbation was associated with reduced PA levels and higher sedentary behaviour in adults with bronchiectasis.15\n\nIn order to assess PA, a wide range of tools are available. These include patient (self) reported outcome measures (PROMs) such as global physical activity questionnaire (GPAQ), recent physical activity questionnaires, international physical activity questionnaire (IPAQ), and self-report activity diaries/logs.16 Alternatively, there are objective methods such as direct observation and device-based measurements (accelerometers, pedometers, heart rate monitors and armbands).16 Recently, mobile phone-based applications are also used to measure PA.17\n\nPhysical activity is an important outcome in pulmonary rehabilitation (PR) as PR is expected to improve movement efficiency, cardiovascular function and skeletal muscle oxidative function, thereby enhancing PA.18 Only a handful of studies have evaluated PA following PR for people with bronchiectasis.19–21 Given the availability of many PA assessment tools, it is a tedious task for the clinician or researcher to choose an outcome measure for clinical practice or research. The evidence on validity and reliability in bronchiectasis are unclear. Therefore, it is important to identify tools that are used to measure PA in people with bronchiectasis and discuss their measurement properties. Furthermore, it is important to identify the feasibility, cost and their limitations. The measurement properties of PA measurement tools examined in this systematic review may inform clinicians and researchers regarding the availability of various PA assessment tools and their validity and reliability, enabling appropriate choices for practice.\n\nTo address the current knowledge gap, this systematic review aims to identify and evaluate the measurement properties of PA assessment tools which have been applied in people with bronchiectasis. The specific objectives of the systematic review are to 1) identify the approaches used to measure PA in bronchiectasis; 2) describe and evaluate the literature available on psychometric properties, including validity, reliability, responsiveness and interpretability of instruments measuring and analysing PA; and 3) provide recommendations on most suitable and effective ways of measuring PA in bronchiectasis.\n\n\nMethods\n\nThe review is registered on PROSPERO, an international prospective register of systematic reviews (CRD42023423087). This systematic review protocol will follow the Preferred Items for Systematic Reviews and Meta-Analyses Protocols (PRISMA-P) reporting guidelines.22 Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines will be used for subsequent systematic review.23\n\nInclusion criteria: Published studies of adult with clinical and/ or radiologically diagnosed bronchiectasis,24 aged ≥18 years, any gender, geographical location and studies that assessed PA and/or if there are reports on measurement properties of PA listed in COnsensus-based Standards for the selection of health Measurement Instruments (COSMIN) taxonomy of measurement properties.25 The review will be limited only to the English language. Studies using mixed respiratory pathology will be included if at least 80% of the included people had primary diagnosis of bronchiectasis or data of sub-group are reported separately for the bronchiectasis population. Studies that include mixed populations (such as adult and paediatric) will also be included only if the data on adult bronchiectasis are provided separately. Studies investigating both acute exacerbations and those in stable conditions will be included. Any reviews of potential relevance to the topic will be screened to identify potentially eligible studies included within that review.\n\nExclusion criteria: Studies using qualitative research methods, narrative review, letters to editors and editorials will be excluded. Studies that report other constructs related to PA such as physical function, mobility, functional status, and activities score from health-related quality of life measures, and activities of daily living will be excluded. Studies that report PA in people with cystic fibrosis will be excluded.\n\nThe definitions of each measurement properties from COSMIN taxonomy of measurement properties25 are listed in Table 1.\n\nThe search will be conducted in PubMed/Medline, Cochrane Central Register of Controlled Studies (CENTRAL), Scopus and EMBASE databases. The keywords that will be used for the search are non-cystic fibrosis bronchiectasis, bronchiectasis, physical activity, questionnaire, self-reported physical activity, pedometer, activity tracker. Search strategy for PubMed database is presented in Table 2. Search filters for PubMed and EMBASE will be developed based on the methods suggested by Terwee et al.26 The references from all the included articles will be screened to identify additional articles.\n\nSelection procedure:\n\nThe articles obtained from these databases will be collated in Rayyan and duplicates will be removed. Two authors (AB, VK) will independently screen the title and abstract of all the articles using Rayyan.27 Any disagreements about inclusion will be resolved through discussions with (AL) as arbitrator. Interrater agreement (IRA) for titles and abstracts will be calculated. Full text articles will be independently reviewed by two authors (AB, VK) to finalize the full text articles which meet the inclusion criteria. Any disagreement will be resolved in the presence of (AL) as arbitrator.\n\nData extraction: A data extraction sheet will be prepared by one author (AB) and will be modified after the discussion with the entire team. Data extraction sheet will be created on Microsoft Excel spreadsheet by one author (AB). The data extraction sheet will contain the following\n\na. Demographic details of the participants such as age, gender, body mass index, severity of the bronchiectasis\n\nb. Characteristics of the study such as name of the first author, country where the study was conducted, year of publication, study design, and sample size.\n\nc. Characteristics of the outcome measure such as name of the measurement tool, abbreviation of the tool, self-reported or clinician administered, original reference for the tool, original language, available translations, recall period, score range, score interpretation, type of PA assessed, setting where it was administered such as hospital or home setting, cost and time taken to administer, equipment needed, training requirement, ease of score calculation, copyright, patient’s physical and mental ability level required to use and ease of standardisation.\n\nd. Measurement properties of the scale: validity (includes content, construct, and criterion validity), reliability (includes reliability measures, measurement error and internal consistency), responsiveness and interpretability. If the psychometric properties have not been assessed in the included study, it will be entered as not applicable.\n\nThe form will be pretested on five studies by study authors prior to finalisation. One of the authors (AB) then will extract data from included studies, and a second author will confirm that the data were extracted correctly. Any discrepancies will be discussed with AL., and the final decision will be made through consensus.\n\nMethodological quality assessment: Two independent reviewers (AB and VK) will rate the methodological quality of the included studies. Based on the design of the study, we will use CASP cohort checklist for cohort design28 and Pedro scale for RCTs.29 For studies including psychometric properties, the standardized COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) Risk of Bias checklist will be used.30 The COSMIN methodology was specially developed and validated for the reviews of patient-reported outcome measures. A newer COSMIN Risk of Bias checklist has been developed for other types of outcome measurement instruments such as performance-based outcome measures, laboratory values and clinician-reported outcome measures. For these reasons, an adapted COSMIN Risk of Bias checklist on reliability and measurement error will be used for performance-based outcome measures.31 Any discrepancies will be discussed with AL., and the final decision will be made through consensus. Methodological quality of each study will be tabulated in the summary of findings table.\n\nEvaluation of outcome measure: The following measurement properties will be evaluated: validity (including content, criterion, construct validity), reliability (including internal consistency, test-retest, inter-rater, intra-rater reliability and measurement error), responsiveness and interpretability using COSMIN Risk of Bias checklists.30,31\n\nData synthesis and analysis: The data will be synthesised narratively and meta-analysis will not be carried out. Finding will be reported in conjunction with the ‘Synthesis Without Meta-Analysis (SWiM)’ guideline where possible.32 The summary of key study characteristics, PA evaluation methods will be tabulated. The outcome measures will be categorised and summarised as self-reported or clinician administered. The psychometric properties of each outcome measure with the statistical values will be summarised. We will summarise the practical considerations for each of the PA evaluation methods as per the clinical and research judgement of the investigator team and existing guidelines.11,33 As the data are not related to treatment effectiveness, a summary of findings via GRADE methodology will not be included.\n\n\nDiscussion\n\nPeople with bronchiectasis often have reduced PA when compared to healthy age-matched peers7,12 In order to assess the PA in adults with bronchiectasis, a list of suitable PA measurement tools is an ideal resource. This list can facilitate the PA assessment in variety of settings like physician’s office, pulmonary rehabilitation centre, hospital, home and occupational setting. This systematic review aims to list all the PA measures used in adults with bronchiectasis. Further, the review aims to list the measurement properties of each tool and quality of the studies that evaluated the measurement properties. Description on ease of use and time required to complete will be summarised, if available. These details will help clinicians to choose outcome measure that will be most feasible in terms of treatment, available resources, cost, time and the settings.\n\nThe PA assessment tools can be broadly classified as self-reported or clinician administered tools. Self-reported PA assessment tools are low cost, easy to administer and low burden method.33 These measurements are often carried out at one time point and may be affected by recall and social desirability bias.33 Although these self-reported tools are simple, easy to use and allow documentation of time spent on specific domain of PA, they may under or overestimate the PA.34 Additionally, the self-reported PA assessment tools that are not primarily developed to assess the individuals with relatively limited amount of PA may not assess the domains of PA these individuals are involved in. Nevertheless, self-reported PA assessment tools can be of great utility in resource limited settings owing to low cost.33 Alternatively, clinician administered outcome measure provide accurate, objective and are less susceptible to bias. However, they are relatively expensive and may involve data reduction and transformation process at the end.33\n\nBy assessing the quality of studies on measurement properties, this review will help researchers choose the outcome measure for their evaluation of the effects of interventions on PA. This review will identify the suite of outcome measures of PA for people with bronchiectasis that can be used for research and clinical purpose.\n\nPiloting of the study selection process.\n\n\nCRediT author statement\n\nAnup Bhat: Conceptualization, methodology, software, writing – Original draft.\n\nAnnemarie L Lee: Conceptualization, validation, Methodology, Writing – Review & Editing, Supervision.\n\nArun G Maiya: Conceptualization, Writing – Review & Editing, Supervision.\n\nVaishali K: Conceptualization, Methodology, validation, Writing – Review & Editing, Supervision.", "appendix": "Data availability\n\nNo underlying data are associated with this article.\n\nFigshare: PRISMA-P for Measurement properties of physical activity in adults with bronchiectasis: a systematic review protocol. DOI: https://doi.org/10.6084/m9.figshare.23599395.v1 35\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nKing PT: The pathophysiology of bronchiectasis. Int. J. Chron. Obstruct. Pulmon. Dis. 2009; 4: 411–419. PubMed Abstract\n\nPolverino E, Dimakou K, Hurst J, et al.: The overlap between bronchiectasis and chronic airway diseases: state of the art and future directions. Eur. Respir. J. 2018; 52(3): 1800328. PubMed Abstract \| Publisher Full Text\n\nOzalp O, Inal-Ince D, Calik E, et al.: Extrapulmonary features of bronchiectasis: muscle function, exercise capacity, fatigue, and health status. Multidiscip. Respir. Med. 2012; 7(1): 3. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGale NS, Bolton CE, Duckers JM, et al.: Systemic comorbidities in bronchiectasis. Chron. Respir. Dis. 2012; 9(4): 231–238. Publisher Full Text\n\nBradley JM, Wilson JJ, Hayes K, et al.: Sedentary behaviour and physical activity in bronchiectasis: a cross-sectional study. BMC Pulm. Med. 2015; 15: 61. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCaspersen CJ, Powell KE, Christenson GM: Physical activity, exercise, and physical fitness: definitions and distinctions for health-related research. Public Health Rep. 1985; 100(2): 126–131. PubMed Abstract\n\nJosé A, Ramos TM, de Castro RAS , et al.: Reduced Physical Activity With Bronchiectasis. Respir. Care. 2018; 63(12): 1498–1505. Publisher Full Text\n\nLavery K, Neill B, Elborn JS, et al.: Self-management in bronchiectasis: the patients’ perspective. Eur. Respir. J. 2007; 29(3): 541–547. PubMed Abstract \| Publisher Full Text\n\nRoyle H, Kelly C: ‘The likes of me running and walking? No chance’: Exploring the perceptions of adult patients with bronchiectasis towards exercise. Chronic Illn. 2022; 19: 157–171. Publisher Full Text\n\nDudgeon EK, Crichton M, Chalmers JD: “The missing ingredient”: the patient perspective of health related quality of life in bronchiectasis: a qualitative study.\n\nKelly CA, Tsang A, Lynes D, et al.: ‘It’s not one size fits all’: a qualitative study of patients’ and healthcare professionals’ views of self-management for bronchiectasis. BMJ Open Respir. Res. 2021; 8(1): e000862. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCakmak A, Inal-Ince D, Sonbahar-Ulu H, et al.: Physical activity of patients with bronchiectasis compared with healthy counterparts: A cross-sectional study. Heart Lung. 2020; 49(1): 99–104. PubMed Abstract \| Publisher Full Text\n\nO’Neill B, McDonough SM, Wilson JJ, et al.: Comparing accelerometer, pedometer and a questionnaire for measuring physical activity in bronchiectasis: a validity and feasibility study? Respir. Res. 2017; 18(1): 16. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlcaraz-Serrano V, Gimeno-Santos E, Scioscia G, et al.: Association between physical activity and risk of hospitalisation in bronchiectasis. Eur. Respir. J. 2020; 55(6): 1902138. PubMed Abstract \| Publisher Full Text\n\nAlcaraz-Serrano V, Arbillaga-Etxarri A, Oscanoa P, et al.: Exacerbations and Changes in Physical Activity and Sedentary Behaviour in Patients with Bronchiectasis after 1 Year. J. Clin. Med. 2021; 10(6): 1190. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSylvia LG, Bernstein EE, Hubbard JL, et al.: Practical guide to measuring physical activity. J. Acad. Nutr. Diet. 2014; 114(2): 199–208. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMurphy J, Uttamlal T, Schmidtke KA, et al.: Tracking physical activity using smart phone apps: assessing the ability of a current app and systematically collecting patient recommendations for future development. BMC Med. Inform. Decis. Mak. 2020; 20(1): 17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTroosters T, Gosselink R, Janssens W, et al.: Exercise training and pulmonary rehabilitation: new insights and remaining challenges. Eur. Respir. Rev. 2010; 19(115): 24–29. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPehlivan E, Niksarlıoğlu EY, Balcı A, et al.: The Effect of Pulmonary Rehabilitation on the Physical Activity Level and General Clinical Status of Patients with Bronchiectasis. Turk. Thorac. J. 2019; 20(1): 30–35. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJosé A, Holland AE, Selman JPR, et al.: Home-based pulmonary rehabilitation in people with bronchiectasis: a randomised controlled trial. ERJ Open Res. 2021; 7(2): 00021–02021. Publisher Full Text\n\nLee AL, Gordon CS, Osadnik CR: Exercise training for bronchiectasis. Cochrane Database Syst. Rev. 2021; 4(4): CD013110-CD. 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. PubMed Abstract \| Publisher Full Text \| Free Full Text\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\nAliberti S, Goeminne PC, O’Donnell AE, et al.: Criteria and definitions for the radiological and clinical diagnosis of bronchiectasis in adults for use in clinical trials: international consensus recommendations. Lancet Respir. Med. 2022; 10(3): 298–306. PubMed Abstract \| Publisher Full Text\n\nMokkink LB, Terwee CB, Patrick DL, et al.: The COSMIN study reached international consensus on taxonomy, terminology, and definitions of measurement properties for health-related patient-reported outcomes. J. Clin. Epidemiol. 2010; 63(7): 737–745. PubMed Abstract \| Publisher Full Text\n\nTerwee CB, Jansma EP, Riphagen II, et al.: Development of a methodological PubMed search filter for finding studies on measurement properties of measurement instruments. Qual. Life Res. 2009; 18(8): 1115–1123. 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\nCritical Appraisal Skills Programme: CASP cohort Checklist. Accessed: 02 May 2023. Reference Source\n\nPEDro: Physiotherapy Evidence Database. Australia: School of Public Health, University of Sydney Institute for Musculoskeletal Health; 2019 [cited 02 May 2023]. Reference Source\n\nMokkink LB, de Vet HCW , Prinsen CAC, et al.: COSMIN Risk of Bias checklist for systematic reviews of Patient-Reported Outcome Measures. Qual. Life Res. 2018; 27: 1171–1179. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMokkink LB, Boers M, van der Vleuten CPM , et al.: COSMIN Risk of Bias tool to assess the quality of studies on reliability or measurement error of outcome measurement instruments: a Delphi study. BMC Med. Res. Methodol. 2020; 20(1): 293. 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. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStrath SJ, Kaminsky LA, Ainsworth BE, et al.: American Heart Association Physical Activity Committee of the Council on Lifestyle and Cardiometabolic Health and Cardiovascular, Exercise, Cardiac Rehabilitation and Prevention Committee of the Council on Clinical Cardiology, and Council. Guide to the assessment of physical activity: Clinical and research applications: a scientific statement from the American Heart Association. Circulation. 2013; 128(20): 2259–2279. PubMed Abstract \| Publisher Full Text\n\nAinsworth B, Cahalin L, Buman M, et al.: The current state of physical activity assessment tools. Prog. Cardiovasc. Dis. 2015; 57(4): 387–395. Publisher Full Text\n\nBhat A, Lee A, Maiya GA, et al.: PRISMA-P for Measurement properties of physical activity in adults with bronchiectasis: a systematic review protocol. figshare. Figure. 2023. (35). Publisher Full Text" }	[ { "id": "186191", "date": "18 Jul 2023", "name": "Jaya Shanker Tedla", "expertise": [ "Reviewer Expertise My expertise is in physical therapy and 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\nThe method paper reads well. Currently, a plethora of physical activity assessment tools are available. This protocol has the potential to address and summarize the available physical activity assessment tools. The following concerns need to be addressed:\nThe title needs to be modified to “Measurement properties of physical activity assessment tool in adults with bronchiectasis: A systematic review protocol.”\n\nAuthors can introduce the prevalence and economic impact of bronchiectasis in the introduction.\n\nIn the eligibility criteria, what about case reports and case series?\n\nDomain-specific physical activity can be discussed in the introduction.\n\nIn the exclusion criteria, qualitative studies are excluded. Qualitative analysis could be one of the steps involved in developing some outcome measures. Would you like to include such studies?\n\nWhat is the procedure if full texts are not available?\n\nQuality assessment tool for qualitative studies.\n\nThe discussion section is important for a full review. The inclusion of this in the method paper is a plus point.\n\nAuthors can discuss remote monitoring of PA using available tools.\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": "186195", "date": "18 Aug 2023", "name": "Vishnu Vardhan G. D.", "expertise": [], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper is about bronchiectasis, a chronic airway disease that causes chronic cough with expectoration and recurrent exacerbations. People with bronchiectasis experience major clinical features such as muscular weakness, loss of muscular endurance, dyspnea, fatigue, and poor quality of life. Due to these symptoms, they often avoid physical activities, which further decondition them. The paper aims to identify and evaluate the literature on psychometric properties of instruments measuring and analyzing physical activity in adults with bronchiectasis.\nThe title needs to be modified.\n\nAge criteria of patients of bronchiectasis with less physical activity to be mentioned in Introduction.\n\nQualitative studies may be included in inclusion criteria.\n\nMention the time duration needed for the review in methods.\n\nMention the year range for selecting the 5 articles in methods.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-801
https://f1000research.com/articles/12-799/v1	10 Jul 23	{ "type": "Study Protocol", "title": "Evaluation of marginal and internal fit of metal crowns made from wax patterns made by conventional technique and CAD CAM milling technique: An in vivo study", "authors": [ "Shubham Tawade", "Mithilesh Dhamande", "Seema Sathe", "Mithilesh Dhamande", "Seema Sathe" ], "abstract": "Introduction: Marginal and internal fit of a metal crown are very important for a successful metal crown prosthesis. This study will evaluate the marginal and internal fit of metal crowns produced from wax patterns that are formed by two different wax pattern fabrication procedures: conventional wax pattern fabrication and wax pattern milled using the computer-aided design and manufacture (CAD CAM) method. Objectives: To evaluate the marginal and internal fit of metal crowns over prepared tooth made from wax patterns made by conventional technique and CAD CAM technique. Methodology: A total of 21 participants with endodontically restored mandibular first molar will be selected. Two all-metal crowns will be made for each participant, thus 42 metal crowns in total will be made. These 42 metal crowns will be divided into two groups based on the method used to create wax patterns: metal crowns made using conventional hand-carved wax pattern technique (Group I, n=21) and metal crowns made using CAD CAM-milled wax pattern technique (Group II, n=21). Then, the marginal and internal fit of metal crowns from both groups will be compared. Expected results: It is expected that metal crowns made by CAD CAM milled wax pattern fabrication method will have better marginal and internal fit than those of conventional method. Conclusions: The clinical acceptability and success of the dental crown will be assessed by this study. Minimal marginal gap and better internal fit of all metal crown are key qualities.", "keywords": [ "Marginal fit", "internal fit", "wax pattern", "CAD CAM" ], "content": "Introduction\n\nLost wax casting technique is used widely in dentistry for production of restoration. The technique involves the production of a wax pattern for required extra coronal restoration over the master cast, which is then invested in a heat-proof investment material. The invested pattern is subjected to a high temperature in a furnace. This eliminates the wax pattern and a mould cavity is created within the investment material. This mould cavity is later filled with liquid molten metal (alloy) which takes up the shape of the required restoration. The accuracy of the wax pattern completely depends on the technician’s skill in manual method. It is a laborious process, and the quality of wax pattern depends on the person performing it. Because the wax is glossy, it can be challenging to spot small flaws during the manual production process when the wax pattern is being removed from the die. Dental crowns can be successful or unsuccessful depending on a variety of factors, including how precisely the crown is fitted and seated.1\n\nClinical acceptability and the success of dental restorations depend heavily on the dental crown prosthesis’s internal fit and small marginal gaps. A dental crown with flawed margins can cause a series of issues, including food build up, gingival inflammation, dental caries and ultimately failure of the crown and tooth.2\n\nAccording to some studies, the marginal gap must be less than 120 μm, while 150 μm is clinically accepted.3 Marginal fit is made up of two components: absolute marginal discrepancy4 and marginal discrepancy, where absolute marginal discrepancy is the misfit between the restoration and the prepared tooth in both the vertical and horizontal directions. Absolute marginal discrepancy is the difference between the axial wall of the prepared tooth and the internal surface of the casting at the margin. The axial and occlusal cement thickness make up the internal fit,5,6 and the luting cement’s internal distribution determines the dental restoration’s stability and retention.7\n\nThe purpose of this study is to evaluate the fit of metal crowns produced from wax patterns that were formed by two different wax pattern fabrication procedures: conventional wax pattern fabrication and wax pattern milled by computer-aided design and manufacture (CAD CAM) method. This study was motivated by the importance of marginal and internal fits and the need for research into the accuracy of new digital technologies in wax pattern production.7,8\n\nTo evaluate the marginal fit and internal fit of metal crowns over a prepared tooth made from wax patterns fabricated by conventional technique and CAD CAM technique.\n\n\n\n1. To evaluate marginal and internal fit of metal crowns made from wax pattern prepared by conventional carving technique.\n\n2. To evaluate marginal and internal fit of metal crowns made from wax pattern prepared by milling technique.\n\n3. To evaluate the difference in marginal fit and internal fit between metal crowns made from wax patterns prepared using the above-mentioned methods.\n\n\nMethods\n\nThe minimum sample size obtained after calculation from parent article for this research is five per group; so 21 participants will be selected per group, i.e., making 42 the total sample size of this study.\n\nA total of 21 participants with endodontically restored mandibular first molar will be selected.\n\nTwo all-metal crowns will be made for each participant, and 42 metal crowns in total will be made. These 42 metal crowns will be divided into two groups based on the method used to create wax patterns: metal crown made using conventional hand carved wax pattern technique (Group I, n=21) and metal crown made using CAD CAM milled wax pattern technique (Group II, n=21).\n\nPreparation of the restored teeth will be performed with chamfer finish line 0.5 mm supragingival following gingival contours with axial walls tapered by 6°-10°, and all the edges will be rounded and smoothened. Gingival retraction will be done with retraction cords. The impressions of the prepared teeth for Group I and Group II will be made using polyvinyl siloxane impression material and will be then poured in Type IV gypsum product to obtain the final master casts. Temporary restoration will be made using a tooth-coloured acrylic (indirect-direct method) and will be cemented using non-eugenol temporary cement at the same appointment.\n\nThe study model is shown in Figure 1.\n\nConventional (hand-formed) production\n\nThe 21 master dies are made from the 21 Group I master casts. To prevent layer overlap and make it simpler to distinguish between them, the die spacer will be applied 1 mm from the margin and in two different colours. According to some articles, four layers of “True Fit” die spacer should be used to create a 25–30 mm gap.9\n\nAfter applying a separator and gently blowing away any excess wax, the dies will be dipped once in molten wax and then covered in medium-hard inlay wax to create the wax patterns.1\n\nComputer-aided design and manufacture (milled)\n\nThe 21 master dies will be obtained from 21 master casts for Group II, which will be scanned using Exoscan scanning software version 3. A cement gap of 30 μm will be set to be 1 mm away from the margin. The crown will be designed over this scanned design of die using Exocad. This final designed file in .stl format will be transferred to a milling machine (inLab MCX5) and the wax pattern will be milled out from Ruthinium CAD CAM Wax Disc (98 mm×14 mm).9\n\nThe wax patterns will be identically sprued using sprue wax (diameter 2.5 mm). The wax pattern will be sprayed with Debubblizers to lower the surface tension, and the casting rings will be lined with ring liner for investments casting and will be mixed according to the manufacturer’s instructions and with the aid of a vibrator, the investment will be poured into the investment rings and all around the wax pattern, then bench-set for 45 to 60 minutes. The mould will then be placed in an oven that has been preheated to about 480°C, held at that temperature for 20 minutes, and then slowly increased to 700°C and held for 30 minutes. The casting machine will be heated in a melting crucible to a temperature of 1050°C. After that, alloy ingots will be heated in a preheated crucible until they are molten. The casting ring will then be taken out of the furnace and seated onto the induction casting machine where crucible and casting ring will be aligned and the induction casting machine will be started. The casting rings will be removed from the casting apparatus after the casting is finished and set aside to bench-cool to room temperature. On cooling, castings will be retrieved from casting ring. The cast crowns will then be finished and polished using standard burs, stones, rubber wheels, and polishing wheels after being de-vested and separated from their sprue. These procedures of casting will remain the same for each participant’s crown.1\n\nMeasurement using silicone replica technique\n\nThe inner surface of the crown will be coated with light-body PVS and positioned onto the prepared tooth with finger pressure for 20 s, and then fixed with cotton roll while the patient close their mouth. Excess silicon material will be removed. After 4.30 min, i.e., after setting the silicon layer, the crown will be removed from the prepared tooth. With a regular set putty material of a different colour, the silicon material that adhered to the internal surface of the crown will be stabilised. Both silicon materials will be removed from each crown in one piece after setting. The resulting impression silicon replicas will then be sectioned into six pieces; one mesio-distal cut and two bucco-lingual cuts using a sharp scalpel. The pieces will be examined under the stereomicroscope to measure four points on each piece: occlusal, upper axial, lower axial, and marginal gap to make the measurements under 10× magnification.10\n\n\n\n1. Light body vinyl polysiloxane impression material (Dentsply Sirona)\n\n2. Heavy body impression material (Zhermack hydrorise)\n\n3. Gingival retraction cord\n\n4. CAD CAM ruthinium wax disc (98 mm×14 mm).\n\n5. Inlay wax\n\n6. Investment Casting material\n\n7. Die spacer\n\n8. Stereomicroscope\n\n\n\n1. Patients with endodontically treated permanent mandibular first molar will be selected.\n\n2. Patient within the age group 15 to 65 years will be selected.\n\n\n\n1. Patients with poor endodontic restoration of first mandibular molar.\n\n2. Patients under 15 years of age.\n\nSample size was calculated using the mean difference formula:\n\nPrimary variable (Marginal fit)\n\nMean ± SD (manual technique) = 160 ± 24\n\nMean ± SD (milling technique) = 110 ± 11\n\nDifference =160-110 = 50\n\nStandard deviation = 24\n\nAs per reference articles.1\n\nMinimum samples size required = 5 per Group.1\n\nThe mean and standard error of the mean will be calculated for each group using Microsoft Excel (Office 2021). The statistical package SPSS will be used and student’s unpaired t-test will be employed in the calculation of statistical significance of marginal and internal fit differences between Groups I and II.\n\n\n\n1. Further study can be conducted on measuring the internal fit of crowns using a large number of samples.\n\n2. More advanced scanners for the cast and advanced milling machine will increase the fit of crowns in the future.\n\nSmall marginal gaps and good internal fit of dental prosthesis are crucial properties of clinical acceptability and success of dental crown.\n\n\n\n1. Some errors can be created in making of die from die stone due to expansion of the gypsum product.\n\n2. The quality of wax pattern made using manual method completely depends on the skill of technicians, and minute cracks on wax patterns cannot be seen with the naked eye because of the glossy surface of wax pattern, which can cause some errors.\n\n\nDiscussion\n\nIn 2012 Paul et al. carried out an in vivo study in which the marginal and internal gap widths of metal ceramic and monolithic zirconia crowns created using conventional and CAD CAM techniques were compared. The study concluded that zirconia crowns made using CAD CAM technology had a better accuracy of fit than metal ceramic crowns made using more traditional methods.1 In 2012, Nawafleh conducted a review and discussed the variables tested and how they affected the results of an investigation in the marginal adaptation of crowns and FPDs. The study came to the conclusion that there is a significant lack of agreement regarding the minimal adaptation of different crown systems because of variations in the testing procedures and experimental design used. The most-used method to reproduce results was direct view technique.2 In 2015 Fathi et al. carried out an in vitro comparison of an internal and marginal fit of crowns made using three different wax production techniques: 3D-printed, milled and conventional, and three different cement gap thicknesses. The conclusion showed that the internal fit of 3D printed wax patterns was far better than the other two fabrication techniques. Regarding internal and marginal fit, wax crown milling is just as precise as traditional hand carving. The most precise internal and marginal fits were produced using the 30 mm offset/die-spacer that the manufacturer recommended.3\n\nIt is expected that metal crowns made by CAD CAM milled wax pattern fabrication method will have better marginal and internal fit than those made with conventional method.\n\nThe results will be published in indexed journal.\n\nThe study has not started yet.\n\nEthical approval was received from Datta Meghe Institute of Higher Education and Research, Sawangi, Wardha (IEC reference number DMIHER (DU)/IEC/2023/854).", "appendix": "Data availability\n\nNo data associated with this article.\n\n\nAcknowledgements\n\nI would like to thank my colleagues and my college.\n\n\nReferences\n\nFathi HM, Al-Masoody AH, El-Ghezawi N, et al.: The accuracy of fit of crowns made from wax patterns produced conventionally (hand formed) and via CAD/CAM technology. J. Prosthodont. Restor. Dent. 2016; 24: 7–10.\n\nHolmes JR, Bayne SC, Holland GA, et al.: Consideration in measurement of marginal fit. J. Prosthet. Dent. 1989; 62: 405–408. Publisher Full Text\n\nGroten M, Axmann D, Pröbster L, et al.: Determination of the minimum number of marginal gap measurements required for practical in-vitro testing. J. Prosth. Dent. 2000; 83: 40–49. PubMed Abstract \| Publisher Full Text\n\nMartínez-Rus F, Suárez MJ, Rivera B, et al.: Evaluation of the absolute marginal discrepancy of zirconia-based ceramic copings. J. Prosthet. Dent. 2011; 105: 108–114. PubMed Abstract \| Publisher Full Text\n\nBoening KW, Wolf BH, Schmidt AE, et al.: Clinical fit of Procera AllCeram crowns. J. Prosthet. Dent. 2000; 84: 419–424. PubMed Abstract \| Publisher Full Text\n\nNakamura T, Dei N, Kojima T, et al.: Marginal and internal fit of Cerec 3 CAD/CAM all-ceramic crowns. Inter. J. Prosth. 2003; 16: 244–248.\n\nNawafleh NA, Mack F, Evans J, et al.: Accuracy and reliability of methods to measure marginal adaptation of crowns and FDPs: a literature review. J. Prosthodont. 2013; 22: 419–428. PubMed Abstract \| Publisher Full Text\n\nPaul N, et al.: Marginal and internal fit evaluation of conventional metal-ceramic versus zirconia CAD/CAM crowns. J. Clin. Exp. Dent. 2020; 12(1): e31–e37. PubMed Abstract \| Publisher Full Text\n\nVaishali K, Prasad DK, Shetty M: A comparative evaluation of application techniques of a paint-on die spacer in grooves: an in vitro study. J. Ind. Prostho. Soci. 2013; 13: 520–524. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRahme HY, Tehini GE, Adib SM, et al.: In vitro evaluation of the replica technique in the measurement of the fit of Procera crowns. J. Contemporary. Dent. Practice. 2008; 9: 25–32." }	[ { "id": "199329", "date": "26 Sep 2023", "name": "Vinod Bandela", "expertise": [ "Reviewer Expertise Fixed Prosthodontics", "Implant Prosthodontics", "Dental Materials" ], "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 clearly mentioned the objectives of the study, the materials used and the methodology followed. In this research the author's will be using the conventional method and the CAD CAM fabricated wax patterns; which are the regular methods of fabrication of wax patterns. As the marginal fit and the internal fit of any prosthesis is important for the long term success of the restoration and the tooth restored, this study will be helpful in the field of fixed prosthodontics. The clinicians will be aware of the beneficial effects of the technique followed during the fabrication.\nI wish the authors good luck.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [ { "c_id": "13269", "date": "05 Feb 2025", "name": "Shubham Tawade", "role": "Author Response", "response": "Thank you so much sir for approving my article." } ] } ]	1	https://f1000research.com/articles/12-799
https://f1000research.com/articles/12-561/v1	30 May 23	{ "type": "Opinion Article", "title": "The rise of preprints in earth sciences", "authors": [ "Olivier Pourret", "Daniel Enrique Ibarra", "Daniel Enrique Ibarra" ], "abstract": "The rate of science information's spread has accelerated in recent years. In this context, it appears that many scientific disciplines are beginning to recognize the value and possibility of sharing open access (OA) online manuscripts in their preprint form. Preprints are academic papers that are published but have not yet been evaluated by peers. They have existed in research at least since the 1960s and the creation of ArXiv in physics and mathematics. Since then, preprint platforms—which can be publisher- or community-driven, profit or not for profit, and based on proprietary or free and open source software—have gained popularity in many fields (for example, bioRxiv for the biological sciences). Today, there are many platforms that are either disciplinary-specific or cross-domain, with exponential development over the past ten years. Preprints as a whole still make up a very small portion of scholarly publishing, but a large group of early adopters are testing out these value-adding tools across a much wider range of disciplines than in the past. In this opinion article, we provide perspective on the three main options available for earth scientists, namely EarthArXiv, ESSOAr/ESS Open Archive and EGUsphere.", "keywords": [ "Open Access", "Preprint", "Open Science" ], "content": "Introduction\n\nA research article’s preprint is its initial draft shared online, which is frequently (but not always) created before submission to a journal and formal peer review (Sarabipour et al., 2019). Preprint archiving services have existed since the 1960s, and thus are not a recent invention (Ginsparg, 2016). A centralized online network called arXiv, pronounced “är kv” (from the Greek letter \"chi\"), was created in August 1991 to exchange physics preprints (Bourne et al., 2017). For more than 30 years, arXiv has assisted the fields of physics, mathematics, and computer science, during which time the rate of scientific knowledge dissemination rapidly accelerated (Ginsparg, 2016; Tennant et al. 2019).\n\nA range of cross-domain or discipline-specific preprint platforms now exist, with exponential growth these last ten years (Kirkham et al., 2020). Preprints as a whole only represent a very small fraction of scholarly publication, but a strong group of early adopters is starting to adopt their use, which is adding value across a much wider range of disciplines than before. Preprint archiving may aid in the modernization of Earth Sciences publishing by removing obstacles to widespread scientific engagement and stumbling blocks to the development of an open and transparent research culture (Pourret et al., 2022).\n\nIn this Opinion Article, we further look at the evolution of three main options for earth scientists, namely EarthArXiv, ESSOAr/ESS Open Archive and EGUsphere and provide opinion on benefits and issues using preprints in earth sciences.\n\n\nPreprints in earth sciences\n\nPreprints have recently gained popularity across a wider range of academic fields, including the Earth Sciences (Nature Geoscience Editorial Board, 2018). The three main preprints servers in Earth Sciences are EarthArXiv, ESSOAr/ESS Open Archive and EGUsphere.\n\n(i) EarthArXiv (Narock et al., 2019) was created in 2018 and initially powered by OSF Preprints, and moved to a new infrastructure as a result of an emerging collaboration with California Digital Library in 2020.\n\n(ii) ESSOAr that recently evolved in ESS Open Archive, was developed in a joint initiative by the American Geophysical Union with financial support from Wiley.\n\n(iii) Earth Scientists who have published in the many journals of the European Geosciences Union (EGU) have already become accustomed to such openness and are posting their work prior to peer-review as a discussion on the Copernicus platform (Voosen, 2017). More than 20 years ago, EGU introduced the unique concept of open discussion and transparent peer review in which preprints were posted online; they now have a centralized preprint service EGUsphere.\n\nAs illustrated on Figure 1, the cumulative numbers of preprints from EarthArXiv, ESSOAr/ESS Open Archive and EGUsphere increased this last five past years; EarthArXiv published 3,429 preprints in five years, ESSOAr/ESS Open Archive published 7,436 in four years and EGUsphere published 326 preprints in less than a year (see Table 1 for details). These numbers still continue to grow and are following a similar track that preprints in biomedical disciplines did ten years ago (Penfold and Polka, 2019) but are not exponential as in medicine during COVID-19 pandemic (Watson, 2022).\n\nSome other regional preprint services also exist as well as more general ones (e.g. Irawan et al., 2022); a list can be found here (Kirkham et al., 2020).\n\n\nBenefits and issues using preprints\n\nPreprints have numerous, well-established advantages for both researchers and the general audience (e.g., Bourne et al., 2017; Sarabipour et al., 2019; Pourret and Irawan, 2022). It is the author’s opinion that preprints, for instance, allow:\n\n• The quick dissemination of research findings, which is important for time-sensitive studies (such as those conducted after natural disasters), for early-career researchers (ECRs) applying for jobs, or for any academic applying for grants or a promotion, given that journal-led peer review can take months or even years (Nguyen et al., 2015);\n\n• Increased visibility and accessibility for research outputs due to the preprint’s free uploading and viewing, especially for individuals who do not have access to paywalled journals or who have restricted access because of remote working (such as during lockdowns);\n\n• Increased visibility may also lead to increased interdisciplinary or transdisciplinary work in fields that would benefit from collaboration between Earth scientists and other disciplines (e.g., Dwivedi et al., 2022). Examples include geologic carbon dioxide removal strategies, water resources management and critical minerals.\n\n• Peer feedback that goes above and beyond what is offered through journal-led peer review (Tennant and Ross-Hellauer, 2020), increasing the likelihood of collaboration through community input and discussion; ECRs can also trained and write their first peer-review of preprints without being asked to.\n\n• Researchers to set priority (or a precedent) for their findings to reduce the possibility of being \"scooped\" by being assigned a digital object identifier (DOI). Some researchers may be afraid or unable to present their results at conferences. Additionally, abstracts available in conference books and proceedings might not always reflect what is presented on the day of the conference. Preprints allow research output to exist, be known and be stored in the digital world;\n\n• Dismantling of silos that traditional journals sustain by exposing us to a wider range of research than we might otherwise encounter and providing a home for works that do not clearly have a traditional peer-review publication as their intended destination (i.e. sharing diverse types of outputs such as data, research code, or methods);\n\n• Openness and transparency in research, with a focus on enhancing the overall standard, reliability, and reproducibility of findings.\n\nDespite these benefits, some authors point out that preprints without peer review raise a host of issues that may vary by discipline and publication type (e.g. Meinert, 2020). In particular, they may come with a caveat that interpretations are subject to change and that they may or may not lead to actual peer reviewed publication. Pourret et al. (2020) pointed out that the increased dissemination effect has the potential to be used to promote non-reproducible scholarship or fake news and adds an extra potential burden on readers. But fake news has plagued climate and environmental science for decades (e.g. Nature Communications Editorial Board, 2017) and it is not specific to just preprinted papers. Preprints may have some other disadvantages, including information overload, insufficient quality assurance, political influence, and outsized impact (e.g. Smart, 2022).\n\nPosting preprints is advantageous for ECRs because they can be shared, cited, and demonstrate productivity. However, the decision to preprint a manuscript must be made by all of the co-authors, and ECRs are frequently not the decision-maker due to power dynamics associated with academia (Ettinger et al., 2022). As a result, ECRs could encounter circumstances in which they are eager to deposit a preprint but are unsure of how to contact their co-authors or bring up the possibility of preprinting to their advisors. It is especially important for those of them leaving their research group after a contractual term. Indeed, in a short time it is not always possible to fully write a research paper in this particular field, as the process of conducting a field study, sampling and geochemical analyses could take years.\n\nBased on policies collated on Sherpa Romeo of the earth sciences journals, a majority of those journals do accept manuscripts preprinted prior to or during submission. As an example 84% of journals in geochemistry allow for preprinting (Pourret et al., 2020). The journals that do not offer a preprint option often do that because their thematic articles are mostly invited, generally review papers, and very rarely include the release of new data. This discrepancy is an example where the style and purpose of a given journal or magazine may influence editors and editorial boards to treat preprints differently based on the objectives of that scientific publication.\n\n\nConcluding remarks\n\nOverall, preprints have played a crucial role in advancing science for the benefit of humanity during the pandemic, according to the opinions of medical and scientific communities as well as the general people (Besançon et al., 2021). They are now included in some major bibliographic databases. Even if not always allowed by some funding agencies (e.g. Australian Research Council, Lanati et al., 2021), preprints are now a recognized step in the publication of scientific research and will continue to be used. For example, on Open Research Europe, the open access platform of Horizon 2020, Horizon Europe and Euratom funded projects, submitted articles are published prior to peer review, similar to preprints. Indeed, preprints are assisting in the modernization of our disciplines by reducing structural hurdles that prevent taxpayers, who frequently support knowledge development, from accessing science and knowledge, as well as by making research findings rapidly available to anybody who might benefit from them. The preprint landscape is moving fast, in early December 2022 PLOS announced in a press release a new partnership with EarthArXiv.\n\nAdditionally, PLOS, in partnership with DataSeer, has just released the first Open Science Indicators dataset, which uses large-scale Natural Language Processing to analyze published research articles to identify and track Open Science practices (Public Library of Science, 2022). The first three indicators included are: data sharing, code sharing, and preprint posting. Importantly, these metrics are not intended to rate or rank journals or publishers, but rather to set benchmarks, monitor changes over time, and better understand the research community’s use of Open Science practices such as preprinting. Even if bioRxiv reports up to 53% of preprints that are later published as papers (Abdill and Blekhman, 2019), Eckmann and Bandrowski (2023) estimated a bigger conversion from preprints to published articles. It is the author’s opinion that preprints are certainly here to stay!", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgments\n\nA preprint version of this article has already been published on EarthArXiv and can be accessed at https://doi.org/ 10.31223/X5936H.\n\n\nReferences\n\nAbdill RJ, Blekhman R: Tracking the popularity and outcomes of all bioRxiv preprints. elife. 2019; 8: e45133. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBesançon L, Peiffer-Smadja N, Segalas C, et al.: Open science saves lives: lessons from the COVID-19 pandemic. BMC Med. Res. Methodol. 2021; 21(1): 117. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBourne PE, Polka JK, Vale RD, et al.: Ten simple rules to consider regarding preprint submission. PLoS Comput. Biol. 2017; 13(5): e1005473. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDwivedi D, Santos ALD, Barnard MA, et al.: Biogeosciences Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science. Earth Space Sci. 2022; 9(3): e2021EA002119. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEckmann P, Bandrowski A: PreprintMatch: A tool for preprint to publication detection shows global inequities in scientific publication. PLoS One. 2023; 18(3): e0281659. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEttinger CL, Sadanandappa MK, Görgülü K, et al.: A guide to preprinting for early-career researchers. Biology Open. 2022; 11(7). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGinsparg P: Preprint Déjà Vu. EMBO J. 2016; 35(24): 2620–2625. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIrawan DE, Zahroh H, Puebla I: Preprints as a driver of open science: Opportunities for Southeast Asia. Front. Res. Metr. Anal. 2022; 7: 992942. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKirkham JJ, Penfold NC, Murphy F, et al.: Systematic examination of preprint platforms for use in the medical and biomedical sciences setting. BMJ Open. 2020; 10(12): e041849. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLanati A, Pourret O, Jackson C, et al.: Research Funding Bodies Need to Follow Scientific Evidence: Preprints Are Here to Stay. OSF Preprint. 2021. Publisher Full Text\n\nMeinert LD: 5. Thoughts on scientific publishing. Geochem. Perspect. 2020; 9(1): 1–133. Publisher Full Text\n\nNarock T, Goldstein EB, Jackson CA-L, et al.: Earth science is ready for preprints. Eos. 2019; 100. Publisher Full Text\n\nNature Communications Editorial Board: Fake news threatens a climate literate world. Nat. Commun. 2017; 8(1): 15460. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNature Geoscience Editorial Board: ArXives of Earth science. Nat. Geosci. 2018; 11(3): 149–149. Publisher Full Text\n\nNguyen VM, Haddaway NR, Gutowsky LF, et al.: How long is too long in contemporary peer review? Perspectives from authors publishing in conservation biology journals. PLoS One. 2015; 10(8): e0132557. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPenfold NC, Polka J: Preprints in biology as a fraction of the biomedical literature (1.0). [Data set]. Zenodo. 2019. Publisher Full Text\n\nPourret O, Irawan DE: Open Access in Geochemistry from Preprints to Data Sharing: Past, Present, and Future. Publications. 2022; 10: 3. Publisher Full Text\n\nPourret O, Irawan DE, Tennant JP: On the Potential of Preprints in Geochemistry: The Good, the Bad, and the Ugly. Sustainability. 2020; 12(8): 3360. Publisher Full Text\n\nPourret O, Jackson C, Goldstein EB, et al.: Modern geoscience publishing. Geoscientist. 2022; 32(2): 22. Publisher Full Text Reference Source\n\nPublic Library of Science: PLOS Open Science Indicators. Public Library of Science. Dataset. 2022. Publisher Full Text\n\nSarabipour S, Debat HJ, Emmott E, et al.: On the value of preprints: An early career researcher perspective. PLoS Biol. 2019; 17(2). Publisher Full Text\n\nSmart P: The evolution, benefits, and challenges of preprints and their interaction with journals. Science Editing. 2022; 9(1): 79–84. Publisher Full Text\n\nTennant JP, Crane H, Crick T, et al.: Ten Hot Topics around Scholarly Publishing. Publications. 2019; 7(2): 34. Publisher Full Text\n\nTennant JP, Ross-Hellauer T: The limitations to our understanding of peer review. Res. Integr. Peer Rev. 2020; 5(1): 6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVoosen P: Dueling preprint servers coming for the geosciences. Science. 2017. Publisher Full Text\n\nWatson C: Rise of the preprint: how rapid data sharing during COVID-19 has changed science forever. Nat. Med. 2022; 28: 2–5. PubMed Abstract \| Publisher Full Text" }	[ { "id": "175861", "date": "15 Jun 2023", "name": "Blanca Rodriguez-Bravo", "expertise": [ "Reviewer Expertise Scientific communication", "Information behaviour", "Knowledge organization" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nCongratulations to the authors for this paper, that is relevant. This is an opinion article that begins by defining and briefly discussing the history of preprints and then focuses on the evolution of three preprint repositories in the field of earth sciences. The article provides quantitative data that confirms the growing interest in the aforementioned platforms, and then addresses the advantages and disadvantages of publishing through preprints. The information about the three preprints platforms is interesting.\nThe authors' vision seems adequate to me, although I believe that in the search for greater symmetry the issues should be presented as the benefits -by means of bullets and with a more complete argumentation-. My view is that benefits are clearly and completely highlighted but this is not the case of the drawbacks. The problems derived by a less formal or less complete peer review process may be expanded as it is the case of information overload, insufficient quality assurance, or non-reproducible research. The main problem can be that the reader is not aware that he/she may have been reading a paper that no one has evaluated yet. I am not familiar with the field of earth sciences but in general there is still a high lack of knowledge about preprints as some of them are eventually published in journals and others are not.\nIn the case of Early Career Researchers (ECRs), to which the authors pay special attention, it is true that the quick dissemination of research findings is a clear advantage for ECRs. However, they are also wary of publications that do not pass prior quality control. Therefore, they often hold back from publishing preprints, and not just because coauthors, senior researchers, prefer to publish in traditional journals. ECRs, due to their competitive circumstances, are sometimes more opposed to publishing preprints that do not lead to a traditional publication than other already tenured researchers. Check, for instance, the paper by Nicholas et al. (2022) published in Profesional de la información, v.31, n.4, e310418.\n\nThe conclusions are appropriate. Open science is a necessity and preprints, as one of its manifestations, are growing in importance as both the subscription model of journals and the APCs model are more and more questioned.\nTo sum up, although the paper is well structured and well argued, the paper will benefit for expanding the \"still\" negative aspects of preprints taking into account the points of view of authors -with particular attention to ECRs- and readers.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Partly\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes", "responses": [ { "c_id": "9860", "date": "10 Jul 2023", "name": "Olivier Pourret", "role": "Author Response", "response": "Thank you for your comments and have reworked our article following your suggestions. We have expanded the drawbacks section (see next response as well). We have added a bullet and have considered the proposed reference: “ECR may wary of publications that do not pass prior quality control. Therefore, they often hold back from publishing preprints, and not just because coauthors, senior researchers, prefer to publish in traditional journals. ECRs, due to their competitive circumstances, are sometimes more opposed to publishing preprints that do not lead to a traditional publication than other already tenured researchers (Nicholas et al., 2022)” Overall, we have refined our article as proposed and expanded the negative aspects of preprints, thank you again." } ] }, { "id": "175864", "date": "20 Jun 2023", "name": "Zhiqi Wang", "expertise": [ "Reviewer Expertise Scientometrics", "science of science", "scientific communication", "preprint", "S&T management" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe opinion paper offers insights into the rise of preprints in earth sciences, focusing on three main preprint servers: EarthArXiv, ESSOAr/ESS Open Archive, and EGUsphere. The authors highlight an increasing trend in the cumulative numbers of preprints posted on these servers, indicating the growing popularity of preprints in the field. They further discuss the benefits and issues associated with preprint publishing.\nTo enhance the overall content, I would suggest the following improvements:\nRegarding the first research problem addressed, the trend in preprint publishing, I suggest the authors to consider additional factors beyond cumulative numbers. In my opinion, factors such as submission rate, citations, and social attention attracted by the preprints can provide a more comprehensive and reliable assessment of the trend.\n\nFor the three preprint servers mentioned, I think it would be valuable to outline their distinct features. This information would help readers understand how to choose the most suitable server for posting or searching preprints.\n\nAs an opinion paper, I suggest the authors to give more further discussion on the specific benefits and challenges unique to preprint publishing in the field of earth sciences, as compared to other disciplines. Considering that the readers of the paper likely come from the field, addressing this topic would provide them with valuable insights. And in the concluding remarks section, the paper will benefit for including comments on the future development of preprints in the field of earth sciences.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Partly\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes", "responses": [ { "c_id": "9861", "date": "10 Jul 2023", "name": "Olivier Pourret", "role": "Author Response", "response": "Thank you for your comments, we have refined our article following your suggestions. The comment is very pertinent, unfortunately we do not have access to data like submission rate, citations, and social attention attracted by the preprints. Certain publishers linked to preprint servers (e.g., AGU journals published in Wiley linked to ESSOAr/ESS Open Archive) would be able to collate such data, but that is outside the scope of our analysis here. Agreed, we have added details in the form of short paragraphs on each of the 3 preprint servers mentioned in our submission. We have added a few more examples dedicated to Earth Sciences and added a sentence on future development of preprints in our discipline in conclusion. Thank you again for all your comments." } ] }, { "id": "175863", "date": "20 Jun 2023", "name": "Daniel J. Dunleavy", "expertise": [ "Reviewer Expertise I am an academic social worker by training (PhD) with an extensive record of publishing on issues related to open science", "peer review", "and issues in scholarly publishing." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have written an opinion piece outlining the rise and use of preprints in the earth sciences. They briefly describe the history of preprints, identify three common preprint platforms used in the field, and articulate the strengths and limitations for researchers and scholars of posting preprints.\nI found the manuscript to fill a somewhat niche, but relevant area of discussion. Its strengths lie in its overall exposition of the strengths and limitations of preprints and overview of the EarthArXiv, ESSOAr/ESS Open Archive, and EGUsphere platforms.\nI hope the following comments, questions, and suggestions help strengthen the overall quality of the manuscript. Additionally, please be advised that any and all references included in this review are suggestive and not meant to be viewed as compulsory.\nIntroduction\n(1) I somewhat disagree with the opening sentence. Though it includes manuscripts that are best described as an \"initial draft shared online\", the term preprint (somewhat unfortunately) appears to encompass many different things (including post-print manuscripts and materials and resources never intended for publication). There's a brief, but decent discussion here:\nhttps://scholarlykitchen.sspnet.org/2017/04/19/preprint-server-not-preprint-server/ (see also the comments)\nand here:\nhttps://doi.org/10.31222/osf.io/796tu.\nYou might consider adding a sentence or two acknowledging this and emphasizing whatever definition you prefer to in the context of this discussion.\n(2) Similarly, though not \"necessary\", the introduction might also make further mention of the history of preprints prior to arXiv. This might help further contextualize and possibly contrast the historical, professional, and institutional factors that (have and continue to) motivate scientists to engage with or refrain from sharing via preprint servers.\n\nSee: https://doi.org/10.1371/journal.pbio.2003995, https://doi.org/10.1002/meet.2014.14505101036,\nand\nhttps://www.science.org/doi/10.1126/science.154.3751.843.a\n\nPreprints in the earth sciences\n(3) This section felt particularly \"thin\". I think it would be strengthened by comparing and contrasting the three servers/platforms in greater detail. As a reader, I did not feel I got a good understanding how these platforms differed and what benefits one might offer over another (in terms of visibility, content moderation, indexing, tools, support, etc.).\n(4) What's more, this section might be improved by a brief discussion of the advantages of discipline-specific servers, compared to using any number of other \"generic\" platforms (e.g., Zenodo or simply OSF Preprints).\nBenefits and issues using preprints\n(5) You've already cited Ginsparg, 2016 - but I think their work provides a nice (if somewhat opinionated) place for expanding and more fully elaborating upon the strengths and limitations of sharing via preprint (see FAQ9 and FAQ15, for example).\n\nData and materials\n(6) The manuscript may benefit from another sentence or two describing how the data for Table 1 and Figure 1 were sourced. As the numbers don't appear (to me) to be readily accessible from the preprint servers, I imagine each site was searched, by year, to generate the total number of preprints. Whatever the case, a bit more explanation may be helpful for enhanced transparency and reproducibility.\nMiscellaneous comments\n(7) I can appreciate that the manuscript was previously published as a preprint on EarthArXiv. If applicable, it might be useful to include a statement or two about whether and how doing so benefited its development or dissemination, if at all.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Partly\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Partly", "responses": [ { "c_id": "9862", "date": "10 Jul 2023", "name": "Olivier Pourret", "role": "Author Response", "response": "Thank you for all your comments and suggestions. We have reworked our article as follows. We have reworked the first paragraph and added some nuances as proposed by reviewer 3. “Though it includes manuscripts that are best described as an \"initial draft shared online\", the term preprint (somewhat unfortunately) appears to encompass many different things (including post-print manuscripts and materials and resources never intended for publication) (see discussion in Tennant et al., 2018). “ We have added some details in the introduction: “In 1961, the USA National Institutes of Health launched a program called Information Exchange Groups, designed for the circulation of biological preprints, but this was shut down in 1967 (Confrey, 1966; Cobb, 2017).” As also suggested by reviewer 2, we have added details on the 3 preprint servers mentioned in our submission. We have added some details of the advantages of discipline-specific servers, compared to using any number of other \"generic\" platforms. We have added some details on Benefits and issues using preprints and further cite the work of Ginsparg (2016). We have added a sentence on the methodology on how the numbers were generated. We have added some words in the acknowledgment section stating that our previous preprint at EarthArXiv let us being invited to submit this opinion paper at F1000Research." } ] } ]	1	https://f1000research.com/articles/12-561
https://f1000research.com/articles/12-794/v1	06 Jul 23	{ "type": "Research Article", "title": "Quantification of microbial risk associated with fecal exposure in a nomadic lifestyle; case study of Turbi ward, Marsabit County", "authors": [ "Batula Jaro", "Sarah Wandili", "Grace Gakii", "Caroline Karani", "Caroline Karani" ], "abstract": "Background: Water, Sanitation and Hygiene (WASH) is the cornerstone for health and growth at all stages of life in helping to maintain health and increase in life span. Poor sanitation as lead to disease causing microorganisms such as E. coli to be on the rise. This study aimed to determine water and milk contamination of E. coli from nomadic community. Methods: A cross-sectional study was conducted on water and milk samples using most probable number method to determine contamination as a result of poor sanitation in this community. Results: The dominant exposure pathway in this study was water pathway with high E. coli positivity, 20% (n=50) for dam water sampled, 20% (n=50) for pan and borehole feed water tanks 20% (n=50). Dam water sources analyzed had presence of 1.05 x1107CFU/ml and pan water sources 1.93x104 CFU/ml, which is above acceptable E. coli level in water for consumption is (10-40 CFU/ml)\n\nConclusions: Microbial contamination noted from this study indicates that there is poor sanitation in nomadic lifestyle. This study reaffirms the need for elaborate sanitation model tailored to the need of pastoralist community to reduce perennial faucal contamination of water sources for the community of Turbi ward. Elaborate sanitation model tailored to the need of pastoralist community to reduce perennial fecal contamination of water sources for the community of Turbi ward.", "keywords": [ "sanitation", "E. coli", "colony forming units" ], "content": "Introduction\n\nSanitation and water management is one of the ways to reduce the spread of enteric pathogens in the urban, peri-urban and rural environmental set up. The most affected are children, women and elderly people especially in a rural set up. The approach of a community to sanitation includes factors such as the perception, feelings and practices involved in defecation and urination, and the disposal of this waste. Their attitude is a result of interconnected factors of cognition as a result of knowledge, perception together with feeling and behaviour that leads to action (Rosenzweig et al. 1962). Sanitation solutions such as flush toilet, piped sewer system, ventilated pit latrines, etc., that prevent direct contact with human excrements are considered improved, while others such as bucket latrines, hanging toilets, and open defecation are not (WHO/UNICEF 2010).\n\nThe goal of SDG 6.2 is to provide access to adequate, equitable sanitation and hygiene for all and put an end to open defecation especially for girls, women and the vulnerable in the society by 2030 (World Bank 2016). Between 2015 and 2020, the population with safely managed sanitation increased from 47 per cent to 54 per cent and the population with access to handwashing facilities with soap and water in the home increased from 67 per cent to 71 per cent. Rates of progress for these basic services would need to quadruple for universal coverage to be reached by 2030.\n\nWater, sanitation and hygiene (WASH) is the cornerstone for health and growth at all stages of life in helping to maintain health and increase in life span. Epidemiological studies has associated poor hygiene practices and lack of water with adverse health outcomes that includes diarrhoeal diseases caused by microorganisms such as E. coli leading to enteric malfunctions that leads to stunted growth. (Pruss-Ustun et al. 2014).\n\nThese exposure pathways can be through water bodies, food, utensils, storage tanks, sewerage system, open drains galleys or seepage. Tens of millions of people across the world, most of them children, die of sanitation related illness (WHO/UNICEF 2019).\n\n\nMethods\n\nPermission was sought through the board of postgraduate studies of Meru University of science and technology, The Meru University of Science and Technology Institutional Research Ethics Review Committee (MIRERC) and County government of Marsabit.\n\nThe study was carried out in the Turbi ward, North Sub-County of Marsabit County, Kenya, with a population of 23,978 (Kenya National Bureau of Statistics 2019). The populations are mostly Cushitic community practicing a pure nomadic lifestyle. The area has land mass of 10,821 km2, and is located at longitude 38°22′25′′E, latitude 3°20′51′′N. Has tropical dry savanna climate. Map for Turbi ward in Northhorr sub county (Figure 1).\n\nThe study employed a cross-sectional study design with an aspect of laboratory analysis. Samples for analysis were collected from dams, pans, camel milk and swabs from milk holding containers. The samples were then transported to the laboratory for analysis. Consent to collect water samples from dams, pans and boreholes was obtained by village elders while milk and swabs from containers consent was given by household heads.\n\nSimple random sampling was conducted to select one village from each center totaling to five villages. Water from dams, pans and boreholes were collected while milk samples were collected from the selected households.\n\nPreparation and analysis of water and milk in the laboratory\n\nWater and milk analysis for most probable number required sterile bottles with MacConkey broth, and Durham tubes for gas collection. Each bottle with sample was appropriately labelled. The water was mixed thoroughly by inverting the bottle many times. The cap of the bottle was removed and the mouth of the bottle flamed. The water samples were then inoculated. After inoculation, the bottles were incubated at 44°C for 24 hours the samples were examined for color change and gas formation.\n\nBiochemical identification of E. coli using Tryptone water\n\nPositive isolates were subjected to biochemical identification using Indole test for E. coli. The test organism was inoculated in a bijou bottle containing 3 mL Tryptone water and incubated at 37°C for 24 hours.\n\nEnumeration of E. coli CFU using colony counter\n\nAll samples that were confirmed to have E. coli were subjected to enumeration in order to calculate the colony forming unit. A serial dilution was performed up to 105 for E. coli. Then 100 μL were transferred into plate count agar plates arranged from 100 to105 respectively. They were incubated for 24 hours at 37°C. The plate that had grown distinct colonies were subjected to counting and colony forming unit calculated. Selected plate was placed on a counting chamber and a colony pointer was used to touch the surface where the colony was had grown on the media and all the colonies will be counted. Colony forming unit was obtained by multiplying number of colonies counted times the dilution factor.\n\nData are presented using tables and bars graphs to compare microbial contamination in different villages.\n\n\nResults\n\nAll the samples taken from all sampled villages had high E. coli bacteria, indicating extent of faecal contamination in water sources used for domestic purposes. Surface water from dams 20% (n=50) and borehole feed water tanks 20% (n=50) had high positivity of E. coli colonies. Table 1 shows the CFU of water samples. Only three samples tested negative for E. coli; these were in Okola. Turbi dam and Okola pan had high E. coli counts colonies both having high positivity of 10% and 8% (n=50) respectively (Table 1).\n\nE. coli was positively identified in milk from Turbi 21%, (n=37), Shurr 19%, (n=37) (Table 2). The lowest burden was Dekuku 5% (n=37) manyattas (small settlements). Out of the 37 samples analysed, 12 tested negative for E. coli (Table 2).\n\n\nDiscussion\n\nThe principle finding of this study is predominance of E. coli in all sources; dam, pan and borehole fed water tanks. Environmental samples collected from the water pathways predominately were from dam, pan, trough, borehole, about 86% (n=50) of samples test positive for E.coli, an indicator of bacteria in faecal contamination. Dam, borehole fed water tanks and pans had positivity of 20% (n=50) showing high presence of E. coli colonies (Table 1). Turbi dam and Okolla pan had high E. coli colony numbers, both having high positivity of 1.05×107 and 1.93×104 CFU/mL, respectively, (Table 1); the acceptable E. coli in water for consumption is 10–40 CFU/mL (WHO 2020).\n\nThe high presence of E. coli detected in these sources used by Turbi, Okolla, and Kambi Nyoka villages could be attributted to that the fact that the research was conducted during the raining season and, during these periods, pastoralist communities depend solely on surface runoff water that feed the dams and pans. Water from boreholes which is retrieved by pumping appliances, such as the one in the Shurr village, are rarely contaminated, but due to poor management of storage tanks and poor hygiene during household water storage processes, tends to increase the likelihood of E. coli exposure in these source of water.\n\nThe results of this study also concur with related study done by Suraja and Raja (2020) on faecal exposure pathways, conducted in low income urban and peri-urban areas that identified contact with open drain water and produce to be the main pathways for exposure both for adults and children. There is limited information and research conducted on exposure pathways among communities that practice a nomadic lifestyle. Due to their mobile lifestyle, the nomadic community lacks basic amenities, such as toilets and safe drinking water (Mohamed 2020). Contamination of water bodies and environment by faecal matter exposes children and adults to water-borne diseases, such as cholera and dysentery.\n\nMilk and milk products are basic foods consumed by people practicing a pastoralist way of life. Milk and milk products are also good media for bacterial growth. Any contamination to these food products affects health and general wellbeing of the population that depend on these food products. Milk samples collected from all manyattas showed contamination with evidence of E. coli. This contamination could be due to use of contaminated water to clean milking utensils and lack of hand washing before milking animals.\n\nThe consumption of raw milk is accepted in some pastoralist communities is associated with cultural beliefs and preference (Tumwine et al. 2015). A study conducted by Samwuel Majalija et al. (2020) in Nakasogola, Uganda, observed that 67.8% respondents reported never or rarely washed hands before milking animals. A related study conducted in India by Lingathurai and Vellathurai (2010) reported high presence of E. coli of 1.25×107 CFU/mL in milk samples collected from farmers. This was linked to poor hygiene, handling, transportation and storage that affects quality of raw milk.\n\n\nConclusion\n\nMicrobial contamination noted from this study indicates that there is poor sanitation in a nomadic lifestyle. This study reaffirms the need for an elaborate sanitation model tailored to the need of pastoralist community to reduce perennial faecal contamination of water sources for the community of the Turbi ward.\n\nThis study reaffirms the need for elaborate sanitation model tailored to the need of pastoralist community to reduce perennial fecal contamination of water sources for the community of Turbi ward.\n\n\nAuthor’s contribution\n\nBJ: Developed the concept, wrote the project proposal, collected the research data, analyzed the data, and wrote the thesis.\n\nSW: Corrected the concept, provided necessary guidance, and corrections at the proposal writing, data analysis, and thesis writing.\n\nGK: Corrected the concept, provided necessary guidance, and corrections at the proposal writing, data analysis, and thesis writing\n\nCK: Mentorship guidance in writing and corrections", "appendix": "Data availability\n\nFigshare: Underlying data for “Quantification of microbial risk associated with faecal exposure in a nomadic lifestyle; case study of Turbi ward, Marsabit county”. https://doi.org/10.6084/m9.figshare.22357084.v1.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgement\n\nI thank the Almighty God for bringing me this far. My utmost gratitude is to my immediate family members with special emphasis to my husband for his continuous support and encouragement during my study. I appreciate my lecturers who have paved way during my coursework that has enabled me to accomplish my study. I would like to thank my colleague students and all people who in their own special ways made this research thesis a success.\n\n\nReferences\n\nBush LM, Vazquez-Pertejo MT: Infection by Escherichia coli O157: H7 and other enterohemorrhagic E. coli (EHEC). MSD Manual Professional Version; 2020. Retrieved October 3, 2021.\n\nHarris L: Trading and exchanges: Market microstructure for practitioners. USA: OUP; 2003.\n\nKenya Population and Housing Census - Volume III: Distribution of Population by Age and Sex. In Kenya National Bureau of Statistics: Vol. II (Issue 1). 2019.\n\nLingathurai S, Vellathurai P: Bacteriological quality and safety of raw cow milk in Madurai, South India. 2010.\n\nMajalija S, Tumwine G, Kiguli J: Pastoral community practices, microbial quality and associated health risks of raw milk in the milk value chain of Nakasongola District, Uganda.2020.\n\nMohamed.: Factors hindering health care delivery in nomadic communities: a cross-sectional study in Ethiopia. 2020.\n\nMuldoon KA, Galway LP, Nakajima M, et al.: Health system determinants of infant, child and maternal mortality: A cross-sectional study of UN member countries. Glob. Health. 2011; 7(1): 1–10. Publisher Full Text\n\nPruss-Ustun A, Bartram J, Clasen T, et al.: Burden of disease from inadequate water, sanitation and hygiene in low-and middle-income settings: a retrospective analysis of data from 145 countries. Trop. Med. Int. Health. 2014; 19(8): 894–905. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRosenberg MR, Krech D, Bennett EL, et al.: Effects of environmental complexity and training on brain chemistry and anatomy: a replication and extension. J. Comp. Physiol. Psychol. 1962; 55(4): 429–437. Publisher Full Text\n\nRosenzweig MR, Krech D, Bennett EL, et al.: Effects of environmental complexity and training on brain chemistry and anatomy: A replication and extension.J. Comp. Physiol. Psychol.1962;55(4):429–437.\n\nSuraj J, Raja B: A quantitative approach for assessing exposure to fecal contamination through multiple pathways in low resource urban settlements.2020.\n\nTumwine G, Matovu E, Kabasa JD, et al.: Human brucellosis;Sero-prevalance and associated risk factors in agro-pastrolist communities of Kibogo District, Central Uganda.2015.\n\nWorld Bank Group: World development report 2016: Digital dividends. World Bank Publications; 2016.\n\nWorld Health Organization: State of the world’s sanitation: an WHO. Guidelines for Drinking-water Quality FOURTH; Escherichia coli Contamination across Multiple Environmental Compartments (Soil, Hands, Drinking Water, and Hand washing Water) in Urban Harare.2020.\n\nWHO/UNICEF: The state of the world’s sanitation to achieve universal sanitation, we need greater investment and higher rates of sanitation coverage. 2019.\n\nWHO, UNICEF: \"UNFPA, The World Bank. Trends in maternal mortality: 1990 to 2008 Estimates developed by WHO, UNICEF.\" UNFPA and The World Bank. Geneva: World Health Organization; 2010." }	[ { "id": "187019", "date": "17 Jul 2023", "name": "Acácio Salamandane", "expertise": [ "Reviewer Expertise Researcher in microbiology", "specializing in food and waterborne 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\nQuantification of microbial risk associated with fecal exposure in a nomadic lifestyle; case study of Turbi ward, Marsabit County\nJaro et al. present the results of an investigation on microbial risk associated with fecal exposure in a nomadic lifestyle; case study of Turbi ward, Marsabit County. Unfortunately, the authors failed to meet important criteria in their methodology, which renders the results unreliable and consequently makes the work useless, at least for now.\nGeneral comments:\nAlthough interesting and contributory to science, the manuscript presents significant flaws in relation to rigorous scientific criteria. The major gaps are related to the methodology used in the microbiological analysis of the selected, which compromises all the obtained results. An example of this is the fact that the authors don’t mention the use of ISO standards guidelines for detecting microorganisms in food and water samples, consequently they use inadequate method to E. coli enumeration, revealing a lack of expertise.\nBelow are listed a few examples.\nSpecific comments:\nIntroduction\nThe introduction should be reformulated and improved to contextualize the problem under study, define concepts that I consider important, such as \"nomadic communities\". The introduction should also include or contextualize the importance of the study for the scientific community and for the community of the region under study. Motivation and objectives of this study.\nMaterials and Methods\nStudy area\nIn this chapter, relevant information on the community under study must be provided, namely, population density, main economic activities and hygiene and sanitation conditions, including the supply of potable water by the local government.\nStudy design\nThis chapter lacks information on the number of samples selected by each village and by each type of sample (Lake, river, dam, swabs, etc.).\nSampling procedure: join with Study design.\nPreparation and analysis\nHow many tubes were used for each sample?\nWhat were the amounts of each sample incubated in each series or group of tubes?\nThe analysis of the microbiological quality of water can be done by two methods: By membrane filtration (the currently most used method) and MPN.\nIn the case of MPN, the recommendation is to use three series of five tubes each (it can be less) that are inoculated in a concentration of 1:1, 1:10 and 1:100.\nIn this study, with MPN being the method used, it was not clear how many tubes were used.\nEnumeration of E. coli CFU using colony counter\nHow do you know that the colonies that were on the PCA were E. coli colonies?\nCounting of E. coli in water is performed by membrane filtration and incubated in chromogenic and differential media such as TBX, ECC and MacConkey agar. In this culture medium it is possible to differentiate colonies of E. coli from other colonies of enterobacteria. In PCA this is not possible, since PCA is a generic medium for bacterial growth.\nResults:\nMicrobiological evaluation\nFigures and tables constructed as results of microbial counts or results from MPN tubes form part of results. Therefore, you must move them from methodology to results.\nDue to the usage of an inappropriate methodology, the validity of all obtained results is highly questionable.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "237738", "date": "07 Feb 2024", "name": "Kun Li", "expertise": [ "Reviewer Expertise Veterinary medicine", "Veterinary parasitology", "Microbiology" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nTitle and Abstract: In title: Why used the term “microbial risk” not E. coli because the study is focusing on just E. coli, also the title is not in justifying the data. In conclusion the “perennial faucal contamination” needs to be checked and should be replaced with “perennial fecal contamination”, also the reason why “perennial” is used here is not clear to me. Keywords: can be extended (if the journal’s format allows) Introduction: “The most affected are children, women, and elderly people, especially in a rural setup. The approach of a community to sanitation includes factors such as the perception, feelings, and practices involved in defecation and urination, and the disposal of this waste”. This line can be revised as it is appropriate to use “verb” after “to” (to sanitize). The sentence structure should be rearranged. “Rates of progress for these basic services would need to quadruple for universal coverage to be reached by 2030”. In this line word “quadruple” is not easy to understand for the reader and can be replaced by some suitable synonym. Overall, in the introduction, some more authentic background information can be added quantitatively. E. coli is not focused in the introduction which is the main point to be discussed. The introduction can be narrowed down from broader to narrow (Starting with some general trends and ending with E. coli the literature review can be made more comprehensive and up to date. What novel did you study? should be here, to capture the reader’s attention. Need to be grammar-checked and spell-checked (complete article). Methodology: Experimental design is questionable. No, strict guidelines were followed in sampling. This is a scientific study and should be in a systematic way, not random, also the transportation conditions of samples from the field to the lab are not clear to me. There is a lack of quantification in the methodology, many details like tube numbers, etc. are not included here. The methodology is too simple and conventional type. How did you differentially diagnose E. coli colonies from other types of bacterial colonies? Figures and tables are not part of the methodology. Methodology and results should be two different sections and should not be mixed. Which software was used to process data, and which statistical model was used?? or in the table presentation is manual is not clear. Results: Results based on colony counting can be misinterpreted and considered not so much authentic. It's a very extreme condition that samples can be negative for E. coli. (Only three samples tested negative for E. coli; these were in Okola.)\n\nDiscussion: “The principle finding of this study is predominance of E. coli in all sources”. This predominance can be replaced by some better synonym. In discussion, there is more general information not specifically focusing on the E. coli count. There is some lack of continuity. The paragraph can be arranged to maintain some continuity. Ascending or descending chronological order can be followed. Clarity and Structure: Results are questionable. Overall Impression: I don’t believe the paper will make a valuable contribution to the field. Strengths and Weaknesses: Need to be much improved. Overall, I don’t consider that this Paper is fulfilling the criteria to be accepted.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "237737", "date": "15 Feb 2024", "name": "Seto Charles Ogunleye", "expertise": [ "Reviewer Expertise Veterinary Medicine", "Infectious disease", "Food Safety", "Veterinary Public Health and 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 research topic is very interesting and the subject matter of E. coli is a global concern that must be dealt with adequately and not peripherally. My comments and suggestions are listed below\n1. The abstract should be reviewed for grammar, and then the content to adequately communicate the subject matter appropriately. A conclusion on presence of fecal contamination primarily to pastoralist is rather inappropriate and the study did not mention a sufficient link between the two variables\n2. The conclusion appears too obsolete- conclusion should be based a more concrete finding\n3. The introduction should be overhauled- there is lack of sufficient background information on E. coli, WASH and fecal contamination.\n4. Overall, the introduction should improved to cover the nearest minimum wealth of information on E. coli.\n5. The method is fails to demonstrate knowledge and application of fundamental bacteriological techniques. There are specific techniques required for the isolation and identification of E. coli. The authors should perform the experiment according to standard laboratory procedures.\n6. The discussion should come from the results findings upon modifications and the word \"high E. coli\" should be avoided- authors should be more scientific in writing and communication.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "237735", "date": "30 Aug 2024", "name": "Mohamed Diab", "expertise": [ "Reviewer Expertise Microbiology", "zoonotic diseases", "One 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\nMore recent articles should be cited in the introduction and in the discussion. Biochemical test for identification of E.coli not based only on Indole Test. The statistical methods should be re-selected to better highlight the results, Do you mean that the only way of milk contamination with E. coli is contaminated utensils or water?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-794
https://f1000research.com/articles/12-517/v1	18 May 23	{ "type": "Systematic Review", "title": "Adolescent Friendly Health Clinics (AFHCS) in India and their compliance with government benchmarks: A scoping review", "authors": [ "Deepika Bahl", "Shalini Bassi", "Subhanwita Manna", "Monika Arora", "Shalini Bassi", "Subhanwita Manna", "Monika Arora" ], "abstract": "Background: Adolescent Friendly Health Clinics (AFHCs) are one of the critical pillars of India’s Adolescent Health Programme-Rashtriya Kishor Swasthya Karyakram. The goal is to empower all adolescents to make informed decisions about their health and to access health services, allowing them to fully reach their potential. A review was conceptualised to assess the compliance of AFHCs with the benchmark proposed by the Government under Rashtriya Kishor Swasthya Karyakram. Methods: Three databases (PubMed, Scopus and Google Scholar) were searched for articles published between 2014 and 2022. A snowball search strategy was also used to retrieve all published articles. Based on the search strategy eight studies were included. Results: Evidence from the primary studies showed that the benchmarks need attention as privacy was lacking (six out of seven studies), unavailability of IEC material (four out of five), signages (two out of four), referrals (one out of two), and judgemental attitude of health care provider (one out of 3). Conclusions: It is crucial to address the existing gaps in order to make the clinics adolescent-friendly, as this could lead to increase utilization of services available in AFHCs and an overall improvement in their health, education, and employment. The improved health will catalyse achieving the Sustainable Development Goals indicators related to nutrition, reproductive health, sexual and intimate partner violence, child marriage, education, and employment.", "keywords": [ "Adolescent Friendly Health Clinic", "AFHC", "Adolescents", "Youth", "Rashtriya Kishor Swasthya Karyakram", "RKSK", "India", "Review" ], "content": "Introduction\n\nAdolescence (10-19 years) is a unique phase of life characterised by rapid changes in physical, biological, cognitive, social, and emotional development.1 Investing intensively in adolescent health and development is not only crucial to improve their survival and well-being but also for India’s development and achievement of Sustainable Development Goals (SDGs) related to health, nutrition, education, gender equality, and food security.1 Investment in adolescent health and wellbeing yields triple benefits, as it benefits adolescents now, into their future adult life and the next generation.2 Health services and policies have largely ignored adolescence but, with the global HIV epidemic among adolescents, policymakers recognised the importance of addressing adolescents’ sexual and reproductive health (SRH)3 needs. Simultaneously, numerous other adolescent health issues were spotlighted by the Lancet series on adolescent health in 2007,4 2012,5 20196 and 2022.7 The latest 2022 Lancet series highlights the global efforts to protect every child from before conception to adulthood.7\n\nIn alignment with the international focus on adolescent health, there are various adolescent health programmes being implemented like the Reproductive and Child Health (RCH) program (I and II)8 and Reproductive, Maternal, Newborn, and Child Health + Adolescents (RMNCHA+A) launched in 2013.9 With these sustained efforts, adolescent health improved which is evident by comparing rounds of the National Family Health Surveys (NFHS) for the reduction in adolescent childbearing, contraceptive knowledge, use of contraceptive methods, mean age at first marriage, etc.10,11 While other health problems persisted such as tobacco use among adolescents, injuries and violence, mental health issues, overweight/obesity, undernutrition, anaemia etc.12 For addressing these concerns, the Ministry of Health and Family Welfare (MOHFW), GOI in 2014 launched a flagship programme ‘Rashtriya Kishor Swasthya Karyakram’ (RKSK). The program aimed to reach out to male and female, rural and urban, married and unmarried, in and out-of-school adolescents with a special focus on marginalised and underserved groups. The program under its ambit has expanded the scope from Sexual Reproductive Health (SRH) to nutrition, injuries, and violence (including gender-based violence), non-communicable diseases (NCDs), mental health and substance misuse, as a one-stop-shop. The strategies include community-based, facility-based, and school-based interventions.13 The facility-based pillar of the programme focuses on providing adolescents with clinical and counselling services through Adolescent Friendly Health Clinics (AFHCs).14\n\nAFHCs are one of the critical pillars of the RKSK that seeks to enable all adolescents to realize their full potential by making informed decisions concerning their health, by accessing the services and support to implement their decisions.15 Services in these clinics are being delivered through trained service providers- Medical officers (MO), Auxiliary Nurse Midwives (ANM), and Counsellors. These clinics have been integrated into medical colleges, district and sub-district hospitals, community health centres (CHCs), and primary health centres (PHCs)14 to bring services ‘closer to home’ for adolescents. At a different level of the health system, manpower and timings of services at the AFHCs vary. As per GOI, there are 7969 AFHCs as of 31st Dec 2019 in India; with the highest number of AFHC in Karnataka (2563) and lowest in Chandigarh (n=4) at various levels of health system catering to diversified health and counselling needs of adolescents.16 Since these clinics have been operational for several years; assessing compliance or alignment with the benchmarks is critical for evaluation and considering further up-gradation if needed. Given this context, a review was conceptualised to assess the compliance of AFHCs to a set of benchmark under RKSK focused. These standards pertain to various aspects such as infrastructure, proximity, operating hours and awareness about the clinic and its services, the competency of health service providers, privacy and confidentiality, community awareness and referral linkage.\n\n\nMethods\n\nTo map the compliance of current adolescent healthcare facilities based on the RKSK benchmark set by GoI, we adopted a scoping review design17 by using Arksey and O’Malley’s five stage scoping review framework.18\n\nStage 1: Identify the research question\n\nIdentifying the research question is the first step in carrying out a scoping review, according to Arksey & O’Malley.18 Therefore, our scoping review addressed the following research question in an effort to synthesise the available knowledge in this field:\n\nWhat is known about the compliance to the RKSK benchmark set by the GOI in various regions of India based on the literature that is currently available?\n\nStage 2: identifying relevant studies\n\nOur search strategy was established after conducting preliminary research to better understand search terms and keywords. We looked up the terms ‘AFHC’ AND “Adolescent Friendly Health Clinics,” “RKSK,” “compliance,” and “India” in PubMed, Scopus, and Google Scholar (Table 1).\n\nStage 3: Selection of literature: Inclusion criteria\n\nThe systematic inclusion of the papers was done in accordance with the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) recommendations.19 Our search approach identified twenty-four papers, which were then imported into Mendeley desktop 1.19.5. Ten duplicate items were deleted, leaving Fourteen articles to be screened. We screened titles, abstracts, and references using the criteria described below. The last search was carried out by two researchers from July 2022 to December 2022. Benchmark of AFHCs as per Government of India guidelines was identified as the outcome of the studies. A copy of the PRISMA flowchart can be found under Extended data.48\n\nTypes and scope of studies\n\nIn this review, studies using both quantitative and qualitative approaches were included from every research setting and region in India. Our search focused on papers published in India between 2014 and December 2022 that contained information on the Indian government’s standards for AFHCs. The studies conducted before 2014 were excluded, as that was the year the RKSK program was launched. A priori, no language or publishing status restrictions were established.\n\nKey concepts\n\nKey concepts pertaining to the AFHC benchmarks established by the GOI under RKSK program were covered in this review.\n\nParticipants\n\nThis review focused on various level health facilities which provide AFHC services to the adolescents aged 10-19 years.\n\nFollowing this, seven full-text papers were evaluated, and four papers were further excluded due to incorrect outcomes and non-availability of the full-text article. To ensure inclusivity and account for diversity, our review did not restrict the search to any specific geographic regions. We only considered articles that had undergone peer review. A snowball search strategy was used to retrieve all maximum possible articles.\n\nStage 4: Data extraction\n\nData related to the benchmarks was extracted on the excel sheet and before retrieving the data, the excel sheet was piloted by the researchers of the team. Information extraction included seven benchmarks set by MoHFW-GOI including infrastructure, clean, bright and colourful, accessibility (proximity and operating hours), awareness about the clinic and range of services it provides (IEC, Proper Sinages), non-judgmental and competent health service providers, privacy and confidentiality, community awareness, and referral from the periphery/community to the higher facilities and speciality clinics.20 Two reviewers (SB and DB) looked over the full texts and abstracts of all the publications as well as their citations to determine each article’s eligibility. Two authors independently evaluate the articles and extracted the data for this review based on the set benchmarks of GOI. Disagreements were resolved by discussion with the third author.\n\nStage 5: Collating, summarizing and reporting the results\n\nTo summarise our data, we used the author and year of publication, AFHC benchmarks. This study presents findings related to infrastructure, community awareness of the services provided, referral from the periphery/community and further referral linkages with higher facilities and speciality clinics, privacy and confidentiality, nonjudgmental and competent health service providers, and accessibility as AFHC benchmark parameters. Furthermore, clinic awareness benchmark includes the provision of IEC and signage. A review synthesis was carried out, taking into account the differences between the various studies in terms of study aims, design, and conclusions.20\n\n\nResults\n\nWe found 24 papers from PubMed(n=0), Scopus(n=14), and Google scholar(n=10) in the initial database search. After removing the duplicates, 14 articles were screened, seven articles were excluded based on title and abstract screening. Only seven articles were eligible for full-text screening. While five articles were included during full-text screening by checking the references. Thus, a total of 12 were reviewed and finally, only eight articles were included in this review (Figure 1).\n\nEight studies from the year 2014 to 2022 were identified and included in the review. Of eight studies, six were cross-sectional, 1 cohort and 1 qualitative was included for review. The included studies had been conducted in different geographical locations of the country like Kashmir,21 Ladakh,21 Leh,22 Uttar Pradesh,23 Ahemdabad,24 Jharkhand,25,26 Maharastra,25 Rajasthan,15,25 Madhya Pradesh,27 Delhi,26 Haryana,26 Punjab,26 and Uttrakhand.26 They covered AFHC15 at various levels of establishment, for example, at Community Health Centre level,25,27 district hospital21 and sub-district hospital.21,25 These studies included, either ‘exit interviews’ of patients23–25,27 availing services at AFHCs or interviews of health care providers/counsellors/staff22 dealing with adolescents in AFHC and ‘Mystery clients’,25,26 to gather information about AFHC.\n\nCompliance of AFHCs with benchmarks enlisted under the RKSK\n\nPrivacy and confidentiality\n\nOut of the eight studies, seven studies evaluated the privacy and confidentiality aspect of AFHCs. Of the available seven studies, six studies reported that privacy and confidentiality in AFHCs were not maintained (Table 2) and below is the evidence from the independent studies to support this statement.\n\nQualitative assessment emphasised seven of the fifteen clients from Jharkhand, Maharashtra and Rajasthan felt that their conversation with the Medical Officer or other staff could have been overheard by others. In addition, four of the nine clients who underwent a physical examination felt that others could have seen them while being examined by the medical Officer.25 Similarly, interaction with mystery clients of Rajasthan reported disturbance from the staff and other patients visiting the clinic during their counselling sessions. In four out of 24 visits, these clients reported that someone was present (besides the practitioner/counsellor) during the sessions. In half of the visits (12/24), the clients reported people coming in between the counselling sessions. This was mainly due to the location of the clinic which led to disturbance and visibility by others.15\n\nQuantitative analysis in the identified studies also showed that confidentiality and privacy were breached. The majority of adolescents (90.91%) did not receive privacy during the consultation and curtains were available only during counselling of 42.42% of adolescent girls24 during their visits to AFHCs of Ahmedabad. During the clinic’s observation, privacy and confidentiality were provided in only 63.6% of the facilities.24 Similarly, in RKSK facilities of Madhya Pradesh, curtains were not there (33%) and conversation could be heard from outside (40%).27 A six-state (Delhi, Haryana, Himachal Pradesh, Jharkhand, Punjab, Uttrakhand) evaluation of AFHCs showed that only 35% of them maintained privacy; with the least being in AFHCs of Himachal Pradesh (0%).26 Adolescents (69%) from Ahmedabad believed that there should be an opportunity for separate private discussions with doctors at AFHCs.28\n\nOn the contrary, there was only one study from Kashmir and Ladakh that showed privacy was maintained. Results showed that 75% of AFHCs operational under RKSK had a dedicated space and the consultation room ensured the privacy of the clients.21\n\nInfrastructure (clean, bright and colourful)\n\nFour out of eight studies did not evaluate the AFHC infrastructure like cleanliness and brightness. The remaining four studies evaluated this benchmark and three studies reported that AFHC infrastructure was maintained well and in only one study the benchmark was not maintained, below is the evidence.\n\nAs per the qualitative results from a study conducted in three states, all the adolescents found the facility to be clean.25 Similar results were reported by all the adolescents (100%) accessing the AFHC in Ahmedabad.24 In another study 17 out of the 24 i.e., 70% of adolescents reported the clinic to be ‘overall clean from inside and outside highlighting the lack of cleanliness in these clinics.15\n\nOn other hand, a study conducted in 10 districts of Madhya Pradesh showed that only 60% of the clinics were clean.27\n\nNon-judgmental and competent health service providers\n\nAnother benchmark of the AFHC is to have non-judgemental and competent healthcare providers. Out of eight studies, only three studies have highlighted the finding around this benchmark. Out of three studies, one study did not meet the benchmark.\n\nOne-third of the adolescents in a study reported some counsellors’ behavior was “judgemental and biased” as the counselor had a judgemental attitude towards unmarried adolescent girls engaging in premarital sexual activity.15\n\nAlthough, in one study almost all adolescent clients, regardless of their sex, or state of residence, reported that the healthcare provider had greeted them cordially when they entered the consultation room (21 of the 24 visits).25 Similarly, in another study adolescents of Ahmedabad reported that 93.9% of health care providers were welcoming during their visits.24\n\nAccessibility (distance and convenient working hours)\n\nThe accessibility of these clinics is defined by the distance and the convenient working hours. Out of eight studies, three studies did not evaluated the accessibility of AFHCs. The remaining five studies evaluated this benchmark, and all (n=5) showed that the clinics were accessible to adolescents, below is the supportive evidence.\n\nAccording to the result of the study conducted in Ahmedabad, 87.8% of adolescents reported that time and days are convenient to seek services24 and similarly 100% of adolescents reported that time was convenient.23 When evaluating the AFHC of Kashmir21 and Madhya Pradesh it showed that they were functional on all days.27 Concerning the distance, AFHC was 5-10 kilometers away from the villages and also the respondents reported that these facilities were easily accessible.25\n\nAwareness about the clinics and range of services (IEC, Proper Signages)\n\nAnother important variable is awareness of the clinic assessed through signboards and Information Education and Communication (IEC) material displayed in the AFHC. Out of eight studies, three studies did not evaluate this benchmark. Of the five studies, four studies showed that the IEC material benchmark was not fulfilled.\n\nEvidence from the studies showed that reading material was available but was readable by only 56.5% of adolescents and less than half of adolescents (43.4%) reported that the material was interesting.29 In results derived through observations in another study, no IEC material was displayed in the AFHC.24 AFHC evaluation from six states of India showed that only 44% of clinics displayed material.26 Similarly, the adolescents reported that only limited IEC material on SRH was displayed in the waiting area of all the AFHCs.15\n\nOn the contrary, only one evaluation from Kashmir and Ladakh regions showed a majority (83.3%) of the facilities had IEC material available.21\n\nRegarding the availability of signages, only four studies evaluated the availability of signboards, and the findings gave a mixed picture (two studies met the benchmarks and the other two did not). In one evaluation, it showed that signboards were only seen in one-fourth of AFHC24 and another evaluation showed that 67% of AFHC from 10 districts of Madhya Pradesh had sign boards.27 On the contrary, evaluation of AFHCs from Ahmedabad showed signboards were available in 100% of the AFHCs21 and similar findings were seen when AFHCs from Jammu and Kashmir were observed.22\n\nReferrals and community awareness\n\nCommunity awareness of the services provided has not been evaluated in the included studies. Another benchmark is the referral from the periphery/community to the higher facility. Out of eight studies, six studies have not evaluated the referral mechanism. The remaining two evaluated, out of which in one study mystery clients reported that they had been referred to a higher facility for SRH issues.25 Similarly in another study, all counsellors reported referring cases of substance abuse, alcohol addiction, STIs, menstrual pain, unwanted pregnancy, and nocturnal emissions to more qualified healthcare providers but the adolescents reported only a few of them were referred to doctors by the counsellors for nocturnal emissions, STIs and teenage pregnancy.15\n\n\nDiscussion\n\nThis review sets out that existing AFHCs are not fully compliant with all the benchmarks proposed by MOHFW, GOI under the National Adolescent Health Programme. The benchmarks that need consideration include privacy in these clinics (six out of seven studies), availability of IEC material (four out of five studies), availability of signages (two out of four studies), referrals (one out of two studies), and non-judgemental attitude of health care providers (one out of three studies). It is important to fill these gaps in the existing AFHCs, especially during the current context of COVID-19 in India due to which the adolescents have become more vulnerable. As per the brief published in 2021, adolescents are vulnerable to a spectrum of issues due to restriction measures that have been put in place such as the closure of schools, restrictions on movement, physical distancing, mask-wearing, and restricted social gatherings.30 The risk of child marriage in India has heightened as a result of the pandemic’s economic fallout, cybercrimes including cyberbullying due to excessive internet use,31 increased mental health issues due to information floated on social media, significant proportions of which were unverified or false.32 The screen time has also increased and physical activity has dwindled among adolescents.30 To overcome health and development issues, AFHCs can be a one-stop clinic as they are intended to be the first point of contact between an adolescent beneficiary and the formal healthcare system.33\n\nStrengthening of AFHCs is crucial for developing the trust of adolescents in availing the services as they are located in their vicinity. Multiple efforts such as a mechanism involving centre, state, block, and village level stakeholders for the constant AFHC evaluations and addressing the gaps identified in each evaluation are needed. In India, a study was previously conducted to evaluate the quality of Adolescent Reproductive Sexual Health services; it assessed if these services met the National Standards of care and utilized periodic program improvement recommendations through the WHO - quality assessment (QA) tools. Periodic interventions resulted in improving the average facility score from 27% to 83% and overall standards score from 28% to 81% at baseline and end line survey, respectively.33 This method can be used across all Indian states to assess the functionality of AFHC at all facility levels and timely and tailor-made intervention can be given to fill the existing lacunae. United Nations agencies’ model can be used for restructuring the AFHCs as used in other countries, like Tanzania. A study conducted in Tanzania described the challenges identified by the Ministry of Health and Social Welfare (MOHSW) and were then addressed with the support of WHO, UNFPA, and other partners in the country.34 Similar methodologies can be adopted in India to strengthen the health system.\n\nThere is also a need for regular booster training of healthcare workers on the importance of maintaining these benchmarks proposed by GOI. This training should give special emphasis on the maintenance of privacy, confidentiality, the importance of displaying the IEC material, signages, the non-judgemental attitude of health care providers, and referrals. Maintenance of privacy is a crucial aspect of adolescent healthcare as they encourage beneficiaries to seek care and disclose sensitive information that allows the service providers to deliver appropriate clinical services.35 Multiple studies have found associations between confidentiality practices and receipt of recommended services.36–38 Additionally, privacy is particularly important for the issues like SRH, and substance misuse, given the possible sensitivity and stigma associated with them.39 IEC is a critical step toward a social behavior change communication approach that motivates people to adopt and sustain healthy behaviors40 in a short time.41 Training is effective and this was evident from the findings of the Tarunya project that provided cascading ARSH training to government staff at secondary care facilities and strengthened outreach activities to enhance community engagement. After 5 years of implementation, the project evaluation showed intervention efforts contributed to improvement in the quality and initial use of ARSH services. The performance of health facilities was appreciated by clients.42 Another aspect that needs attention is the non-judgemental attitude of the health providers. According to the World Health Organization,41 if an adolescent feels unwelcome, it is unlikely that they would utilize the services. Adolescents are an age group that needs to be treated with respect and dignity. The aforementioned characteristics determine the friendliness and acceptability of services provided to adolescents, and hence their propensity to utilise the available services.43 Capacity building of service providers in providing counselling services tailored to the age, life stage and health problem. Thus, there is a dire need for the booster training of the service providers at AFHCs to strengthen their skills further to provide services in non-judgemental and sensitive manner. Another concern was the signboards and the IEC materials in the AFHCs. A marked signboard indicating if the facility has an AFHC and the timing as an important indicator as per the RKSK operational guidelines. With the presence of these signages, it is easy for adolescents to locate.44 The presence of this will help in adolescents’ knowledge enhancement. IEC materials can be Charts/Posters/Leaflets/Wall paintings, etc. on six thematic areas of RKSK and other adolescent health issues.45 The presence of IEC in all the clinics will be a valuable addition, as they are a means of imparting knowledge, disseminating health information, and positively modifying health attitudes and behaviours46 in a short period.\n\nFor the training of health care providers existing systems can be used. For instance, the Karnataka state involves mentoring network for the capacity building of health care providers for quality care. Across India, 900 health professionals were connected to NIMHANS ECHO.47 Multi-point video conferencing was used to conduct virtual sessions with healthcare providers to improve their self-efficacy, further enhancing their interest and optimism in helping persons with addiction. This included case-based learning and didactic lecture by experts, also seeking clarification regarding standard management. Through this, 500 doctors from the district and PHC have been trained.47 These existing establishments can be used as an opportunity for organizing booster trainings.\n\nDespite employing a rigorous methodology in this review, its generalizability was limited due to the scarcity of studies across various regions of India.\n\n\nConclusion\n\nUnder RKSK’s facility-based approach, AFHC constitutes a crucial pillar, and addressing the existing gaps in this area could lead to increased utilization of available services by adolescents, resulting in improved health outcomes. The improved health of our young population will also help in achieving Sustainable Development Goals indicators related to nutrition, reproductive health, sexual and intimate partner violence, child marriage, education, and employment.\n\n\nAuthors contribution\n\nDB and SB conceptualized the idea. DB and SB conducted the screening and data extraction. DB and SM design the methodology. DB, SB and SM drafted the manuscript and MA critically reviewed the manuscript. All the authors approved the final version of the manuscript.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: Adolescent Friendly Health Clinics (AFHCS) in India and their compliance with benchmarks: A scoping review. https://doi.org/10.6084/m9.figshare.22132022.v1. 48\n\nThis project contains the following extended data:\n\n- PRISMA flowchart.pptx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nGeorge A, Jacobs T, Ved R, et al.: Adolescent health in the Sustainable Development Goal era: are we aligned for multisectoral action? BMJ Glob. Health. 2021 Mar 1; 6(3): e004448. 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Publisher Full Text\n\nChandra-Mouli V, Mapella E, John T, et al.: Standardizing and scaling up quality adolescent friendly health services in Tanzania. BMC Public Health. 2013; 13(1): 579. Publisher Full Text\n\nBrittain AW, Williams JR, Zapata LB, et al.: Confidentiality in Family Planning Services for Young People: A Systematic Review. Am. J. Prev. Med. 2015 Aug 1; 49(2 Suppl 1): S85–S92. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLeichliter JS, Copen C, Dittus PJ: Confidentiality Issues and Use of Sexually Transmitted Disease Services Among Sexually Experienced Persons Aged 15-25 Years - United States, 2013-2015. MMWR Morb. Mortal. Wkly Rep. 2017 Mar 10; 66(9): 237–241. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nO’Sullivan LF, McKee MD, Rubin SE, et al.: Primary care providers’ reports of time alone and the provision of sexual health services to urban adolescent patients: results of a prospective card study. J. Adolesc. Health. 2010 Jul; 47(1): 110–112. Publisher Full Text\n\nThrall JS, McCloskey L, Ettner SL, et al.: Confidentiality and adolescents’ use of providers for health information and for pelvic examinations. Arch. Pediatr. Adolesc. Med. 2000; 154(9): 885–892. PubMed Abstract \| Publisher Full Text\n\nPampati S, Liddon N, Dittus PJ, et al.: Confidentiality matters but how do we improve implementation in adolescent sexual and reproductive health care?. J. Adolesc. Health. 2019 Sep 1; 65(3): 315–322. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGOI: Social and Behavior Change Communication (SBCC) Training for Information, Education, and Communication (IEC) Officers.2013. Reference Source\n\nWHO: Making health services adolescent friendly Developing national quality standards for adolescent-friendly health services. World Health Organization. Reference Source\n\nBarua A, Chandra-Mouli V: The Tarunya Project’s efforts to improve the quality of adolescent reproductive and sexual health services in Jharkhand state, India: A post-hoc evaluation. Int. J. Adolesc. Med. Health. 2017 Dec 20; 29(6): 20160024.\n\nKapoor N: Adolescent Friendly Health Clinics in India-Are They Friendly Enough? Int. J. Policy Sci. Law. 1(4): 2114–2134. Reference Source\n\nPastrana-Sámano R, Beatriz Heredia-Pi I, Olvera-García M, et al.: Adolescent Friendly Services: quality assessment with simulated users. Rev. Saude Publica. 2020 Apr 6; 54: 36. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNHM, GOI: Operational Guidelines For Implementation “Rashtriya Kishor Swasthya Karyakram” (RKSK) Programmes for strengthening Adolescent Health.Reference Source\n\nAgnes T: Use of Information, Education and Communication (IEC)-Based Materials: An Effective Teaching-Learning Strategy in Nutrition Education. 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Publisher Full Text" }	[ { "id": "174956", "date": "08 Jun 2023", "name": "Palak Gupta", "expertise": [ "Reviewer Expertise Public health", "Nutrition", "Hunger", "food and nutrition insecurity" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIt is a well-written document and is of great interest in public health in India. Some of my comments are:\nSome of the abbreviations are not explained by the author, and it will be helpful if they can be expanded upon. Example: GoI, IEC etc. IEC is expanded somewhere in the middle of the study; it will be better to explain when it is used for the first time in the manuscript.\n\nThe authors utilize benchmarks proposed by the Government under Rashtriya Kishor Swasthya Karyakram. It will be helpful to know what the benchmarks are, how those benchmarks are measured (which indicators are used). Also, if there is a report or website which have those benchmarks listed, adding that will be helpful.\n\nThis review has a limitation on the number of manuscripts available, and not all the studies have measured the benchmarks, which makes it hard to be replicated and results must be used with caution.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [ { "c_id": "9766", "date": "20 Jul 2023", "name": "Deepika BAHL", "role": "Author Response", "response": "Comment 1: Some of the abbreviations are not explained by the author, and it will be helpful if they can be expanded upon. Example: GoI, IEC etc. IEC is expanded somewhere in the middle of the study; it will be better to explain when it is used for the first time in the manuscript. Response: The abbreviation of GOI added in the 10th line of the second para of Introduction. IEC expanded at the first place in method section and subsequently acronym IEC has been used. Comment 2: The authors utilize benchmarks proposed by the Government under Rashtriya Kishor Swasthya Karyakram. It will be helpful to know what the benchmarks are, how those benchmarks are measured (which indicators are used). Also, if there is a report or website which have those benchmarks listed, adding that will be helpful. Response: Citation added in the 1st line of Design segment. All the details regarding benchmarks already exist in the data extraction segment of the manuscript. “Information extraction included seven benchmarks set by MoHFW-GOI including Infrastructure, clean, bright and colourful, accessibility (distance and convenient working hours), awareness about the clinic and range of services it provides (Information, Education and Communication, Proper Sinages), non-judgmental and competent health service providers, privacy and confidentiality, awareness of the services to the community members, their need and referral from the periphery/community to the higher facilities and speciality clinics” Comment 3: This review has a limitation on the number of manuscripts available, and not all the studies have measured the benchmarks, which makes it hard to be replicated and results must be used with caution. Response: Added to the limitation section of the manuscript." } ] } ]	1	https://f1000research.com/articles/12-517
https://f1000research.com/articles/12-342/v1	28 Mar 23	{ "type": "Research Article", "title": "Endothelin-1 as predictor of major adverse cardiovascular events in chronic coronary syndrome patients undergoing coronary intervention", "authors": [ "Trisulo Wasyanto", "Ahmad Yasa", "Nimas Ayu", "Ahmad Yasa", "Nimas Ayu" ], "abstract": "Background: Major adverse cardiovascular events (MACE) are predicted to be low in chronic coronary syndrome (CCS) patients who have undergone percutaneous coronary intervention (PCI). Endothelin-1 has been considered a pro inflammatory biomarker and\n\nsuggested as a novel prognostic indicator in CCS. The objective of this research was to prove endothelin- 1 as predictor of MACE within 1-year evaluation in CCS patients undergoing PCI. Methods: This research was an analytic observational study with a cohort design. The participants were CCS patients who had undergone PCI. Endotelin-1 levels were checked before the patient underwent PCI. Occurrences of MACE were observed within 1 year. The comparison between normally distributed continuous data was performed with a T-test, and the Mann–Whitney test was used for not normally distributed data. A comparison between categorical data was performed with the Chi-square test. The cut-off point of endothelin-1 levels to predict MACE was analyzed by receiver operating characteristics (ROC). Results: Participants in this study were 63 patients. Six patients experienced MACE within 1 year (9.5%) and 57 patients were included in the non-MACE group (90.5%). Mann Whitney T test showed there were significance differences in endothelin-1 levels from the two groups (p=0.022). The ROC curve showed cut off point the endothelin-1 is 4.07 ng/dl with a sensitivity of 83.3%, specificity of 75.4% and accuracy of 76.2%. Based on the area under curve (AUC) value and the accuracy of this study, endothelin-1 was able to detect MACE within 1 year of follow-up. Conclusions: Endothelin-1 can be used as predictor of MACE within 1-year evaluation in CCS patients undergoing coronary intervention.", "keywords": [ "endothelin-1", "major adverse cardiovascular events", "chronic coronary syndrome", "coronary intervention" ], "content": "Introduction\n\nCoronary heart disease (CHD) is a type of heart disease caused by the narrowing of the coronary arteries due to the atherosclerosis process. CHD can be divided into acute coronary syndrome (ACS) and chronic coronary syndrome (CCS).1–3 The diagnosis of CCS includes identification of risk factors for atherosclerosis, clinical evaluation, and supporting examinations.4,5\n\nEndothelin-1 is derived from endothelial cells and several studies have reported its associated with endothelial dysfunction.6–8 Endothelial dysfunction has been reported as an atherosclerotic risk factor associated with future cardiovascular events,9–11 and therefore has been considered a pro inflammatory factor12–14 and suggested as a novel prognostic indicator in ACS. However, its role in predicting cardiovascular events in stable coronary artery disease is unclear.15–17 Endothelin-1 in the cardiovascular system is produced not only by vascular endothelial cells but also by vascular smooth muscle cells, cardiomyocytes, and fibroblasts.18–20 Levels of endothelin-1 in blood plasma are very low under normal conditions, but the levels increase 100 times higher when the vascular wall shows increased cellular activity.21–23 Endothelin-1 is a potent endogenous vasoconstrictor produced primarily by the vascular endothelium.24–26 As a vasoconstrictor it contributes to increased tone in atherosclerotic coronary arteries and is involved in endothelial dysfunction, inflammation, and vascular remodeling.27–29\n\nA meta-analysis by Windecker et al. reported a reduction in mortality and incidence of acute myocardial infarction (AMI) with revascularization vs. medical therapy alone, in CCS patients when revascularization was performed with a coronary artery bypass graft (CABG) or a new generation of drug-eluting stent (DES) instead of the earlier DES (bare metal stent) or balloon angioplasty alone.30 In patients with stable coronary artery disease, an initial fractional flow reserve (FFR)-guided PCI strategy was associated with a significantly lower rate of the primary composite end point of death, myocardial infarction, or urgent revascularization at five years than medical therapy alone. Patients without hemodynamically significant stenosis had a favorable long-term outcome with medical therapy alone.31\n\n\nMethods\n\nThe protocol of the research was approved by the Medical and Health Research Ethics Committee of Dr. Moewardi Hospital Surakarta Indonesia No.71/II/HREC/2021 on November 12, 2021. Participants provided signed informed consent to participate.\n\nThe design of the research was a prospective cohort study conducted in December 2021 – December 2022. The population were patients diagnosed with chronic coronary syndrome (CCS) who underwent cardiac catheterization (PCI) and were admitted in the intensive cardiovascular care unit (ICVCU) and cardiology ward of Dr. Moewardi Hospital, Surakarta, Indonesia. This study recruited 63 patients, consisting of 46 (73%) male patients and 17 (27%) female patients. We included subjects with a diagnosis of chronic coronary syndrome aged between 30 and 75 years old. We excluded subjects with acute myocardial infarction (AMI), previous history of PCI, severe heart valve abnormalities, history of chronic heart failure with New York Heart Association (NYHA) class ≥II, chronic renal failure, hepatic cirrhosis, and malignancy; with concomitant infection and sepsis; with concomitant acute stroke and acute inflammatory state (such as acute arthritis and pericarditis) during hospitalization; and acute heart failure. All subjects gave signed informed consent to participate in the study.\n\nUpon admission, before the patient underwent catheterization, a peripheral antecubital venous blood sample was obtained from each subject during the supine position. The blood sample was centrifuged at 4000 r.p.m for 20 minutes and stored at −80°C in a freezer until analysis for endothelin-1 measurement. Endothelin-1 was detected and quantified with endothelin-1 immunoassay Quantikine® ELISA kit (R&D Systems, Minneapolis, USA) according to manufacturer procedure instructions (CV%: 23). The ELISA method was performed once by a skilled technician in the clinical pathology laboratory at Dr. Moewardi Hospital Surakarta Indonesia.\n\nThe subjects’ clinical data were collected during hospitalization. The treatments for subjects was at the discretion of attending cardiologists, without any interference of this research. Subjects were observed from admission until one year after hospital discharge for the occurrence of major adverse cardiac events (MACE). After the patient was discharged from the hospital, they are asked to carry out routine check-ins every month (if there are no complaints), or immediately check-in if there are complaints. If it is time for a check-in and the patient does not attend, they will be contacted by telephone or if necessary, a visit to the patient's home is made. The adverse cardiac event was the composite of cardiac death, acute heart failure, cardiogenic shock, reinfarction, and resuscitated ventricular arrhythmia. Cardiac death was fatal due to cardiac disease. Acute heart failure was defined as the occurrence of signs/symptoms of congestion and the use of intravenous diuretics. Cardiogenic shock was defined as the signs of reduced peripheral perfusion and the use of vasopressors drugs. Reinfarction was defined as the recurrent chest pain, recurrent ST-segment elevation, and an elevation of cardiac enzymes. Resuscitated ventricular arrhythmia was the return of spontaneous circulation after resuscitation for lethal arrhythmias.\n\nFor statistical analysis, SPSS 26.0 for Windows (SPSS Inc., Chicago, IL, USA) was used. The subjects were divided into two groups based on the presence of adverse cardiac events. The normal distribution was tested with the Kolmogorov-Smirnov test. The comparison between normally distributed continuous data was performed with Student's T-test, while the Mann–Whitney test was used for not normally distributed continuous data. A comparison between categorical data was performed with the Chi-square test. A receiver operating characteristic (ROC) curve was designed to determine the cut-off point of endothelin-1 level to predict adverse cardiac events. A univariate and multivariable analysis with logistic regression test were performed to determine the independent predictor of an adverse cardiac event. A p value < 0.05 was set as statistical significance.\n\n\nResults\n\nThis study was conducted in the emergency room, polyclinic, intensive cardiovascular care unit (ICCU), and cardiac care ward, clinical pathology laboratory, and cardiac catheterisation laboratory hospital. 63 samples from patients with CCS were obtained. The 63 patients were then monitored for one year for the development of major adverse cardiovascular events (MACE). The results of this study listed in the Table 1.\n\nFor variables related to coronary angiography results, 28 (44.4%) persons involved one coronary vessel, 16 (25.4%) persons involved two vessels, and 19 (30,2%) person involved three vessels. The characteristic variable descriptions and coronary angiography are presented in Table 2.\n\na Independent t test (numerical data fulfils normality assumptions).\n\nb Chi-squared test/Fisher exact test (nominal categorical data).\n\nOf the 63 patients in the study, six patients experienced MACE within 1 year (9.5%), and 57 patients were included in the non-MACE group (90.5%). MACE occurred in the evaluation of six patients (9.5%), in the form of acute myocardial infarction, heart failure, and death in two (33.3%), one (16.6%), and three (50%) patients, respectively. In male patients who underwent MACE, two patients experienced AMI, one patient experienced heart failure, and two patients died. Only one female patient experienced MACE due to death. Two patients were not routinely monitored for evaluation, due to busyness of the patients, insurance issues, or geography\n\nEndothelin-1 levels generally ranged from 2.15 pg/ml to 6.90 pg/ml, with a mean of 3.66 pg/ml and a standard deviation of 1.09 pg/ml (3.66 ± 1.09 pg/ml). In the non-MACE sample group, endothelin-1 levels ranged from 2.15 pg/ml to 6.90 pg/ml, with a mean of 3.59 pg/ml and a standard deviation of 1.09 pg/ml (3.59 ± 1.09 pg/ml). In the MACE sample group, endothelin-1 levels ranged from 3.52 pg/ml to 5.84 pg/ml, with a mean of 4.37 pg/ml and a standard deviation of 0.78 pg/ml (4.37 ± 0.78 pg/ml). The description and testing of endothelin-1 level variables are presented in Table 3.\n\n* significant at the 5 percent significance level.\n\nThe calculation of endothelin-1 levels as a predictor of 1-year MACE variables was done by using the receiver operating characteristic (ROC) curve. The area under the curve (AUC) for the ROC curve on the incidence of MACE for the variable endothelin-1 level as a predictor was 0.785. The interpretation of the variable endothelin-1 level can detect the incidence of MACE well. Based on the ROC curve, the cut-off point value of the endothelin-1 level variable was 4.07ng/dl, and the occurrence of MACE can be detected from the endothelin-1 level variable with a sensitivity rate of 83.3% and a specificity rate of 75.4% and a diagnostic accuracy rate of 76.2%. The results of sensitivity, specificity, and diagnostic accuracy are presented in Table 4.\n\nThe relationship between endothelin-1 levels and 1-year MACE (cut-off point = 4,07) are presented in Table 5.\n\n** Significant at 1 % significance level.\n\nThe statistical test results of the relationship between endothelin-1 levels and MACE with a probability of p = 0.008 indicate that the relationship is significant at a 1% significance level (p 0.01). The odds ratio reached 15.36, with a 95% confidence interval of 1.65 142.84, indicating that the relation between endothelin-1 levels and MACE was truly significant (convincing). The ROC curve on MACE events for variable endothelin-1 levels as a predictor resulted in an AUC value of 0.785 with an accuracy rate of 76.5%. All of this demonstrates that endothelin-1 levels are a good predictor of MACE within a year.\n\n\nDiscussion\n\nMACE or major adverse cardiovascular event is often used as a composite outcome of an observational study. Various definitions of MACE show different components in each study; some define MACE into three, four of five components.32–34 From all studies, it can be concluded that the most common components are acute myocardial infarction, stroke, and death. In addition, there were 15 studies that included heart failure as a component of MACE.35–37\n\nZhou's study included 3154 patients with stable CHD who were followed for 24 months. This study showed that endothelin-1 levels were associated with major cardiovascular events in CHD patients who were not revascularized. Endothelin-1 plays a prognostic role in stable CHD patients.38–40 An increase in endothelin-1 levels caused vasoconstriction and decreased coronary blood flow, thus causing and exacerbating myocardial ischemia. Haug's study showed that endothelin-1 production increases in conditions where there are atherosclerotic plaques in the coronary arteries. Endothelin-1 release stimulates smooth muscle cell proliferation in a paracrine or autocrine manner, which may contribute to the development of coronary artery disease.41–45\n\nIn our study, MACE occurred in six patients in the study sample. The low incidence of MACE could be due to several reasons. Firstly, the level of patient compliance with treatment was quite good at the 1-year follow-up. In addition, 63 patients underwent percutaneous coronary intervention (PCI). PCI is associated with a significant reduction in the primary composite risk of death, acute myocardial infarction, and urgent revascularization within five years, when compared with medical therapy alone.46–51\n\nIn one retrospective cohort study, it was demonstrated that sex has an impact on subsequent adverse cardiovascular outcomes among patients over 60 years of age with atherothrombotic disease.52\n\nResearch by Hata J and Kiyohara Y, 2013 in Asia reported that adverse cardiovascular events including ACS, all strokes, vascular procedures, and death in hospital were significantly lower in female patients than in males, both with univariate and multivariate analysis. Traditional atherosclerotic risk factors are age, hypertension, dyslipidemia, diabetes mellitus, and smoking.53\n\nIn contrast to some previous meta-analyses, Zimmermann et al’s 2019 meta-analysis of 2400 subjects reported that reduced MACE was confirmed in patients undergoing PCI procedures, showing significant reductions in cardiac death and MI after a median follow-up 33 months with fractional flow reserve (FFR)-guided PCI vs. medical therapy (hazard ratio 0.74, 95% CI 0.56-0.989, P=0.041).54\n\nThe ROC curve on MACE events for variable endothelin-1 levels as a predictor resulted in an AUC value of 0.785 with an accuracy rate of 76.5% in our study, which showed that endothelin-1 can act as a predictor for major cardiovascular events within 1 year. Diagnostic test research will be improved if the AUC value is close to 1. Criteria for interpreting the AUC value are as follows: >0.5-0.6 = very weak, >0.6-0.7 = weak, >0.7-0.8 = moderate, >0.8-0.9 = good, >0.9-1 = very good. The following criteria are used to interpret the accuracy score categories: 50-60% is very weak, 60-70% is weak, 70-80% is medium, 80-90% is strong, and 90-100% is very strong.55 This can be interpreted to mean that endothelin-1 levels can detect the occurrence of MACE in patients with CCS after a 1-year follow-up.\n\nThe limitations of this study were that it was only conducted in one center, and two patients were not routinely monitored for evaluation, due to busyness of the patients, insurance issues, or geography. Thus, the follow-up of patients cannot be fully monitored properly. Another limitation of this study is the small sample size, which is clearly insufficient to accurately describe the situation.56–57\n\n\nConclusion\n\nEndothelin-1 can be a predictor of major adverse cardiovascular events within 1 year in patients with CCS who had coronary intervention.", "appendix": "Data availability\n\nData are not able to be made publicly available due to the hospital’s confidentiality and patient privacy policies. Readers and reviewers who wish to access the data (underlying source data and analysis software output) should contact the corresponding author (trisulo.wasyanto@staff.uns.ac.id).\n\n\nAcknowledgements\n\nWe would like to thank to Dr. Moewardi Hospital for giving permission to collect the data.\n\n\nReference\n\nZipes DP, Libby P, Bonow RO, et al.: A Textbook of Cardiovascular Medicine. 11th ed. Elsevier Inc; 2018.\n\nNaz A, Billah M: COVID-19 and Coronary Heart Disease. Encyclopedia. 2021; 1(2): 340–349. 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "174144", "date": "09 Jun 2023", "name": "Ahmed Shawky Elserafy", "expertise": [ "Reviewer Expertise Cardiology" ], "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\nVery nice manuscript actually and a sound hypothesis.\nThe introduction is clear; however, I would remove the word “earlier DES (bare metal stent)” and just keep it bare metal stents.\nThe methods were constructive but when comparing the patients that had a MACE to the non-MACE group was very faulty as the numbers are not close enough for a statistical analysis.\nThe results were clearly presented; however, the amount of contrast, number of balloon dilatations, stents are not included which can increase inflammation and increase mortality. Also, what is the reason for some of the patients being transferred to the CCU? Were they including those who suffered a MACE? What was the LVEF comparison between the two groups? Most literature don’t classify occurrence of heart failure as MACE. Why did you do that? And when did the MACE occur in those 6 patients? Very early on or later?\nThe manuscript is a good idea with a clear hypothesis and constructed in a very good manner and minor language and grammar mistakes. I would recommend extensive revision before accepting this manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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?\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": "9854", "date": "06 Jul 2023", "name": "Trisulo Wasyanto", "role": "Author Response", "response": "Responses (1) AUTHOR RESPONSE Comment 1 The introduction is clear; however, I would remove the word “earlier DES (bare metal stent)” and just keep it bare metal stents. Response 1: Thanks so much for the comments. We revise it according to your suggestion. Comment 2 The methods were constructive but when comparing the patients that had a MACE to the non-MACE group was very faulty as the numbers are not close enough for a statistical analysis. The results were clearly presented; however, the amount of contrast, number of balloon dilatations, stents are not included which can increase inflammation and increase mortality. Also, what is the reason for some of the patients being transferred to the CCU? Were they including those who suffered a MACE? What was the LVEF comparison between the two groups? Most literature don’t classify occurrence of heart failure as MACE. Why did you do that? And when did the MACE occur in those 6 patients? Very early on or later? Response 2: Thanks so much for the comments. The objective of this research was to prove endothelin- 1 as predictor of MACE within 1-year evaluation in CCS patients undergoing PCI. So our study was to see the occurrence of MACE in CCS patients who underwent PCI and was associated with high endothelin 1 levels (≥4.07) compared to low endothelin 1 levels (<4.07), from various clinical variables such as demographic variables and accompanying risk factors. Some patients after procedures are transferred to the CCU due to complex procedures involving intervention of more than or equal to 2 coronary arteries, or there are periprocedural complications. They are not included in the MACE category in our study. MACE or Major Adverse Cardiovascular Event is a major cardiovascular event that is commonly used as a composite outcome of observational studies. Various definitions of MACE show different components in each study. Based on several studies, some defined MACE into 3, 4, or 5 components. From all studies, it can be concluded that the most commonly found components are acute myocardial infarction, stroke, and death. In addition, there are some studies that include heart failure as a component of MACE. According to AHA (American Heart Association), MACE is defined as a composite of all causes of death; myocardial infarction, stroke, heart failure requiring hospitalization and revascularization, including percutaneous coronary intervention or coronary artery bypass graft. We included heart failure as an indication for hospitalization as it occurred in the sample population referring to several literatures. MACE may occur in the late phase, or during outpatient. We compare LVEF on the incidence of MACE (+) and MACE (-) with no significant difference in the result and these are added to Table 2 (to view this table please open the link below). https://tinyurl.com/table2research" } ] }, { "id": "181207", "date": "26 Jun 2023", "name": "Josip A Borovac", "expertise": [ "Reviewer Expertise Acute coronary syndrome", "heart failure", "interventional cardiology" ], "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 Abstract section, authors present data on ROC curve and provide sensitivity and specificity info, however, they do not make explicit statement to what does this sensitivity and specificity refer to. It might be implicative this is MACE, however, that should be clearly stated.\n\nThe number of patients examined is low, as well as the number of events – only six patients experienced MACE. Do the authors think this is enough to provide validity in their observations? This is a major limitation to this study.\n\nI am not sure that endothelin-1 as a biomarker is able to detect MACE within 1-year follow-up, this is not substantiated with data – number of events was extremely low.\n\nPredictive value of endothelin-1 for these purposes is even more burdened by the heterogeneity of events contained within the MACE outcome – so what does the endothelin-1 measure? Two patients had AMI, one patient had heart failure, and two death events. Even if the endothelin-1 was predictive of adverse events, we do not know for which one. Similarly, this would challenge the pathophysiology of these events and authors would need to make a significant burden of proof to show how would this pathophysiologically relate to the events.\n\nAgain diagnostic power of this test cannot be substantiated at the event rate of 6 patients – with such a low number of events, albeit, so heterogeneous as well, statisticall associations might be due to chance.\n\nAuthor state that this was a prospective cohort study, how did they come up with such a sample size? Did they perform any a-priori testing of the study size and sample size. This needs to be thoroughly elaborated since it is important from methodological standpoint.\n\nExact timing on when endothelin-1 levels were sampled needs to be provided.\n\nSimilarly, why before PCI and why not after PCI sampling – authors would need to provide sound rationale for this.\n\nDid any of the patients in your study had CTO? This needs to be disclosed.\n\nWhat about other biomarkers measured in this cohort? Why no examination of association of endothelin-1 with troponin or NT-proBNP?\n\nPeriprocedural and stenting dana would need to be provided – we only have information on stented vessel number distribution.\n\nPlease change \"ureum\" to \"urea\" in the table.\n\nSince authors followed and monitored patients for 1-year pharmacotherapy at discharge is a very potent and important modifier of outcomes. Authors did not provide any information on post-discharge pharmacotherapy which is a major limitation of these results. Even more, authors mentioned good compliance of patients as one of the potential reason of having low MACE, however, they provide no specificities of such treatment.\n\nWhat were indications to revascularize these patients? We need to know more on who were these patients and why was revascularization initiated.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "9855", "date": "06 Jul 2023", "name": "Trisulo Wasyanto", "role": "Author Response", "response": "Responses (2) AUTHOR RESPONSE Comment 1 In the Abstract section, authors present data on ROC curve and provide sensitivity and specificity info, however, they do not make explicit statement to what does this sensitivity and specificity refer to. It might be implicative this is MACE, however, that should be clearly stated. Responses 1 Thank you, you are right. This is indeed the sensitivity, specificity and accuracy of the MACE based on the ROC curve. We have confirmed this in the abstract. Comment 2 The number of patients examined is low, as well as the number of events – only six patients experienced MACE. Do the authors think this is enough to provide validity in their observations? This is a major limitation to this study. I am not sure that endothelin-1 as a biomarker is able to detect MACE within 1-year follow-up, this is not substantiated with data – number of events was extremely low. Response 2 Our study met the minimum sample size required to make the results valid. Sample size was calculated using Open Epi Version 3 software to calculate sample size in a test that compared two means with reference literature for differentiation and standard deviation of groups 1 and 2 according to a previous study by Abdelrazek et al., 2020. Comment 3 Predictive value of endothelin-1 for these purposes is even more burdened by the heterogeneity of events contained within the MACE outcome – so what does the endothelin-1 measure? Two patients had AMI, one patient had heart failure, and two death events. Even if the endothelin-1 was predictive of adverse events, we do not know for which one. Similarly, this would challenge the pathophysiology of these events and authors would need to make a significant burden of proof to show how would this pathophysiologically relate to the events. Again diagnostic power of this test cannot be substantiated at the event rate of 6 patients – with such a low number of events, albeit, so heterogeneous as well, statistical associations might be due to chance. Response 3 In one study, endothelin-1 levels were associated with major cardiovascular events in coronary heart disease (CHD) patients who were not revascularized. Increased endothelin-1 causes vasoconstriction and decreases coronary blood flow thereby causing and exacerbating myocardial ischemia. In another study, it showed that endothelin-1 production increased in conditions where there was atherosclerotic plaque in the coronary arteries. Endothelin-1 release stimulates smooth muscle cell proliferation in a paracrine or autocrine manner, thereby contributing to the development of coronary artery disease. Endothelin-1 originates from endothelial cells and according to several studies, is associated with endothelial dysfunction. Endothelial dysfunction has been reported as an atherosclerotic risk factor associated with future cardiovascular events. Therefore, endothelin has been considered as a proinflammatory factor. Endothelin-1 acts as a vasoconstrictor which plays a role in increasing atherosclerotic coronary artery tone. Endothelin-1 is involved in endothelial dysfunction, inflammation, and vascular remodeling. Comment 4 Author state that this was a prospective cohort study, how did they come up with such a sample size? Did they perform any a-priori testing of the study size and sample size. This needs to be thoroughly elaborated since it is important from methodological standpoint. Response 4 Sample size was calculated using Open Epi software version 3 to calculate the sample size in a test that compared two means with reference sources for differentiation and standard deviation of groups 1 and 2 according to a previous study by Abdelrazek et al., 2020. Comment 5 Exact timing on when endothelin-1 levels were sampled needs to be provided. Similarly, why before PCI and why not after PCI sampling – authors would need to provide sound rationale for this. Response 5 Blood samples were taken when the sample population met the inclusion criteria and before coronary angiography was performed. Because endothelin 1 is a biomarker that detects pro-inflammatory factors, blood sampling after PCI would confound the study results. Comment 6 Did any of the patients in your study had CTO? This needs to be disclosed. Response 6 In our study none of the patients had CTO. OK, we will include this in the manuscript. Since none of the patients had CTO, this may have resulted in a low MACE. Comment 7 What about other biomarkers measured in this cohort? Why no examination of association of endothelin-1 with troponin or NT-proBNP? Response 7 The aim of this study is to prove that endothelin-1 can act as a new predictor of MACE within 1 year in CCS patients undergoing coronary intervention. Due to cost and insurance limitations, we did not compare endothelin 1 and other cardiac biomarkers. Comment 8 Periprocedural and stenting dana would need to be provided – we only have information on stented vessel number distribution. Response 8 The patient underwent PCI with stent implantation using DES according to the size of the blocked coronary artery. Comment 9 Please change \"ureum\" to \"urea\" in the table 1. Response 9 Thank you, we've changed it to urea in Table 1. Comment 10 Since authors followed and monitored patients for 1-year pharmacotherapy at discharge is a very potent and important modifier of outcomes. Authors did not provide any information on post-discharge pharmacotherapy which is a major limitation of these results. Even more, authors mentioned good compliance of patients as one of the potential reason of having low MACE, however, they provide no specificities of such treatment. Response 10 All patients have been educated for control and come to our heart polyclinic every month. Patient compliance with taking medication at home is one of the factors we cannot control. This is one of the limitations of the research. Patients are treated with standard drugs according to Guideline Directed Medical Therapy, namely in the form of double antiplatelet, Beta blockers, ACE inhibitors or Angiotensin receptor blockers, and MRA as indicated. Comment 11 What were indications to revascularize these patients? We need to know more on who were these patients and why was revascularization initiated. Response 11 1. Patients with suspected CHD, symptoms of stable angina and/or dyspnea. 2. Patients with new heart failure, left ventricular dysfunction, and suspected CHD. 3. Patients with or without symptoms, stable condition of duration <1 year after the incident ACS. 4. Asymptomatic subjects, where CHD is detected on examination." } ] } ]	1	https://f1000research.com/articles/12-342
https://f1000research.com/articles/12-783/v1	05 Jul 23	{ "type": "Research Article", "title": "Determinants of fruit consumption in adult women in Indonesia", "authors": [ "Ibnu Malkan Bakhrul Ilmi", "Muhammad Nur Hasan Syah", "Utami Wahyuningsih", "Yessi Crosita Octaria", "Muhammad Nur Hasan Syah", "Utami Wahyuningsih", "Yessi Crosita Octaria" ], "abstract": "Background: Fruit consumption in Indonesia is low, while diet related diseases are climbing, including among adult women where obesity prevalence is the highest. This study aimed to analyze determinants of fruit consumption among adult women aged 19–49 years in the country. Methods: Analysis was done to secondary data on food consumption obtained from a cross sectional survey of the national Basic Health Research 2010. The potential determinants analyzed were nutritional status (body mass index, BMI), age, formal education, marital status, economic status (quintile), and region. The logistic regression model was applied. Results: The results showed that adult women in Indonesia had higher odds of consuming more fruits if they were with higher BMI (OR BMI > 25=1.093, CI:1.026–1.165), in the older age group (OR middle-aged adult=1.079, CI:1.013–1.150), had higher educational status (OR completed elementary School or higher=2.070, CI:1.909–2.244), from higher economic status (OR high=2.258, CI:2.112–2.413), and resided in urban regions (OR urban area=1.305, CI:1.230–1.385). Meanwhile, being married appeared to hinder fruit consumption (OR=0.915, CI:0.849–0.986). Conclusions: Fruit consumption among adult women in Indonesia showed disparities between socioeconomic and sociodemographic characteristics. Thus intervention to improve fruit consumption should involve improving nutritional knowledge, especially among those with lower level of consumption (e.g married women), as well as improving access and availability of fruit for women from lower socioeconomic status and rural areas. This could include the use of locally available fruits that is less expensive and more accessible.", "keywords": [ "Adult", "Consumption", "Fruit", "Risk Factor", "Women" ], "content": "Introduction\n\nEasy access and advanced information push modern society to lead a life that dominantly involves mild activities and consume fast food with high fat, sugar, salt, and low fiber (WHO, 2002). Based on WHO review (2021), such meal plans increase the risk of having obesity and non-infection diseases.\n\nIn Indonesia, the prevalence of obesity is considerably high, especially for adult women. In 2010, the prevalence percentage of adult women with obesity presented 15.4% (Ministry of Health, 2010) and considered higher numbers in 2013 with 32.9% (Ministry of Health, 2013). Obesity prevalence is higher in urban areas compared to rural areas, and the number of women affected by obesity is higher compared to their male counterparts (Ministry of Health, 2013). Based on the WHO report (2020), 73% of deaths in Indonesia happen due to non-infectious diseases. One of the non-infectious diseases that contribute to the highest numbers of death in Indonesia is diabetes mellitus (DM), according to the Ministry of Health of Indonesia (2020). Diabetes mellitus can happen to anyone, though the higher risk applies from adults to elders, and can reduce life expectancy (Magliano et al., 2018). Diabetes mellitus can also affect workers’ productivity, as workers who have diabetes mellitus have lower productivity than those who do not (Tabano et al., 2018). Diabetes mellitus can consecutively decrease the productivity-adjusted life years (PALY) for 11.6% in men and 10.5% in women (Magliano et al., 2018). Also, based on the American Diabetes Association (2018), workers who have diabetes mellitus have higher cost burdens. Diabetes economic cost in the US based on the calculation from direct medical costs and reduced productivity costs, increased by 26% in 5 years (2012–2017) due to the increased prevalence of diabetes mellitus.\n\nTo prevent obesity and non-infectious diseases, consuming a sufficient quantity of fruits helps. Fruits are good to avoid weight gain (Bes-Rastrollo et al., 2006) and helps to reduce blood low-density lipoprotein cholesterol (Djoussé et al., 2004), chronic disease risks (Riboli and Norat, 2003), cardiovascular disease risks (Dauchet et al., 2006), cancer risks (Pavia et al., 2006; Boffetta et al., 2010), and help to enhance women’s bone health (McGartland et al., 2004).\n\nAccording to WHO (2003) and Ministry of Health Republic Indonesia (2014), the advised balanced nutrition guide to consuming fruits and vegetables is 400 grams/person/day. Among those numbers, 150 grams are fruits. In general, fruits contain phytonutrients, potassium, and fibers that help fight against non-infectious chronic diseases (WHO, 2003). On the other hand, having less than five portions of fruits and vegetables per day affects a higher rate of deaths (Bellavia, 2013). In Indonesia, as much as 93.6% of the population aged 10 years old or more have fruits and vegetable consumption deficiency (Ministry of Health, 2007). There are many factors that determine a person’s consumption of fruit, including: sensory factors, social interactions, fruit price, time, personal principles, media and health advertising (Pollard et al., 2003).\n\nSo far, there has been no national-scale research that analyzes determinants of fruit consumption in Indonesia for adult women, a socio-demographic with the highest prevalence of obesity in Indonesia. Thus, this research aims to analyze the determinants of fruit consumption for adult people aged from 19–49 years old.\n\n\nMethods\n\nThis research uses secondary data from Basic Health Research 2010, collected by Health Research and Development Agency, Ministry of Health, Republic of Indonesia. Basic Health Research 2010 uses a cross-sectional study design. Data has been collected from May 2010 to August 2010 by professionals. This analysis of research of fruit determinant factors was conducted from May 2021 to June 2021 in Universitas Pembangunan Nasional (UPN) Veteran Jakarta. This study was approved by Ethical Approval Involving Human Respondents Universitas Pembangunan Nasionan UPN Veteran Jakarta (Protocol number: 02/UN61/PT.01.06/2021).\n\nThis research follows Basic Health Research 2010 method to collect sampling numbers and methods. The Basic Health Research data collected in 2010 comes from 441 regions/cities among 33 provinces. The numbers of households were 69,300, the number of household members were 251,388, and the number of women aged 19–49 years old were 54,178. The cleaning of data was conducted by eliminating subjects that have no height data (143 people), weight data (135 people), food consumption data (228 people), and pregnancy status data (466 people). We eliminated subjects with calorie intakes numbers of <0.3 and >0.3 times to basal energy (536 people), nutrients adequacy of >400% (635 people), body mass index (BMI) of <12.5 and BMI of >40 (123 people) and unusual consumption (1292 people). The total subjects were 50,620 adult women.\n\nFrom the Basic Health Research e-file in 2010, the collected data consists of individual characteristics, economic status characteristics, anthropometric, and food consumption. The individual characteristic data consists of age, origin, education, and jobs. The anthropometric data uses weight and height. The food consumption data uses fruits types and numbers of consumed fruits.\n\nData processing was conducted after data cleaning. The cleaned data was used to calculate the total grams of fruit consumption and to create new variables or derivatives. The bivariate analysis uses the chi-square test to see the correlations of food consumption level to nutritional status, education, region, jobs, and economic status. The overview of the variables and their descriptions are presented in Table 1, and t test used for calculating the average gram per capita per day in fruit consumption and the difference between groups.\n\nThe cutoff point used for fruits was 75 g/day or half of fruit consumption recommendation based on balanced nutrients guidelines (150 g/day). This was because the average number of fruit consumption in Indonesia only reaches up to 76.4 g/day (Ministry of Health, 2010). Thus, to analyze the cut-off point, the number of recommended consumptions should be lowered to half point. The multiple logistic regression analysis was used to know the determinant factors of fruit consumption in adult women. All data cleaning and statistical analysis were done using the IBM SPSS version 17. The multiple regression model applied in the research is shown below:\n\n\nResults and discussion\n\nThe analysis results show that the number of adult women in Indonesia who consume less than half of the fruit consumption recommendation reaches 88%. Socioeconomic characteristic consists of nutritional status, age, education, marital status, jobs, economic status, and region type as shown in Table 2.\n\n* Chi Square test sig<0.05.\n\nTable 2 shows that women with BMI<25 tend to consume fruits less than 75 g/day (65.4% of all women). Both young adults (32.6% of all women) and middle-aged women (56.5% of all women) tend to consume fruits less than 75 g/day. This showed that fruits consumption in women in Indonesia is low. In addition, women who have elementary school education (82.7% of all women) and are married (72.5% of all women) tend to consume fruits less than 75 g/day. Higher percentage of women who are employed (6.4% of all women) consume more than 75 g/day of fruit compared to only 4.5% of all women among women who are unemployed. More women who are coming from the upper middle-income bracket and those living in urban areas consume fruits more than 75 g/day.\n\nAs it was mentioned earlier, the average number of fruit consumption in Indonesia only reaches up to 76.4 g/day (Ministry of Health, 2010). This average consumption per capita is even lower among adult women, which was only around 23 g/day. The t test results presented in Table 3 showed that all socio demographic characteristics significantly correlated to total average consumption of fruit per capita per day. Total average consumption of fruit among women with BMI>25 kg/m2, older women aged 30–49 years old, women with higher education of elementary school or higher, women who are single and employed, women coming from upper middle quintile of income bracket as well as women living in urban areas all show significantly higher average of fruit consumption per capita per day. Sadly, despite fruit consumption being significantly higher among these sociodemographic groups, the total average was very low compared to the national recommendation of 150 g/day and only one third of the national average of fruit consumption which is around 76 g/day. In addition, the calculation also showed very high standard deviation. Thus, caution should be applied in reading the result which indicates low consumption and large disparities.\n\n* T-Test sig<0.05.\n\nMultiple logistic regression results showed (Table 4) that adult women in Indonesia had higher odds of consuming more fruits if they were with higher BMI (OR BMI>25=1.093, CI: 1.026–1.165), in the older age group (OR middle-aged adult=1.079, CI: 1.013–1.150), had higher educational status (OR completed elementary School or higher=2.070, CI: 1.909–2.244), from higher economic status (OR high=2.258, CI: 2.112–2.413), and residing in urban regions (OR urban area=1.305, CI: 1.230–1.385). Meanwhile, being married appeared to hinder fruits consumption (OR=0.915, CI: 0.849–0.986).\n\n* Significant (p<0.05).\n\nOur findings showed a similar picture in comparison to previous studies regarding the topic. In the USA, a study on consumption pattern among different socioeconomic groups and demographics showed that consumption of fruit and fruit juices are higher among more affluent communities and among those with active lifestyles (Deshmukh-Taskar et al., 2007). Regarding the correlation between education level and fruit consumption, it is assumed that people with higher education levels have better knowledge and awareness to consume healthier foods (Elfhag, 2008). Having a good understanding of nutrition significantly relates to fruit and vegetable consumption (Wardle, Parmenter & Waller, 2000). On the other hand, an individual with lower education may be less likely to consume fruit every day (Giskes et al., 2008) which affects low fruit and vegetable consumption (Darmon & Drewnowski, 2008). The research result of Dynesen et al. (2003) shows that adult women with higher education levels and those who live with two members at the house both have higher frequencies of consuming fruits.\n\nIn contrast to reviews from Ab Karim et al. (2012) which shows that marital status has a significant and positive impact on fruit and vegetable consumption, our study showed the opposite where being single was correlated with significantly higher fruit intake. Married people tend to have a higher income than those who are single or those who are unmarried (Friel et al., 2005). Research by Pollard et al. (2001) shows that being married and having smaller number of members living in one house share a positive impact on fruit consumption level, while the mixed result are shown with children. In our case, it is likely that importance of body image and higher agency of choosing better diet may contribute to the higher intake of fruits among unmarried adult women in Indonesia.\n\nThe multivariate test result shows that job status is not significant as fruit consumption determinants. The research result from Shohaimi (2004) shows there are strong and independent relations between a social class of work and education level to fruit consumption. Women from lower working social class and have less educational background have less fruit consumption. These findings link to higher awareness of the benefits of consuming fruits (McIntosh et al., 1990). The effect of peer pressure in the workplace are considered non-significant (Shohaimi, 2004).\n\nOur findings show that in adult women with low economic status, the fruit consumption level is lower than upper-middle-class women. This is in line with research on adolescents (Riediger et al., 2007). Both populations in the USA (Rose & Richards, 2004) and Canada (Riediger et al., 2007) show that higher family economic status showed higher fruit and vegetable diet than those with lower economic status. People with lower economic status tend to spend their income for basic needs than for fruits and vegetables, as may be considered as non-beneficial products (Ab Karim et al., 2012). Research in the UK also shows that fruit and vegetable consumption or healthy food in general are considered costly (Thompson, 2008). Based on research held by WHO (2005), the cost of fruits and vegetables had a negative impact on the consumption of fruits for both people with higher and lower incomes. In line with this, Indonesia has similar condition, as a case study from Hartini et al. (2003) shows that fruit consumption in women in urban areas are higher than in women in rural areas. Thus, systematic education and transformation in the food system to change this point of view is needed.\n\nResiding area types also influence the consumption of fruits. Our study found that women who live in rural areas have lower levels of consumption than those who live in urban areas. Gustafson et al. (2007) reports that there are different numbers of fruit and vegetable consumption between people who live in rural areas to urban areas. This is also related to different job statues and workloads from both areas (Devine et al., 2003), despite the assumption that in urban areas, the probabilities of increased price impact to low demand, the availability and accessibility to various type of fruits may result in increased consumption (WHO, 2005).\n\nThis research used a cross-sectional study from the Basic Health Research 2010, collected by Health Research and Development Agency of the Ministry of Health of Indonesia, and has limited views to differentiate cause and effects in variables. Furthermore, it used 24 hours recall calculating data about food consumption, which gives less detailed food consumption habits. However, this research generally shows results that are in line with other previous works.\n\n\nConclusions and suggestions\n\nThe study examined the determinants of fruit consumption among adult women in Indonesia. The finding revealed that fruit consumption among adult women in Indonesia remains low, with nutritional status, age, education level, and income as the determinants of adequate fruit consumption. Based on this research, fruit consumption can elevate in several ways. This includes upgrading information related to nutrition and improving the availability of fruits in each area at an affordable price. Health promotion interventions to scale up fruit consumption should pay attention to the factors identified in this study. The results of this study are expected to provide input to existing government policies. The Indonesian government so far has had guidelines for fruit consumption for the community, but it must continue to be socialized regarding this matter in increasing fruit consumption. Further research is necessary to analyze other determinant factors related to fruit consumption.", "appendix": "Data availability\n\nThe data of this study are from the Indonesian Ministry of Health. The data can be obtained trough the following process:\n\n1. Submit an application and proposal to the Indonesian Ministry of Health Balitbangkes (https://www.badankebijakan.kemkes.go.id/)\n\n2. Assessment of proposals by the data owner of the Indonesian Ministry of Health’s Balitbangkes\n\n3. If approved, raw data are given according to what is needed in the research\n\n4. Authors are required to sign disclaimer which prohibits data sharing by data owner (Indonesian Ministry of Health Balitbangkes) and only allowed to share results of analysis\n\n\nAcknowledgements\n\nWe thank Arini Nurul Fikri who has supported accessing and processing data and the Ministry of Health, Republic of Indonesia for data support.\n\n\nReferences\n\nAb Karim MS, Othman KI, Karim R, et al.: Factors influencing fruits and vegetables consumption behaviour among adults in malaysia. J. Agric. Mark. 2012; 5: 29–46. Faculty of Food Science and Technology, Universiti Putra Malaysia.\n\nAssociation AD: Economic costs of diabetes in the US in 2017. Diabetes Care. 2018; 41: 917–928. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBes-Rastrollo M, Sánchez-Villegas A, Gomez-Gracia E, et al.: Predictors of weight gain in a Mediterranean cohort: the Seguimiento Universidad de Navarra. Am. J. Clin. Nutr. 2006; 83: 362–370. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDevine CM, Connors MM, Sobal J, et al.: Sandwiching it in: spillover of work onto food choices and family roles in low- and moderateincome urban households. Soc. Sci. Med. 2003; 56(3): 617–630. PubMed Abstract \| Publisher Full Text\n\nDynesen AW, Haraldsdottir J, Holm L, et al.: Sociodemographic differences in dietary habits described by food frequency questions—results from Denmark. Eur. J. Clin. Nutr. 2003; 57(12): 1586–1597. PubMed Abstract \| Publisher Full Text\n\nElfhag K, Tholin S, Rasmussen F: Consumption of fruit, vegetables, sweets and soft drinks are associated with psychological dimensions of eating behaviour in parents and their 12-year-old children. Public Health Nutr. 2008 Sep; 11(9): 914–923. PubMed Abstract \| Publisher Full Text\n\nFriel S, Newell J, Kelleher C: Who eats four or more servings of fruits and vegetables per day? Multivariate classifications tree analysis of data from 1998 survey of lifestyle, attitudes and nutrition in the Republic of Ireland. Public Health Nutr. 2005; 8: 159–169. PubMed Abstract \| Publisher Full Text\n\nGiskes K, van Lenthe VJ , Kamphuis CBM, et al.: Household and food shopping environments: do they play a role in socioeconomic inequalities in fruit and vegetable consumption? A multilevel study among Dutch adults. J. Epidemiol. Community Health. 2008; 63; 113–120. 2009.\n\nGustafson A, Cavallo D, Paxton A: Linking homegrown and locally produced fruits and vegetables to improving access and intake in communities through policy and environmental change. J. Am. Diet. Assoc. 2007; 107(4): 584–585. PubMed Abstract \| Publisher Full Text\n\nHartini TNS, Winkvist A, Lindholm L, et al.: Food patterns during an economic crisis among pregnant women in Purworejo District, Central Java, Indonesia. Food Nutr. Bull. 2003; 24(3): 256–267. PubMed Abstract \| Publisher Full Text\n\nLautenschlager L, Smith C: Understanding gardening and dietary habits among youth garden program participants using the Theory of Planned Behavior. Appetite. 2007; 49(1): 122–130. PubMed Abstract \| Publisher Full Text\n\nLuc Djoussé, Arnett DK, Coon H, et al.: Fruit and vegetable consumption and LDL cholesterol: the National Heart, Lung, and Blood Institute Family Heart Study. Am. J. Clin. Nutr. 2004; 79: 213–217. PubMed Abstract \| Publisher Full Text\n\nMagliano DJ, Martin VJ, Owen AJ, et al.: The productivity burden of diabetes at a population level. Diabetes Care. 2018; 41: 979–984. PubMed Abstract \| Publisher Full Text\n\nMcGartland CP, Robson PJ, Murray LJ, et al.: Fruit and vegetable consumption and bone mineral density: the Northern Ireland Young Hearts Project. Am. J. Clin. Nutr. 2004; 80: 1019–1023. PubMed Abstract \| Publisher Full Text\n\nMcIntosh WA, Kubena KS, Walker J: The relationship between beliefs about nutrition and dietary practices of the elderly. J. Am. Diet. Assoc. 1990; 90: 671–676. Publisher Full Text\n\nMinistry of Health: Riset Kesehatan Dasar. Indonesia: Badan Penelitian dan Pengembangan Kesehatan; 2007.\n\nMinistry of Health: Riset Kesehatan Dasar. Indonesia: Badan Penelitian dan Pengembangan Kesehatan; 2010.\n\nMinistry of Health: Riset Kesehatan Dasar. Indonesia: Badan Penelitian dan Pengembangan Kesehatan; 2013.\n\nMinistry of Health: Penyakit Tidak Menular Kini Ancam Usia Muda. 2020. Reference Source\n\nPavia M, Pileggi C, Nobile CG, et al.: Association between fruit and vegetable consumption and oral cancer: a meta-analysis of observational studies. Am. J. Clin. Nutr. 2006; 83: 1126–1134. Publisher Full Text\n\nPollard J, Greenwood D, Kirk S, et al.: Lifestyle factors affecting fruit and vegetable consumption in the UK Women’s Cohort Study. Appetite. 2001; 37: 71–79. PubMed Abstract \| Publisher Full Text\n\nPollard J, Kirk SL, Cade JE: Factors affecting food choice in relation to fruit and vegetable intake: a review. Nutr. Res. Rev. 2003; 15(2): 373–387. Publisher Full Text\n\nRiboli E, Norat T: Epidemiologic evidence of the protective effect of fruit and vegetables on cancer risk. Am. J. Clin. Nutr. 2003; 78: 559S–569S. Publisher Full Text\n\nRiediger ND, Shooshtari S, Moghadasian MH: The influence of sociodemographic factors on patterns of fruit and vegetable consumption in Canadian adolescents. J. Am. Diet. Assoc. 2007; 107: 1511–1518. PubMed Abstract \| Publisher Full Text\n\nRose D, Richards R: Food store access and household fruit and vegetable use among participants in the US Food Stamp Program. Public Health Nutr. 2004; 7: 1081–1088. PubMed Abstract \| Publisher Full Text\n\nTabano DC, Anderson ML, Ritzwoller DP, et al.: Estimating the impact of diabetes mellitus on worker productivity using self-report, electronic health record and human resource data. J. Occup. Environ. Med. 2018; 60: e569–e574. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShohaimi S, Welch A, Bingham S, et al.: Residential area deprivation predicts fruit and vegetable consumption independently of individual educational level and occupational social class: a cross sectional population study in the Norfolk cohort of the European Prospective Investigation into Cancer (EPIC-Norfolk). J. Epidemiol. Community Health. 2004; 58: 686–691. PubMed Abstract \| Publisher Full Text\n\nThompson J: Health Survey for England 2007 Knowledge, attitudes and behaviours. Vol. 2008. . London: NHS Information Centre; 2008; pp. 107–148.\n\nWardle J, Parmenter K, Waller J: Nutrition knowledge and food intake. Appetite. 2000; 34(3): 269–275. Publisher Full Text\n\n[WHO] World Health Organization: Globalization, Diets and Noncommunicable Diseases. Geneva: World Health Organization; 2002.\n\n[WHO] World Health Organization: Diet, nutrition and the prevention of chronic diseases: report of a joint WHO/FAO expert consultation. Geneva: World Health Organization; 2003.\n\n[WHO] World Health Organization: Effectiveness of interventions and programmes promoting fruit and vegetable intake. Geneva, Switzerland: WHO; 2005.\n\n[WHO] World Health Organization: Obesity and overweight.update article 9 June 2021. Reference Source\n\n[WHO] World Health Organization: Noncommunicable diseases progress monitor 2020. Geneva: 2020." }	[ { "id": "184683", "date": "11 Jul 2023", "name": "Al Mukhlas Fikri", "expertise": [ "Reviewer Expertise Food and Nutrition" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 analyzed and found an interesting result using a huge data from national study. However, several points below must be clarified before its indexing:\n\nThe used data were from a survey in 2010. It is too old.\n\nAbstract must consist of the number of involved subjects.\n\nSeveral presented data in introduction are also too old.\n\nIntroduction does not include the reasons of why this study evaluated on adult women.\n\nPlease provide some literature supporting your speculation regarding the reason for unmarried women having higher fruit consumption.\n\nPlease also provide the reason why women who live in rural have lower levels of consumption. The reason of the result of BMI correlation with fruit consumption also needs to be discussed.\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": "226104", "date": "18 Dec 2023", "name": "Rian Diana", "expertise": [ "Reviewer Expertise Community Nutrition" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nComments to authors:\nTitle: This study analyzed socioeconomic factors as determinants of fruit consumption. Therefore, a more specific title would be more appropriate. It is advisable to use references from the last three to five years due to the abundance of relevant studies conducted in low, middle, and high-income countries. Introduction:\nIn the introduction, it would be helpful to include information about global fruit consumption, particularly in low and middle-income countries. Comparing Indonesia's situation to these nations can provide insight into the current scenario. This comparison helps readers understand that the issue of low fruit consumption is widespread, affecting numerous countries, including Indonesia. Low fruit and vegetable intake is a risk factor for non-communicable diseases. This study, in particular, emphasizes fruit consumption. Hence, it is imperative to provide a robust rationale for the exclusive focus on fruit consumption in this investigation\n\nResults & Discussion:\nIn the methods section, it is explicitly indicated that fruit consumption was acquired via a 24-hour recall. As a result, this investigation allows delineating details regarding the specific fruits (fruits types) commonly consumed in dietary practices, thereby allowing the manuscript to provide a more comprehensive understanding of the quantity and predominant varieties of fruits ingested by adult women. This, in turn, facilitates a nuanced examination of nutritional compositions and underpins strategies aimed at fostering fruit consumption that is more attuned to the preferences and socioeconomic conditions of adult women. Please provide information on the prevalence of adequate fruit consumption (150 g/day) among adult women, followed by the prevalence of half of the recommended intake (75 g/day), to emphasize the magnitude of the issue. Table 3 shows a standard deviation exceeding the mean, signifying a non-normal distribution of the data. Therefore, the use of parametric statistics is considered unsuitable for this dataset. It is advisable to consider employing non-parametric methods when presenting results and conducting inferential analysis. Please check the decimal numbers. The total percentage should be 100%, but several data points do not sum up to 100%, including nutritional status (99%), age (100.1%), education, etc. When presenting a p-value of 0.000, it should be expressed as p < 0.001. Please provide information on how fruit consumption could benefit adult women. Specifically, elaborate on the nutritional content of fruits that can confer these benefits, especially in preventing non-communicable diseases as mentioned in the introduction. Kindly provide a comprehensive discussion of the association between fruit consumption and factors, including income, education, urban residency, marital status, and BMI. Consider these factors comprehensively rather than as individual components. Additionally, explore whether income and educational attainment demonstrate a more robust correlation or serve as the main predictors for fruit consumption when contrasted with other socioeconomic variables.\n\nStrength and limitation. This study utilizes data from the 2010 Basic Health Survey, which was conducted 13 years ago. Therefore, it is necessary to address the strengths and limitations of the study and explain why this data was chosen. Is the current situation still relevant? Are there no more recent data available for use, Conclusions & suggestions: Low fruit consumption was identified in this study. Please rephrase the implications to align with the findings. How can the government develop strategies to increase fruit consumption among adult women? Which characteristics of adult women need enhancement to increase their fruit consumption?\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-783
https://f1000research.com/articles/9-759/v1	22 Jul 20	{ "type": "Research Article", "title": "Intensive care nurses' knowledge of enteral nutrition at public hospitals in Sana'a, Yemen: a cross-sectional survey", "authors": [ "Talal Ali Hussein Al-Qalah", "Gamil Ghaleb Alrubaiee", "Talal Ali Hussein Al-Qalah" ], "abstract": "Background: Nurses have a pivotal role in initiating and managing enteral nutrition (EN) and monitoring any potential complications. Yet, it is unclear whether Yemeni nurses have adequate knowledge to deliver and manage enteral nutrition safely. Therefore, the aim of this study was to assess the level of ICU nurses’ knowledge regarding the management of EN. Methods: A descriptive cross-sectional study was conducted from February 2019 to March 2019. A probability sampling method was used to recruit 174 nurses from four public hospitals in the capital city of Yemen. A self-administered 17-item questionnaire related to ICU nurses' knowledge regarding EN intervention was used to collect the data. Results: Out of the 174 respondents, 60.9% were females, 48.9% were aged between 20 and 25 years and 66.1% had a 3-year nursing diploma. Most respondents (79.3%) had one to five years of working experience as nurses, while almost two-thirds (70.7%) had one to five years of working experience as an ICU nurse. Above half (59.2%) of the respondents had never attended training courses on EN management and 65.5% specified that the college or institute of nursing was the source for their knowledge about EN management. Only 10.9% of the respondents had an adequate level of knowledge, while (43.1%) of them had a moderate level of knowledge and 46.0% of them had an inadequate level of knowledge regarding the EN management. Significant associations between the level of ICU nurses' knowledge of EN management and their level of education and the sources of knowledge were detected. Conclusions: The significant gap in ICU nurses’ knowledge regarding EN management identified implies the need to upgrade and refresh of the ICU nurses' knowledge by implementing a regular training program concerning EN management.", "keywords": [ "Enteral nutrition", "tube feeding", "nurses’ knowledge", "intensive care units", "public hospitals", "Yemen" ], "content": "Introduction\n\nCritically ill patients need regular enteral nutrition (EN) as an essential intervention to fulfil the body’s dietary and physiological requirement1. EN is the recommended method of nutritional support for ICU ill patients who need extra nutritional calories because of the increased metabolic rate2. It is considered as a medical therapy in law; hence, it should not be initiated only after ethical considerations have been made.\n\nPreviously, delivering of EN to critically ill patients was considered as a type of supportive care and not a therapeutic intervention3. Based on its benefits, it is more than a supportive therapy. It has been found that EN protects critically ill patients from malnutrition and subsequently improves body immunity and healing of tissues, which decreases their physiological stress effect, peptic ulcer, rates of infection4,5, the inflammatory response and maintains the function and integrity of the bowel3,6. Although maintaining balanced feeding via EN improves patients' health-related-outcomes, overfeeding leads to an increase in the mortality rate and must be avoided7.\n\nMalnutrition among ICU ill patients is a universal public health concern, with a prevalence rate ranging from 40 to 60%8. According to previous studies, almost 70% of ICU patients acquired malnutrition during hospitalization9. To overcome this serious problem, EN should be initiated as early as possible for critically ill patients to avoid any risk of morbidity and mortality, which usually increases due to long patient hunger10. Previous studies and nutritional guideline have recommended that EN should be started within 24 to 48 hours of patients' admission to the ICUs or after the stability of the hemodynamic state, specifically after cardiac resuscitation11. In other words, once critically ill patients are admitted to ICUs, delivering appropriate nutrition becomes imperative12.\n\nDespite the benefits of EN to critically ill patients, this process is usually associated with many complications, particularly if performed without an adequate level of knowledge13,14. Inappropriate delivering and poor management of EN can result into several complications, such as tube blockage or mal-positioning, nausea, vomiting, pulmonary aspiration, overfeeding, diarrhoea, treatment-related complications and delivery-site related complications like infection and agitation15. ICU nurses play a significant role in preventing such complications because they are responsible for identifying patients' nutritional risk, the calories needed, initiating and managing EN and monitoring any potential complications16,17. Accordingly, they must be knowledgeable enough to administer EN to critically ill patients safely14,16. Therefore, the aim of the present study was to explore Yemeni ICU nurses’ knowledge regarding management of EN. Specifically, our study aimed to answer the following two research questions:\n\n1. What is the level of Yemeni ICU nurses’ knowledge regarding EN management?\n\n2. Are there differences in the ICU nurses’ knowledge level regarding EN management based on their socio-demographic characteristics?\n\n\nMethods\n\nA descriptive cross-sectional study design was used to assess the knowledge level of ICU nurses regarding EN management.\n\nThe study was conducted from February to March 2019 in ICUs at four public hospitals in Sana'a, the capital city of Yemen. The four public hospitals are Al-Thawra Modern General Hospital, Al-Kuwait University Hospital, Al-Sabeen Maternity and Child Hospital, and the Republican Teaching Hospital Authority. These hospitals were selected as they are the referral hospitals for most people and the service fees are low.\n\nAccording to Al-Hawaly, Ibrahim, and Qalawa results, 71.1% of the respondents had a satisfactory total level of knowledge about EN18. Because our study was a cross-sectional, the following equation was used to calculate sample size: N=4pq/d2, where; N: required sample size, p: expected proportion of sample (from previous studies), q = 100 – p, and d= wanted precision (10% was taken in this study). Accordingly, a sample of 163 nurses was calculated. Assuming attrition of 10% = 16 + 163 = 179 nurses was required.\n\nStratified sampling was utilized to select the participants from the above-mentioned public hospitals. A list of the ICU nurses’ name was obtained from each hospital. The required sample was drawn randomly from each list using a systematic random technique. All ICU nurses who had at least 6 months working experience, including both males and females with different educational qualifications, who were involved directly in ICU patients care, full-time employees and had agreed to participate were eligible to take part in this study. Nurses who included in the pilot study and those who were unwilling to participate were excluded. Based on these criteria, the eligible participants were approached by the researchers at their workplace. Out of 384 ICU nurses, 174 nurses were included in this study.\n\nBased on a comprehensive review of the previous related studies, a self-administered questionnaire was developed by the researchers. The questionnaire consists of 17 questions with four possible options to be answered. The final questionnaire (see Extended data19 for a blank copy) is divided into two sections as follow:\n\nThe first section is related to the socio-demographic characteristics of the participants: age, sex, level of education, working experience as a nurse, working experience as ICU nurse, training courses on EN and sources of knowledge about EN.\n\nThe second section is related to knowledge of ICU nurses regarding EN management and is divided into three subsections:\n\n1. Knowledge of ICU nurses regarding before EN administration, which includes eight questions with a total of 32 responses.\n\n2. Knowledge of ICU nurses regarding during EN administration, which involves four questions with a total of 16 responses.\n\n3. Knowledge of the ICU nurses regarding after EN administration, which involves five questions with a total of 20 responses.\n\nThe 17 questions related to knowledge were assessed with “Yes” and “No” options. After correction of some reverse statements, a score of 1 was given for each correct response, while a score of 0 was given for each “incorrect” response. The maximum score for all correct answers was 68. Correct answers were calculated to obtain total scores for all questions of the three subsections. A score of 50% or less was considered inadequate, 51–75% moderate, while 76% and above was considered as adequate20.\n\nThree experts in the EN from hospitals and Al-Razi University were invited to participate in examining the content validity for the instrument used in this study. Their comments concerning the tool accuracy, relevance, consistency, comprehensiveness and applicability for implementation were taken in consideration. A pilot study was conducted on 40 ICU nurses. Cronbach’s alpha test was performed to examine the reliability of the questionnaire items. The result of the alpha was 0.78, which is acceptable.\n\nA self-administered questionnaire was distributed during the period of February to March 2019. The ICU nurses in the selected hospitals were invited to fill the questionnaire. Out of 179 questionnaires distributed, 174 were completed correctly and included in the final analysis.\n\nThe participants' responses were entered, cleaned, checked and explored using statistical software (IBMSPSS), version 22.0. The analyzed data was described using the mean values and standard deviations for continuous variables as well as the frequency and percentages for the categorical variables. A multinomial logistic regression and Chi-square tests were conducted to find out the associations between the ICU nurses’ knowledge and the selected socio-demographic variables. A p-value of ≤0.05 was reported as statistically significant.\n\nEthical clearance from the Ethics Committee of Al-Razi University was obtained for the current study. Then, an official written permission was also obtained from the managers of the selected hospitals prior to conducting the study. A written consent from all involved nurses was obtained prior to conducting the study.\n\n\nResults\n\nAlmost half of the participants' age (48.9%) ranged from 20 to 25 years with a mean ±SD of 26.94±4.31. Most of them (60.9%) were females and had a 3-year nursing diploma (66.1%). Regarding their previous experience, 79.3% of the participants had 1 to 5 years of working experience as nurses, while 70.7% of them had working experience as ICU nurses for the same duration. More than half of the nurses (59.20%) had never attended training courses on EN, whereas 61.5% of them specified that colleges or institutes of nursing were a source for their knowledge about EN. Further details of socio-demographic characteristics of the participants are presented in Table 1. De-identified socio-demographic characteristics, in addition to individual-level responses to the questionnaire, are available as Underlying data21.\n\nThe results showed that only 16.1% of the participants had an adequate level of knowledge, while 44.80% of them had a moderate level of knowledge and 39.10% reported an inadequate level of knowledge about pre-administration of EN. Concerning the level of the participants’ knowledge on administration of EN, the results showed that the majority (49.40%) of them had an inadequate level of knowledge regarding administration of EN. However, 5.80% of the participants had an adequate level and 44.80% of them reported a moderate level of knowledge on administration of EN. Regarding the level of knowledge of EN following administration, the results revealed that most (47.70%) of the ICU nurses had an inadequate level of knowledge, and 9.20% had an adequate level, while 43% of them had a moderate level of knowledge about management following adminsitration of EN. The detailed results are demonstrated in Figure 1.\n\nConcerning the overall level of ICU nurses’ knowledge on the different items of EN management, the results of the current study showed that the most (46.0%) of the participants had an overall inadequate level of knowledge and only (10.9%) had an overall adequate level of knowledge, while (43.1%) had an overall moderate level of knowledge regarding the EN management. The results are illustrated in Figure 2.\n\nThe current results indicated that there was a significant association between the level of education and sources of knowledge about EN and the overall level of participants’ knowledge of EN management (P=0.011 and P=0.030, respectively). However, there were no significant associations between the participants’ age, sex, experience as nurses, experience as ICU nurses and training courses and the overall level of knowledge regarding EN management (P= 0.276, 0.626, 0.425, 0.204 and 0.714, respectively). The detailed results of the association are presented in Table 2.\n\n* P-value is significant at ≤ 0.05 level\n\n\nDiscussion\n\nThe results of the current study revealed that the age of the majority of the ICU nurses’ was 20 years old and above. This result indicate that most participants were fresh graduates who were assigned together to work in ICUs. This finding is consistent with the result of a previous study16 which reported that over half of participants’ age ranged between 26 and 35 years old. However, our result is inconsistent with the result of another study22 which revealed that the majority of nurses’ age were 35 years old and above. Furthermore, the results showed that the majority (60.9%) of the ICU nurses were female. The high proportion of female nurses could be related to the fact that the profession of nursing remains a female-dominant profession. This finding is similar to a previous study16 that showed the majority (75%) of the participants were female nurses in the context of Egypt.\n\nThe current study revealed that more than half of the ICU nurses had a three-year nursing diploma and five years or less of work experience, either as general nurses or as ICU nurses. This could be because studying nursing education is more accessible in many nursing institutes all over Yemen, while there are a limited number of nursing colleges that have opened in the last few years. This finding is nearly in line with a previous study16 that reported most nurses had a diploma with one to four years of working experience. The results also revealed that 59.20% of ICU nurses had never taken any previous training courses on EN and 61.5% of them specified colleges and nursing institutes as the main sources of knowledge about the management of EN for them. This result is consistent to that of Mula22, who found that 72.5% of the participants obtained knowledge about EN during college studying or nursing schools. However, our results contradict the results by Ramuada23 who found that in-service training courses (24.9%) was the most frequent source for knowledge, followed by collages or schools of nursing education (20.6%).\n\nThe key finding in the current study was that the ICU nurses exhibited an inadequate level of knowledge concerning EN management. However, only 10.90% of the ICU nurses had an overall adequate level of knowledge regarding the EN management as a whole and the levels of adequate knowledge of it before administration, during administration and after administration were (16.10%, 5.80% and 9.20%, respectively). Such an inadequate knowledge among most Yemeni ICU nurses might be due to the inadequacy of in-service refreshing training’ courses or because hospitals have not a clear and updated guideline protocol that ICU nurses can access and adhere to at work. As mentioned above, 59.20% of ICU nurses had never engaged in training courses about EN, and most had a three-year nursing diploma and had five-years working experience or less, which supports our speculation. Our findings highlighted the gap in ICU nurses’ knowledge regarding the EN management, which indicates the necessity for conducting in-service training courses that focus on EN management. The results are consistent with an earlier study10 which assessed knowledge and practice among 85 nurses working in ICU concerning EN management. The result revealed that ICU nurses had a low and inadequate level of knowledge about EN management. In another similar study24 that assessed nurses’ knowledge and practice regarding use of a nasogastric tube (NGT) in medications administration for ICU patients, an unsatisfactory level of knowledge among nurses was found. Additionally, another study25 assessing nurses’ knowledge level about nutrition revealed that nurses had poor knowledge of nutrition. However, the results of the current study are inconsistent with the result of Al-Hawaly, Ibrahim and Qalawa18 who found that the majority of the respondents had a satisfactory overall level of knowledge concerning NGT nutrition administering. Likewise, the result disagrees with the result of Carlos, Costa and Simino26, who registered a satisfactory level of nurses’ knowledge concerning nutritional therapy.\n\nAnother key finding of this study is that the level of ICU nurses’ knowledge regarding EN management was significantly associated with the educational level (χ2 = 13.141, P= 0.011). In other words, a high educational level in nursing was associated with a higher level of knowledge. This could be attributed to the fact that faculties of nursing focus more on the theoretical aspect, while health institutes pay considerable attention to the practical aspect. This finding is similar to those of Abdullah et al.,24, Shahin et al.,10 and Taha and Said16, who found that the educational level was positively significant associated with the level of the nurses’ knowledge about EN, whereas those who had a bachelor degree achieved a higher level of knowledge compared to those with less educational level. However, our finding was inconsistent with the results of Aml, Manal and Fatamah27, who reported no difference in knowledge level based on the nurses’ educational qualifications. This discrepancy is possibly because of the differences in the curriculum of educational institutions. Furthermore, it was found that a significant association between the knowledge level and the sources of information related to EN management (χ2= 13.948, P= 0.030). The result implied that colleges and institutes of nursing represent the main source for respondents' knowledge about EN management. This result could be supported by the result of the present study as the majority (59.2%) of the respondents had never attended training courses related to EN management and only 7.5% of them used other resources for gaining knowledge about EN. Our result is in line with those of Abdullah et al.24, who found that doctors and previously working experience were the major sources for the nurses’ knowledge regarding EN management. The result also agrees with that of Morphet et al.17 concerning colleagues as the main source of respondents' knowledge. Yet, this disagrees with that result concerning the hospital policies and protocols as the source for the respondents’ knowledge about EN. In contrast, the result is incompatible with that found by Al Kalaldeh, Watson and Hayter28, as the researchers reported that the internet was the major source of knowledge about EN among the other sources for nurses.\n\nOn the other hand, there were no significant associations between the level of ICU the gap in ICU nurses’ knowledge regarding EN management and their age, sex, working experience and training courses about EN management. The results are consistent with those of Penland29 in relation to the respondents’ age, as the researcher reported that the respondents’ knowledge level was not significantly associated with age. However, our results are in disagreement with the results of studies by Taha and Said16 and Mooi30 in relation to the nurses’ age and years of working experience, as the researchers found that there was a highly statistically significant association between knowledge level regarding EN management and the respondents' age and previous working experience. This discrepancy might be attributed to the nature of training courses provided and the differences in the respondents' data, where it was found that young and newly graduated nurses had been more receptive, more tolerant and have a more potent memory.\n\nThe current study has some limitations that should be addressed in future research. The study was exclusive to assessment of nurses’ knowledge in ICUs at public hospitals in Sana'a, the capital city of Yemen. Thus, the findings should be dealt with caution. Besides, future studies should evaluate nurses’ practices in different hospitals and settings.\n\n\nConclusions\n\nBased on the findings of this study, it can be concluded that Yemeni ICU nurses had an inadequate level of knowledge about EN management. Accordingly, improving such knowledge regarding EN management is extremely needed. To this end, holding an in-service training courses in EN management among ICU Yemeni nurses and conduct such training courses on a regular basis are highly recommended.\n\n\nData availability\n\nFigshare: ICU nurses’ knowledge about EN. https://doi.org/10.6084/m9.figshare.1254232721\n\nThis file contains the individual-level responses of all participants to each question asked.\n\nFigshare: Questionnaire on ICU nurses’ knowledge regarding EN. https://doi.org/10.6084/m9.figshare.1264398819.\n\nThis file contains an English-language blank copy of the questionnaire used in this study.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Author contributions\n\n\n\nGGA and TAHA developed the idea and design of the study. TAHA was responsible for data collection and data analysis. GGA has write up the manuscript. Both authors contributed to reviewing, drafting the manuscript and approved the final version.\n\n\nAcknowledgement\n\nThe authors would like to thank the hospitals’ managers for their kind cooperation and also all those who helped in data collection.\n\n\nReferences\n\nTaylor CR, Lillis C, LeMone P, et al.: Fundamentals of Nursing Care: The Art and Science of Nursing Care. 2011; Walters Kluwer. Reference Source\n\nSánchez CÁ, de Aguirre Zabarte MM, Bordejé LL: [Guidelines for specialized nutritional and metabolic support in the critically-ill patient. Update. Consensus of the Spanish Society of Intensive Care Medicine and Coronary Units-Spanish Society of Parenteral and Enteral Nutrition (SEMICYUC-SENPE): gastrointestinal surgery]. Med Intensiva. 2011; 35: 42–47. PubMed Abstract \| Publisher Full Text\n\nJarden RJ, Sutton LJ: A practice change initiative to improve the provision of enteral nutrition to intensive care patients. Nurs crit care. 2015; 20(5): 242–255. PubMed Abstract \| Publisher Full Text\n\nColaço AD, Nascimento ERPd: Bundle de intervenciones de enfermería en nutrición enteral en la terapia intensiva: una construcción colectiva. Revista da Escola de Enfermagem da USP. 2014; 48(5): 844–850. Publisher Full Text\n\nTaylor B, Brody R, Denmark R, et al.: Improving enteral delivery through the adoption of the \"Feed Early Enteral Diet adequately for Maximum Effect (FEED ME)\" protocol in a surgical trauma ICU: a quality improvement review. Nutr Clin Pract. 2014; 29(5): 639–648. PubMed Abstract \| Publisher Full Text\n\nFriesecke S, Schwabe A, Stecher SS, et al.: Improvement of enteral nutrition in intensive care unit patients by a nurse-driven feeding protocol. Nurs crit care. 2014; 19(4): 204–210. PubMed Abstract \| Publisher Full Text\n\nLooijaard WGPM, Denneman N, Broens B, et al.: Achieving protein targets without energy overfeeding in critically ill patients: A prospective feasibility study. Clin Nutr. 2019; 38(6): 2623–2631. PubMed Abstract \| Publisher Full Text\n\nVanBlarcom A, McCoy MA: New Nutrition Guidelines: promoting enteral nutrition via a nutrition bundle. Crit care nurse. 2018; 38(3): 46–52. PubMed Abstract \| Publisher Full Text\n\nHarvey SE, Parrott F, Harrison DA, et al.: Trial of the route of early nutritional support in critically ill adults. N Engl J Med. 2014; 371(18): 1673–1684.PubMed Abstract \| Publisher Full Text\n\nShahin MA, Mohamed WY, Sayed M: Nurses’ knowledge and practices regarding enteral nutrition at the critical care department of Al-Manial university hospital in Egypt: Impact of a designed instructional program. Journal of American Science. 2012; 8(1): 397–405. Publisher Full Text\n\nMarshall AP, Cahill NE, Gramlich L, et al.: Optimizing nutrition in intensive care units: empowering critical care nurses to be effective agents of change. Am J Crit Care. 2012; 21(3): 186–94. PubMed Abstract \| Publisher Full Text\n\nBlackburn GL, Wollner S, Bistrian BR: Nutrition support in the intensive care unit: an evolving science. Arch Surg. 2010; 145(6): 533–538. PubMed Abstract \| Publisher Full Text\n\nKrenitsky J: Full Force Enteral Nutrition: A New Hope, or the Dark Side? A Critical Look at Enhanced Enteral Feeding Protocols. PRACTICAL GASTROENTEROLOGY. 2018; 17: 16. Reference Source\n\nAl-Jalil T, Gray G, Rasouli M, et al.: Auditing of enteral nutrition nursing care in critical care patients. Nursing Practice Today. 2019; 6(1): 25–18. Publisher Full Text\n\nHouston A, Fuldauer P: Enteral feeding: Indications, complications, and nursing care. American Nurse Today. 2017; 12(1): 20–24. Reference Source\n\nMohammed EK, Taha AS: Critical Care Nurses’ Knowledge and Practice Regarding Administration of Total Parenteral Nutrition at Critical Care Areas in Egypt. Critical Care. 2014; 4(13). Reference Source\n\nMorphet J, Clarke AB, Bloomer MJ: Intensive care nurses’ knowledge of enteral nutrition: a descriptive questionnaire. Intensive Crit Care Nurs. 2016; 37: 68–74. PubMed Abstract \| Publisher Full Text\n\nAl-Hawaly M, Ibrahim MH, Qalawa SA: Assessment of nurses’ knowledge and performance regarding feeding patients with nasogastric tube in Ismailia General Hospital. Med J Cairo Univ. 2016; 84: 99–105. Reference Source\n\nAlrubaiee GG: Questionnaire on nurses’ knowledge about EN .pdf. figshare. Online resource. 2020. http://www.doi.org/10.6084/m9.figshare.12643988.v1\n\nBloom BS: Taxonomy of educational objectives. Vol.1: Cognitive domain. New York: McKay, 1956; 20: 24.\n\nAlrubaiee GG: ICU nurses’ knowledge about EN-dataset 2020.sav. figshare. Dataset. 2020. http://www.doi.org/10.6084/m9.figshare.12542327.v1\n\nMula CT: A descriptive study of nurses’ knowledge and practice about adult enteral nutrition in special care units of a referral Hospital in Malawi. University of KwaZulu-Natal, Durban. 2011. Reference Source\n\nRamuada LG: Assessment of knowledge, attitude and practice of nurses regarding Enteral Nutrition at a Military hospital. 2017. Reference Source\n\nAbdullah M, Mohammed WY, Ismail M: Nurses’ knowledge and practices about administration of medications via nasogastric tube among critically ill patients. Journal of Education and Practice. 2014; 5(1): 147–159. Reference Source\n\nYalcin N, Cihan A, Gundogdu H, et al.: Nutrition knowledge level of nurses. 2014. Reference Source\n\nCarlos CM, Costa RF, Simino GPR: Knowledge of nurses about nutritional therapy. Bahiana. 2020; 9(1): 33–40. Reference Source\n\nAml AK, Manal SI, Fatimah SA: Assessment of Critical Care Nurse's Knowledge and Practices Regarding Care of Patients Receiving Total Parenteral Nutrition. Med J Cairo Univ. 2018; 86: 2763–2773. Publisher Full Text\n\nAl Kalaldeh M, Watson R, Hayter M: Jordanian nurses’ knowledge and responsibility for enteral nutrition in the critically ill. Nurs Crit Care. 2015; 20(5): 229–241. PubMed Abstract \| Publisher Full Text\n\nPenland KS: The relationship between nurse nutrition knowledge and unintentional weight loss in nursing home residents. 2010. Reference Source\n\nMooi NM: Knowledge of intensive care nurses regarding the monitoring of early enteral nutrition. Afr J Nurs Midwifery. 2018; 20(2): 1–14. Publisher Full Text" }	[ { "id": "67783", "date": "03 Aug 2020", "name": "Khaled Mohammed Al-Sayaghi", "expertise": [ "Reviewer Expertise Critical Care and Emergency Nursing", "Medical surgical Nursing", "nutritional support in ICU" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 results part in the abstract should focus on the main results such as the areas with high level of knowledge and areas with lower level of knowledge. Remove the excessive description of the sample socio-demographic characteristic.\n\nConclusion part has been written as a recommendation only. It will be better if you summarize the findings then make a brief recommendation.\n\nMethods:\n\nUnder the setting subtitle no need to mention the names of the hospitals. Maintaining the confidentiality of participant hospitals. No need to mention the duration of the study under the setting subtitle, it is mentioned under data collection.\n\nDelete this ‘According to Al-Hawaly, Ibrahim, and Qalawa’ and write : according to a previous study(..) ….\n\nInstead of citing the tool they have developed and used, authors must mention and cite the references and literature that had been used in developing the tool.\n\nPer authors, the second part of data collection instrument contains three subsections which are the before EN administration, during EN administration, and after EN administration. Accepting that this categorization is correct, it is not clear which items are under each subsection. Moreover, most of the 17 items are not related to the before, during, and after EN management, they are related to general knowledge about the EN (such as the indications, goals, benefits, complications, routs, methods, types and contents of EN formula, …….. etc.), even there is an item asking about the types of nutritional support in general (enteral, parenteral, combination, ..etc.). More suitable grouping and categorizing must be used to organize the instrument or to leave it without any categorization it will be better.\n\nValidity and reliability: delete the word ‘ reliability’ and replace it by ‘ internal consistency’.\n\nUnder the data analysis subtitle, they mentioned that a multinomial logistic regression test was conducted. In fact, no multinomial logistic regression test was done. So , delete ‘ multinomial logistic regression’.\n\nResults:\nIn results, the use of some terms (such as most, majority) in describing the results need a revision. For example: 49.40% is not a majority.\n\nTable 2 presents the frequency and percentage of the participants and compares between the subgroups using the Chi-square tests. I think it will be better if the table presents the knowledge means scores and standard deviations of the subgroups and compare between them by the t or f tests. After that multiple regression can be performed.\n\nDiscussion:\nDiscussion must be on the main important findings based on the objectives of the study. No need to write two paragraphs at the beginning of the discussion about the participants' characteristics such as age, gender, educational levels, and work experience. Describing those characteristic in results part is enough.\n\nGeneral\n\nThe paper needs English language editing.\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": "8944", "date": "30 Nov 2022", "name": "Gamil Ghaleb Alrubaiee", "role": "Author Response", "response": "COMMENT # 1: Abstract: The results part in the abstract should focus on the main results such as the areas with high level of knowledge and areas with lower level of knowledge. Remove the excessive description of the sample socio-demographic characteristic. RESPONSE: Thank you for your comment. The results section has been rewritten based on your recommendation. Please see the abstract's results section. COMMENT # 2: Conclusion part has been written as a recommendation only. It will be better if you summarize the findings then make a brief recommendation. RESPONSE: Thank you for your comment. Indeed, the findings were summarized in the results section, and the conclusion section focused on the main result, the knowledge gap, and the recommendations based on that result. COMMENT # 3: Methods: Under the setting subtitle no need to mention the names of the hospitals. Maintaining the confidentiality of participant hospitals. No need to mention the duration of the study under the setting subtitle, it is mentioned under data collection. RESPONSE: Thank you for your comment. We have followed your recommendations. COMMENT # 4: Delete this ‘According to Al-Hawaly, Ibrahim, and Qalawa’ and write : according to a previous study(..) RESPONSE: Thank you for your comment. We have followed your recommendations. COMMENT # 5: Instead of citing the tool they have developed and used, authors must mention and cite the references and literature that had been used in developing the tool. RESPONSE: Thank you for your comment. The references for adapted tool were cited as recommended. COMMENT # 6: Per authors, the second part of data collection instrument contains three subsections which are the before EN administration, during EN administration, and after EN administration. Accepting that this categorization is correct, it is not clear which items are under each subsection. Moreover, most of the 17 items are not related to the before, during, and after EN management, they are related to general knowledge about the EN (such as the indications, goals, benefits, complications, routs, methods, types and contents of EN formula, ........ etc.), even there is an item asking about the types of nutritional support in general (enteral, parenteral, combination, ..etc.). More suitable grouping and categorizing must be used to organize the instrument or to leave it without any categorization it will be better. Instead of citing the tool they have developed and used, authors must mention and cite the references and literature that had been used in developing the tool. RESPONSE: Thank you for your comment. The items under each subsection were mentioned to be clear for the potential readers. We also replace the word \"management\" by \"care\" to be consistent with the general knowledge about the care of EN. COMMENT # 7: Validity and reliability: delete the word ‘reliability’ and replace it by ‘internal consistency’. RESPONSE: Thank you for your comment. We removed the word \"reliability\" and replaced it with \"internal consistency.\" COMMENT # 8: Under the data analysis subtitle, they mentioned that a multinomial logistic regression test was conducted. In fact, no multinomial logistic regression test was done. So, delete ‘multinomial logistic regression’. RESPONSE: Thank you for your comment. We apologize for mistyping a multinomial logistic regression test. We have removed the term \"multinomial logistic regression\". COMMENT # 9: Results: In results, the use of some terms (such as most, majority) in describing the results need a revision. For example: 49.40% is not a majority. RESPONSE: Thank you for the comment. We have corrected some terms as recommended. COMMENT # 10: Table 2 presents the frequency and percentage of the participants and compares between the subgroups using the Chi-square tests. I think it will be better if the table presents the knowledge means scores and standard deviations of the subgroups and compare between them by the t or f tests. After that multiple regression can be performed. RESPONSE: Thank you for your comment. Following the recommendation of Reviewer 1, we re-analyze the data in Table 2 using the Fisher exact test rather than the Chi-square test. Please see Table 2. COMMENT # 11: Discussion: Discussion must be on the main important findings based on the objectives of the study. No need to write two paragraphs at the beginning of the discussion about the participants' characteristics such as age, gender, educational levels, and work experience. Describing those characteristic in results part is enough. RESPONSE: Thank you for your comment. Based on your recommendation, the two paragraphs about socio-demographic characteristics were removed from the discussion section. COMMENT # 12: General: The paper needs English language editing. RESPONSE: Thank you for your comment. The manuscript was reviewed and edited as your recommendation." } ] }, { "id": "75190", "date": "10 Dec 2020", "name": "Hiroyuki Ohbe", "expertise": [ "Reviewer Expertise Nutrition support in critically ill patients. Clinical epidemiology." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript \"Intensive care nurses' knowledge of enteral nutrition at public hospitals in Sana'a, Yemen: a cross-sectional survey\" by Talal Ali Hussein Al-Qalah, et al. is a descriptive cross-sectional study from four public hospitals in the capital city of Yemen. The authors intended to assess the level of ICU nurses’ knowledge regarding the management of enteral nutrition. The authors recruit 174 nurses in 2019. The authors found that 46% of them had an inadequate level of knowledge regarding enteral nutrition management. From my impressions, the aim of this study may not be interested in countries other than Yemen.\nIntroduction: Please clearly state “what is unknown” in their topic. It is unclear why the authors did this study.\n\nMethods: Sample size determination: I’m not familiar with the equation the authors used. Can the authors provide the reference to support this sample size calculation?\n\nMethods: Did the authors use the questionnaire which was previously developed or which was newly created? If the authors use the questionnaire which was newly created, how and why the authors could define that a score of 50% or less was considered inadequate, 51–75% moderate, while 76% and above was considered adequate. The cut-off score should be carefully selected.\n\nMethods: Please clearly describe how to perform the multinomial logistic regression. How to obtain the p-values in Table 2? Multinomial logistic regression? Chi-square test?\n\nMethods: Because the cells in Table 2 contained under <5, Fisher exact test is more suitable than chi-square test.\n\nDiscussion: If the authors used the different questionnaire used in the previous study, how and why the authors could compare the results?\n\nConclusions: Is there any evidence that training courses in EN management improve clinical outcomes? Based on the results of your study, the only thing the authors revealed was that low SES was associated with inadequate knowledge. Experience and training courses were not associated with improved knowledge. Therefore, the conclusion should be based on their results.\n\nDiscussion: What is new in this study? What can the readers act from this paper all over the world?\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": "8945", "date": "02 Mar 2023", "name": "Gamil Ghaleb Alrubaiee", "role": "Author Response", "response": "COMMENT # 1: Introduction: Please clearly state “what is unknown” in their topic. It is unclear why the authors did this study. RESPONSE: Thank you for your comment. We agree with your comment that it was unclear in the introduction why the authors conducted the study, but it is stated clearly in the abstract. Please refer to lines 2–4 in the background section. In response to your comment, we have clarified in the introduction why the authors conducted this study. Please see paragraph 4, lines 10, 11, and 12 of the introduction. COMMENT # 2: Methods: Sample size determination: I’m not familiar with the equation the authors used. Can the authors provide the reference to support this sample size calculation? RESPONSE: Thank you for your comment. The equation we used to determine sample size in our study was found in many textbooks and cited by many other previous studies. We have included a reference according to your comment. Please see sample size determination section, lines 3. COMMENT # 3: Methods: Did the authors use the questionnaire, which was previously developed, or which was newly created? If the authors use the questionnaire which was newly created, how and why the authors could define that a score of 50% or less was considered inadequate, 51–75% moderate, while 76% and above was considered adequate. The cut-off score should be carefully selected. RESPONSE: Thank you for your comment. We did, in fact, use an adapted questionnaire and didn't develop a new one. The word \"developed\" is used incorrectly in this statement (A self-administered questionnaire was developed). We have changed the word “developed” by “adapted” to be clear. In addition, we have added cited studies based on Reviewer 2's comment. Please see study instrument section, lines 2. The cut-off score used in this study as a scoring system was determined by previous studies rather than by the authors themselves. We already included the reference (Reference #22). Furthermore, many previous studies used a Bloom-based knowledge scoring system, we have added one of these studies. Please see the reference #23. COMMENT # 4: Methods: Please clearly describe how to perform the multinomial logistic regression. How to obtain the p-values in Table 2? Multinomial logistic regression? Chi-square test? RESPONSE: Thank you for your insightful observation and comment. In fact, we did not use multinomial logistic regression in our data analysis; instead, we used the Chi-square test to determine the relationships between ICU nurses' knowledge and the selected socio-demographic variables and obtain p-values. Based on your valuable input and that of Reviewer 2, the phrase \"multinomial logistic regression\" has been removed, and the analysis statement has been corrected. Please see data analysis section, lines 4. COMMENT # 5: Methods: Because the cells in Table 2 contained under <5, Fisher exact test is more suitable than chi-square test. RESPONSE: Thank you for your comment. We fully agree with you. We use the Fisher exact test to re-analyze the data in this table and re-write the table results accordingly. Please see Table 2. Please also see line 4 for the addition of this test to the data analysis section. COMMENT # 6: Discussion: If the authors used the different questionnaire used in the previous study, how and why the authors could compare the results? RESPONSE: Thank you for your comment. Our questionnaire was not significantly different from those used in previous studies. We simply modified an existing questionnaire rather than creating a new one. As a result, we compared our study findings to those of related studies with similar intended outcomes. COMMENT # 7: Conclusions: Is there any evidence that training courses in EN management improve clinical outcomes? Based on the results of your study, the only thing the authors revealed was that low SES was associated with inadequate knowledge. Experience and training courses were not associated with improved knowledge. Therefore, the conclusion should be based on their results. RESPONSE: Thank you for your comment. Thank you for your comment. Our conclusion is derived from our results and there is no sentence implied that training courses in EN management improve clinical outcomes but improve the awareness and knowledge. this is what we concluded based on our findings and this is supported by many previous studies. Please see our conclusion section. COMMENT # 8: Discussion: What is new in this study? What can the readers act from this paper all over the world? RESPONSE: Thank you for your comment. This study, like many others around the world, has clear objectives. These are stated clearly at the end of the introduction section. These are explicitly stated at the end of the introduction. According to the study findings, we believe that the situation regarding Yemeni nurses' enteral nutrition care knowledge becomes clear. This would help decision makers develop a plan to fill this knowledge gap, and as a result, Yemeni nurses' knowledge would grow professionally, and they would be able to provide safe health care services. Furthermore, the findings of this study will serve as a data base for future research and will provide potential readers with information about the current situation of Yemen's nurses. We've added a paragraph to explain the study's implications. Please see the discussion section, paragraph 4, Lines 1-6." } ] } ]	1	https://f1000research.com/articles/9-759
https://f1000research.com/articles/12-38/v1	10 Jan 23	{ "type": "Systematic Review", "title": "Thermal performance of gasifier cooking stoves: A systematic literature review", "authors": [ "Md Insiat Islam Rabby", "Md Wasi Uddin", "Mahafuzur Rahman Sheikh", "Humayun Kabir Bhuiyan", "Tazeen Afrin Mumu", "Fabliha Islam", "Afsana Sultana", "Md Wasi Uddin", "Mahafuzur Rahman Sheikh", "Humayun Kabir Bhuiyan", "Tazeen Afrin Mumu", "Fabliha Islam", "Afsana Sultana" ], "abstract": "A systematic literature review was conducted to summarize the overall thermal performance of different gasified cooking stoves from the available literature. For this purpose, available studies from the last 14 years (2008 to 2022) were searched using different search strings. After screening, a total of 28 articles were selected for this literature review. Scopus, Google Scholar, and Web of Science databases were used as search strings by applying “Gasifier cooking stove” AND “producer gas cooking stove” AND “thermal performance” keywords. This review uncovers different gasified cooking stoves, cooking fuels, and fabrication materials besides overall thermal performances. The result shows that the overall thermal performance of different gasified cooking stoves was 5.88% to 91% depending on the design and burning fuels. The premixed producer gas burner with a swirl vane stove provided the highest overall thermal performance range, which was 84% to 91%, and the updraft gasified stove provided the lowest performance, which was 5.88% to 8.79%. The result also demonstrates that the wood pellets cooking fuel provided the highest thermal performance and corn straw briquette fuel provided the lowest for gasified cooking stoves. The overall thermal performance of wood pellets was 38.5% and corn straw briquette was 10.86%.", "keywords": [ "Gasified cooking stoves", "thermal performance", "cooking fuels and literature review." ], "content": "Introduction\n\nOne of the largest energy-consuming sectors in developing nations is the cooking sector, and this sector requires a large amount of energy and effort as it is a commonplace daily activity. Biomass fuel, natural gas, oil, and coal are the predominant sources of energy for cooking sector, and the majority of the inhabitants in developing countries rely on conventional fuels, typically wood and agricultural residues. Approximately three billion people worldwide, 41% of households, rely on solid biomass fuels (biomass such as wood, crop residues, dung, charcoal, and coal) for cooking due to the affordability or availability of these fuels, especially in developing countries in Asia and sub-Saharan Africa (Bonjour et al., 2013). The majorities of the conventional cooking are perpetrated over open flames, which burn inefficiently and result in significant emissions. It is worth to be mentioned that, in 2010, about 3.5 million premature deaths globally were caused by household air pollution (Lim et al., 2012), and it also contributed to outdoor air pollution, which resulted in an additional 370,000 deaths and 9.9 million disability-adjusted life worldwide (Chafe et al., 2014). Furthermore, household emissions can stimulate lung cancer, chronic obstructive pulmonary disease and chronic bronchitis, cardiovascular diseases, low birth weight, stillbirth, and acute lower respiratory infections (Amegah & Jaakkola, 2016). Excessive uses of solid fuels have pernicious effects on human health, regional environment, and global climate (Smith et al., 2004). Due to the pernicious impact on human health that results in sophisticated diseases, global temperature rise, hazardous gas emissions, and excessive time waste in conventional cooking, the advancement of heat generation techniques in cooking stoves become significant.\n\nTo concoct an improved cooing stove, it must requires substantial improvements in combustion efficiency as well as increased fuel efficiency compared to conventional stoves (Venkataraman et al., 2010). In the first decade of the 1940s, the development of biomass-based cooking stoves commenced in India, and these stoves were known as improved mud cooking stoves. Then another study (Raju, 1954) reported the development of the upgraded multi-pot mud cooking stoves for Indian rural households. Afterwards, an upsurge in better cooking stoves appeared due to the world's focus shifted to environmental concerns and energy conservation measures. These cooking stoves were created and built using engineering principles, making them more effective and long-lasting than the conventional open fired cooking stove. Investigators are currently attempting to design cooking stoves that are more ecologic and sustainable as well as more energy and thermally efficient. To date, several different types of improved cooking stoves have been designed and investigated, i.e. patsari cooking stoves (Cynthia et al., 2008), mirt cook stove (Dresen et al., 2014), gasifier cook stove (Carter et al., 2014), wick stove (Dinesha et al., 2019), pellet stoves (Boman et al., 2011), radiant stoves (Pantangi et al., 2011), etc. From the above verities, gasifier cook stove is one of the potential energy efficient and environment friendly cook stove.\n\nThe process of transforming solid or liquid feed stocks into usable gaseous or other chemical fuels that may be combusted to produce thermal energy is known as gasification. Fuel with a small amount of air is delivered into a closed container so that the fuel can be partially combusted to generate the required heat for gasification. The fundamental idea of gasification is that it is a thermochemical process that uses the reactions of drying, pyrolysis, oxidation, and reduction to turn solid fuel into a combustible gas (producer gas) (Basu, 2010). In a gasifier cook stove, biomass is gasified in the reactor to generate syngas, thereafter, syngas is burned in the burner in order to obtain producer gas flame (Susastriawan et al., 2021). On the contrary, biomass is directly combusted with the presence of excess air and produced heat and flue gas.\n\nDue to the eclectic amount of highly appealing characteristics of gasifier cookstoves, including high efficiency, smoke-free safe combustion, uniform and steady flame, simplicity of controlling the flame, and operational capability for long periods (Raman et al., 2014), the advancement of gasifier cooking stoves became significant. Therefore, to date, several research studies had been performed on the design and development of gasifier cooking stoves with the goal of increasing efficiency and dwindling emission such as producer gas stove with bluff-body shape in burner (Susastriawan et al., 2021), producer gas stove (Panwar et al., 2011; Punnarapong et al., 2017), Chinese gasifier stove (Carter et al., 2014), natural-draft gasifier cookstoves (Hailu, 2022; Tryner et al., 2014), fixed bed advanced micro-gasifier cook stove (Sakthivadivel & Iniyan, 2017), inverted downdraft gasifier (Narnaware & Pareek, 2016; Ojolo et al., 2012; Osei et al., 2020), biomass gasifier cookstove (Panwar & Rathore, 2015), top-lit updraft gasifier cookstove (Scharler et al., 2021), advance micro-gasifier stove (Sakthivadivel et al., 2019; Wamalwa et al., 2017), rice husk gas stove (Ndindeng et al., 2019), natural and force draft gasifiers stove (Getahun et al., 2018), and natural cross draft (Nwakaire & Ugwuishiwu, 2015). However, to the authors’ best knowledge, no proper systematic reviews have already been conducted on the overall thermal performance of gasifier cook stoves, with an emphasis on types of gasifier stoves, cooking fuels, location of investigation, and materials to fabricate stoves. Therefore, in this study, a systematic review has been performed to consolidate all the technical works published on the thermal performance of gasifier cooking stoves as well as further analyse the areas on which additional studies should be focused for future research trajectory.\n\n\nMethods\n\nA typical research methodology steps for systematic review of Tranfield et al. (2003) are considered which are given in Figure 1 wherein the 1st stage is known as “Define” which is subdivided by steps as “Identification of need for a literature review” and “Development of a literature review protocol”. The 2nd stage known as “Collect and Select” which is also consist of two steps- “Identification of documents” and “Selection of relevant documents”. Simultaneously, the 3rd stage is “Analyse” which is categorized as documents and Data extraction steps. Meanwhile, the final stage is “Result” indicates the last steps “Documents Finding” wherein collected all documentation are reviewed significantly for extracting knowledge from gathered information.\n\nA literature search was conducted to cover the period from January 2008 to August 2022. Scopus, Web of Science, Google Scholar and Science Direct databases were selected as search strings. EndNote X 9.0 software was used to exclude duplicates from searched data. The protocol of the review discussed in Table 1. Moreover, the system for search string database is presented in Table 2 where the process to search articles in different considered database is discussed.\n\nTo conduct this study, the author, date, name and types of study, study location, stoves types, material used, fuels/energy sources, thermal performances and emission of pollutants were reported by using Microsoft Excel.\n\n\nResults and discussion\n\nA total of 1153 articles initially identified. After removing duplicates, checking title, abstract and full text, 28 were found eligible based on the predetermined exclusion and inclusion criteria for this study. Among the 28 selected articles, all conducted their investigation on gasified cooking stoves experimentally and only 3 articles performed numerical/computational analysis beside experimental study.\n\nThe publications year of the selected articles is summarized in Figure 2, which was obtained from Table 3. The figure shows that the selected articles were published in 2022, 2021, 2020, 2019, 2017, 2016, 2015, 2014, 2012 and 2008. The result also highlights that the highest amount of research on gasified cooking stoves was conducted in 2019 at 18% and the lowest amount of research was conducted in 2012 at only 4%. From the beginning to the mid of the current year 2022 almost 14% studies were identified from the selected literature which reflects that the investigation demand on gasified cooking stoves is recently also a high priority to researchers.\n\nFrom the literature search, this review identified different types of gasified cooking stoves wherein modification and improvement were applied. Based on the findings from Table 2 the identified gasified cooking stoves are summarized in few categories, which are:\n\n1. Downdraft gasified stove: reverse-downdraft, inverted downdraft and biomass downdraft\n\n2. Natural draft gasified stove: Natural draft and Natural cross draft\n\n3. Forced draft gasified stove: forced draft, forced-draft pellet-fed semi gasifier, forced draft with separate secondary and primary air fans\n\n4. Micro gasified stove: fixed bed advanced micro, advanced micro\n\n5. Updraft gasifier cook stove: top-lit updraft (TLUD), Portable Top-Lit Up Draft, top-lit updraft (TLUD) with remote burner and fuel reactor, Chinese model (HX-20) updraft institutional\n\n6. General gasified cooking stove: biomass, Chinese, biochar\n\n7. Others: producer gas stove with bluff-body shape in burner, rice husk gasifier stove\n\nThe percentages of selected publications on the gasified cooking stoves are presented in Figure 3. The figure shows that the maximum articles worked on general gasified cooking stoves was 23%, while only 12% articles performed investigation on micro, and other gasified cooking stoves. Due to the easy design consideration and fabrication most of the studies considered general gasified cooking stoves for their investigation.\n\nMost of the identified articles on different gasified gas stoves are conducted in Asian and African continents as due to energy security and crisis people in these continents for which people of these continents mainly depend on the biomass fuel driven cooking system. Country wise identified published articles from Table 3 are presented in Figure 4. Among the selected articles 71% mentioned their study location. The figure shows 11 different countries from Asian and African continent where the investigation on gasified cooking stoves were conducted. The figure also highlights that 21% published articles performed their studies in India, which is the highest while the lowest study was performed in Thailand, which was only 3%. The design, configuration and burning fuels for any cooking stoves usually develop and investigate based on the geographical locations, climate, environment and materials availability. Therefore, this finding will help researchers, organizations and government to investigate and implement this type of cooking stoves based on the geographical location so that the adoption rate of the research can increase.\n\nCast iron, mild steel, metal, ceramic fiber, steel sheet, carbon steel and stainless steel were mainly used to make gasified cooking stoves. Among the selected articles for the current review, only 60% articles addressed the materials they used to fabricate their experimental gasified stove. The usage percentages of these materials in the published articles are presented in Figure 5. The figure shows that 15% published articles used mild steel which is the highest while 3% used ceramic fiber which is the lowest. The availability of mild steel in the investigated locations and higher thermal properties of stainless steel for cooking devices are the key reasons for applying it in production.\n\nThe fuels used in the cooking stoves are categorized in four types from the Table 2 and presented in Figure 6. The categories are wooden fuel, animals manure, cereals, charcoal and others. However, wooden fuels are classified in seven types, which are pellets, cassava peel, coconut shell, sized, shavings, chip and sawdust. Among the fuels wooden pellets fuels were used maximum. Peanut shell, cornstalk and cow dung, from pine patula, saw dust pellets, tamarind pellet, wood pellets and rice hull pellets are identified as wooden pellets fuels from selected articles. Moreover, Babul wood (Prosopis Juliflora), mango (magnifera indica), babul (prosopis julifera) and nim (azadirachta indica) wood, eucalyptus, bamboo and pinusroxburgii (Salla) wood are identified as sized wooden fuels. The rice husk, wheat straw and corncobs are categorized as cereal fuels while gas and briquettes are categorized in other types. In briquette fuels rice husk, sawdust-cow dung and corn straw are identified. This finding highlights the potential fuels to run a gasified cooking stove through which general people and research will be benefited.\n\nThe overall thermal performance of different gasified cooking stoves from Table 1 is identified 5.88% to 91% depends on the design and burning fuels. The thermal performances of the cooking stoves usually determine by using three approaches named water-boiling test, control cooking test and kitchen performance test. The overall thermal performance of different gasified cooking stoves obtained from selected studies is presented in Figure 7 and Table 4. Figure 7 shows that natural draft semi gasified cooking stove provide the highest overall thermal performance which was 42% while Mayon rice husk gasified stoves shows the lowest performance which was 11%. In the meantime, the overall thermal performance of stove was presented as range in the literature therefore this performance is summarized in Table 5. Table 5 shows that premixed producer gas burner with a swirl vane stove provided the highest overall thermal performance range which was 84% to 91% and updraft gasified stove provided the lowest performance which was 5.88% to 8.79%. This overall thermal performance of the stoves usually varied due to the design and fuels applied in the experimental tests.\n\nDue to the different mechanical properties such as fuel consumption rate, calorific value, heating rate and fire point different cooking fuels provided different thermal performance presented in Table 3. To understand the insight of the thermal performance of different stoves for different cooking fuels a summarization table is created. The Table 5 presents the overall thermal performance for some cooking fuels that are directly mentioned in Table 1. From Table 5 it can be seen that wood pellets provided the highest thermal performance and corn straw briquette provided the lowest. The overall thermal performance of wood pellets was 38.5% and corn straw briquette was 10.86%.\n\n\nConclusion\n\nIn this current literature review the overall thermal performance of different gasified cooking stoves were explored. For this purpose, available literature from past 14 years from 2008 to 2022 were search by using different search strings and after screening a total of 28 articles were selected for this literature review. The key findings from the review are as follows:\n\ni. Maximum studies on gasified cooking stoves were conducted on 2019, which was 18%, and the least minimum researches were conducted on 2012, which was only 4%. From the beginning to the mid of the current year 2022 almost 14% studies were identified from the selected literature which reflects that the investigation demand on gasified cooking stoves is recently also in high priority to researcher.\n\nii. The identified gasified cooking stoves from literature are classified in six groups named downdraft, updraft, natural draft, forced draft, micro, general gasified and others whereas the maximum articles worked on general gasified cooking stoves, which was 23%.\n\niii. 21% published articles on gasified cooking stoves performed their studies in India, which is the highest while the lowest study was performed in Thailand, which was only 3%.\n\niv. 15% published articles used mild steel to make gasified stove, which is the highest while only 3% used, ceramic fiber, which is the lowest.\n\nv. The identified cooking fuels for gasified stoves are classified in four group which are wooden fuel, animals manure, cereals, charcoal and others whereas wooden fuel was applied most of the studies.\n\nvi. The overall thermal performance of different gasified cooking stoves was 5.88% to 91% depends on the design and burning fuels. The premixed producer gas burner with a swirl vane stove provided the highest overall thermal performance range, which was 84% to 91%, and the updraft gasified stove provided the lowest performance, which was 5.88% to 8.79%.\n\nvii. Among the coking fuels, the wood pellets provided the highest thermal performance and corn straw briquette provided the lowest for gasified cooking stove. The overall thermal performance of wood pellets was 38.5% and corn straw briquette was 10.86%.\n\nThe review recommends to analysis the impact of pollution rate of the identified gasified stove on women and children health. Moreover, the adoption rate among general, economic sustainability and lifecycle analysis of the identified gasified stoves can be more valuable for our community.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: PRISMA checklist and flowchart for ‘Thermal performance of gasifier cooking stoves: A systematic literature review’, https://doi.org/10.6084/m9.figshare.21747020.v2 (Uddin et al., 2022).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nAhmad R, Zhou Y, Zhao N, et al.: Performance investigation of top-lit updraft gasifier stove using different biomass fuels. Fresenius Environ. 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Publisher Full Text\n\nVenkataraman C, Sagar AD, Habib G, et al.: The Indian National Initiative for Advanced Biomass Cookstoves: The benefits of clean combustion. Energy Sustain. Dev. 2010; 14(2): 63–72. Publisher Full Text\n\nWamalwa P, Nyaanga D, Owino G: Development of an experimental biomass micro gasifier cook stove. IOSR J. Mech. Civ. Eng. 2017; 14(5): 6–10." }	[ { "id": "161508", "date": "07 Feb 2023", "name": "Shabnam Konica", "expertise": [ "Reviewer Expertise Mechanical Engineering", "Solid Mechanics" ], "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 work presents a statistical review of the thermal performance of gasifier cooking stoves. While the content of this article is important to understand the aspects of designing and energy performance evaluation of gas stoves for the countries where this type of stoves are still in use, it does not have a clear conclusion or future recommendations regarding how to improve the performance in terms of energy efficiency and environmental pollution. There should be more concise action words to address this issue. Below are some of my concerns:\nI am against putting Table-2 altogether. Everyone knows how to search, and it should not be on the table. The references are included, which should suffice the explanation of the search method.\n\nWhat are the authors' conclusions about the different types of cooking stoves? Which design is better and why? More explanations are necessary. Also, I advise including their design and working principles.\n\nThe authors mention, \"this finding will help researchers, organizations and government to investigate and implement this type of cooking stoves based on the geographical location so that the adoption rate of the research can increase.\" If these stoves are already in use in those locations, it is unclear why the government should implement them. They are already in use.\n\nThe authors talk about different materials. While it is clear why steel stoves are widely used for fabricating gas stoves, I am not clear why other materials are there. Do those materials improve the design and efficiency? More explanation is necessary.\n\nFor each fuel, there should be sufficient research on the health impact and environmental pollution. The authors should conduct a review in these areas and add it to this work, and it should not be left for future recommendations.\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? No", "responses": [ { "c_id": "9583", "date": "05 Jul 2023", "name": "Md Insiat Islam Rabby", "role": "Author Response", "response": "Thank you very much for reviewing the manuscript. The paper has been revised according to the reviewer suggestions and comments. The responses for reviewer comments are as follows: 1. I am against putting Table-2 altogether. Everyone knows how to search, and it should not be on the table. The references are included, which should suffice the explanation of the search method. Response: Thank you for the suggestion. The table has been removed. 2. What are the authors' conclusions about the different types of cooking stoves? Which design is better and why? More explanations are necessary. Also, I advise including their design and working principles. Response: Thank you for the suggestion and advice. Authors added the design, working principal and reason of performance for different identified gas stoves. 3. The authors mention, \"this finding will help researchers, organizations and government to investigate and implement this type of cooking stoves based on the geographical location so that the adoption rate of the research can increase.\" If these stoves are already in use in those locations, it is unclear why the government should implement them. They are already in use. Response: This review only summarized the articles those are experimentally conducted in laboratory by different researchers and identified thermal performances. Authors did not get any evidence from the literature that those are implanted and used in big scale in those geographical areas therefore authors mentioned that statement based on the findings from literature. However, for readers continence authors made the following revisions: “this finding may help researchers, organizations and government to investigate and implement this type of cooking stoves based on the geographical location so that the adoption rate of the research can increase” 4. The authors talk about different materials. While it is clear why steel stoves are widely used for fabricating gas stoves, I am not clear why other materials are there. Do those materials improve the design and efficiency? More explanation is necessary. Response: Thank you for looking on it. During discussing materials authors missed some points therefore this section seems unclear. For manufacturing stoves steel was used in all studies, while other mentioned materials usually used for insulation purposes. Authors revised the “Materials to fabricate stoves” section accordingly. 5. For each fuel, there should be sufficient research on the health impact and environmental pollution. The authors should conduct a review in these areas and add it to this work, and it should not be left for future recommendations. Response: Thank you for the valuable suggestion. Authors also believe that health impact and environmental pollution are very concerning factors for cooking stoves. However, the current systematic literature review only limited to thermal performance of gasifier cooking stoves. Health impact and environmental pollution are not scope of this review. Therefore, authors only showed the relationship between fuels and thermal performances for gasified cooking stoves. This is a systematic literature review, which was structured and maintained according to the guidelines of a typical systematic review followed by “PRISMA Diagram & Checklist - Systematic Reviews”. Additionally, most of the identified literature for this review did not discuss health impact and environmental pollution are not scopes of this review. Therefore, it will be now very difficult for authors to add health impact and environmental pollution, which were not the scopes for this review. Authors are now writing another critical review article on cooking stoves wherein health impact and environmental pollution are considered and given priority, therefore authors do not want to include health impact and environmental pollution in this systematic review." } ] }, { "id": "161509", "date": "10 Feb 2023", "name": "Nawshad Arslan Islam Arslan Islam", "expertise": [ "Reviewer Expertise Advanced Energy Systems", "Carbon Negative/Carbon Neutral Hydrogen", "Blue Hydrogen", "Green Hydrogen", "Advanced Power Cycle", "Gasification Systems", "High speed Flow dynamics", "High Pressure Combustion", "SCO2 power cycles", "High Turbulence Combustion", "Digital Engineering", "Digital Twin", "Smart Grid", "Microgrid", "V2G", "V2L", "V2H", "V2X", "Digitally Interconnected Energy Infrastructure", "CFD", "FEA. Experimental Thermo-fluids" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 focuses on gasifier stoves and their thermal performances. I applaud the hard work of the authors, however there are significant improvements required.\n\nAlthough the literature may be limited due to the technology being limited to use in certain parts of the world, a wide range of technical resources can be found based on gasification process and biomass power generation. the review fails to merge the scientific relations between such processes and hence does not provide any technical information behind statistical data? For example, the article states wood pellet shows better efficiency but fails to analyze the reason behind it.\nAlthough a review article, it should necessarily go over adequate amount of technology description. For example the article provides no background on how thermal performances are measured, what experiments are usually performed, examples of such set ups. For a small review of 28 literatures, it was possible to have in depth discussion of some of the technical aspects and design aspects.\nIn addition, the review focuses a lot on how the articles were searched and geological location of research and how often research was published. However, I do not think these are relevant and provide any scientific merit to the work.\nI have several recommendations for the authors, if followed will greatly improve the quality of the article. My recommendations are listed below-\nAbstract should not contain how articles were searched. this is irrelevant for technical paper review. It should focus on how many types of stoves you reviewed, how many fuels (feeds) reviewed, some of the technical challenges, methods used to calculate efficiency and a few line summary of why some setups and fuels perform better than others.\n\nIn introduction it would be better to talk about biomass fuel types. There is a broader category of fuel types based on source - Agricultural, Forest, Animal Residue, Solids and Plastic Waste, MSW. And then by constituent of organic matter - Lignin, lignocellulosic, cellulosic, hemi cellulosic etc. Author may want to define the types based such technical norms and then set up the review based on such fuel types. Otherwise the comparisons will not have any common variable. for example woodchip always performs better while agricultural waste will always perform worse due to organic constituent. Thus comparing two different types over several types of stoves will not provide much technical understanding\n\nInstead of Dung authors may want to write Animal Waste. It covers a broader area.\n\nThe Methods section is completely irrelevant to the technical purpose of the article. If it is not required by the Journal Guideline, it is best to remove this section.\n\nReview papers do not contain Results and Discussion. Since authors are describing what is already published in brief.\n\nInstead of Methods and Results and discussion sections, authors may want to have sections as Stove Types - overviewing different stoves and their design and challenges. Types of Experiments Conducted to measure efficiency. Efficiency by fuel type and how it changes, reasoning behind and how stove design influences it.\n\nSimilar to the reasons stated above, Figure 1-4, 6 and Table 1 and 2 does not have any meaningful technical contribution and thus should be removed if not required by Journal guideline.\n\nIn addition, the data for figure 2-6 are questionable. Since the author filters a lot of literatures, such numbers do not reflect actual scenario. Thus it is best to avoid it.\n\nThere is a tremendous scope to add technical reasoning for this review. For example, each type of cooking stove efficiency should be backed up by how it was measured and what setup was used and how to calculate it.\n\nSimilar reasoning should also be used to describe efficiency issues for fuels\n\nWhy was swirl vane producer gas burner was not included in gasified stoves comparison in figure 7. Essentially Gasification or Gasified process results in producer gas?\n\nWhy does the premixed producer gas with swirl vane have a very high efficiency compared to other technologies? Please describe\n\nSimilarly why does wood pellets perform better than corn straw? Please describe\n\nSimilar descriptions should be provided for all cases presented in Table 3, 4 and 5\nI wish the authors best of luck with their future 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? No\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", "responses": [ { "c_id": "9582", "date": "05 Jul 2023", "name": "Md Insiat Islam Rabby", "role": "Author Response", "response": "Thank you very much for reviewing the manuscript. The paper has been revised according to the reviewer suggestions and comments. The responses for reviewer comments are as follows: 1. Abstract should not contain how articles were searched. this is irrelevant for technical paper review. It should focus on how many types of stoves you reviewed, how many fuels (feeds) reviewed, some of the technical challenges, methods used to calculate efficiency and a few line summary of why some setups and fuels perform better than others. Response: Thank you for the concern. This is actually a systematic literature review paper not a technical review paper. Therefore, reviewer might me confused on about the current review. Authors maintained PRISMA systematic literature review process, which was provided by the journal to make a good systematic literature review. In published other systematic review papers it is common to mention how articles were searched and how many articles were selected for review. However, authors added the number of stoves and fuels identified from literature in the Abstract section. 2. In introduction it would be better to talk about biomass fuel types. There is a broader category of fuel types based on source - Agricultural, Forest, Animal Residue, Solids and Plastic Waste, MSW. And then by constituent of organic matter - Lignin, lignocellulosic, cellulosic, hemi cellulosic etc. Author may want to define the types based such technical norms and then set up the review based on such fuel types. Otherwise the comparisons will not have any common variable. for example woodchip always performs better while agricultural waste will always perform worse due to organic constituent. Thus comparing two different types over several types of stoves will not provide much technical understanding Response: Thank you for the nice suggestion. As this study, mainly focus on revising gasified cooking stoves and its thermal performance therefore in the introduction section talk about fuel types is beyond the scope of the review. The main focus of the literature review is gasified cooking stoves and thermal performance not fuel types. Even those published articles we reviewed from literature they also did not discuss on fuel types and physical characteristics of fuels. Therefore, authors want to keep the arrangement of introduction section as it is. However, authors added working principal and design of different gasified cooking stoves in results and discussion section to make the review more standard. 3. Instead of Dung authors may want to write Animal Waste. It covers a broader area. Response: Thank you so much for the suggestion. Authors changed dung to animal waste. 4. The Methods section is completely irrelevant to the technical purpose of the article. If it is not required by the Journal Guideline, it is best to remove this section. Response: This is actually a systematic literature review paper not a technical review paper. Therefore, reviewer might me confused on about the current review. Authors maintained PRISMA systematic literature review process, which was provided by the journal to make a good systematic literature review. In published all systematic review papers reviewer can easily find method section. It is a mandatory part for systematic literature review according to PRISMA guideline. Therefore, authors added this section otherwise it will not be a systematic review. 5. Review papers do not contain Results and Discussion. Since authors are describing what is already published in brief. Response: This is actually a systematic literature review paper not a technical review paper. Therefore, reviewer might me confused on about the current review. Authors maintained PRISMA systematic literature review process, which was provided by the journal to make a good systematic literature review. In published all systematic review papers reviewer can easily find result and discussion section. It is a mandatory part for systematic literature review according to PRISMA guideline. Therefore, authors added this section otherwise it will not be a systematic review. 6. Instead of Methods and Results and discussion sections, authors may want to have sections as Stove Types - overviewing different stoves and their design and challenges. Types of Experiments Conducted to measure efficiency. Efficiency by fuel type and how it changes, reasoning behind and how stove design influences it. Response: This is actually a systematic literature review paper, not a technical review paper. Therefore, the reviewer might be confused about the current review. Authors maintained PRISMA systematic literature review process, which was provided by the journal to make a good systematic literature review. In published all systematic review papers reviewer can easily find result and discussion sections. It is a mandatory part for systematic literature review according to PRISMA guidelines. Therefore, authors added this section otherwise it will not be a systematic review. However, the authors added a subsection on different cooking stoves according to reviewer's suggestion where design and working principles were discussed. 7. Similar to the reasons stated above, Figure 1-4, 6 and Table 1 and 2 does not have any meaningful technical contribution and thus should be removed if not required by Journal guideline. Responses: Authors removed Table 2 and Figure 3. The authors want to keep others' figures and tables to maintain the systematic review protocol. 8. In addition, the data for Figure 2-6 are questionable. Since the author filters a lot of literature, such numbers do not reflect the actual scenario. Thus it is best to avoid it. Responses: Authors want to keep these figure and tables to maintain systematic review protocol. As the search and article selection protocol maintained a systematic method therefore the presented scenario is actual. 9. There is a tremendous scope to add technical reasoning for this review. For example, each type of cooking stove efficiency should be backed up by how it was measured and what setup was used and how to calculate it. Response: The measurement process of efficiency and setup were not scope of the review. Authors working on a general technical review on cooking stoves where these will be added. 10. Similar reasoning should also be used to describe efficiency issues for fuels Response: The measurement process of efficiency and setup was not the scope of the review. Authors working on a general technical review on cooking stoves where these will be added. 11. Why was swirl vane producer gas burner was not included in gasified stoves comparison in figure 7. Essentially Gasification or Gasified process results in producer gas? Responses: Thank you for the comment. The performance of swirl vane producer gas burner was identified as range (84% to 91% ) in literature therefore it was not included in Figure 7. In Figure 7, only those stoves' performance that was not in range was plotted. However, in discussion, the performance of swirl vane producer gas burner is included. 12. Why does the premixed producer gas with swirl vane have a very high efficiency compared to other technologies? Please describe Response: Thank you for the suggestions. The reason has been included in “Thermal performance of different gasified cooking stoves” section. The added part is as follows: “Swirl vanes use in stoves are usually a flame retardant device that highlights the recirculation zone formation to improve the mixing of flame stabilization and reactants compared to other stoves. Due to the improvement in flame stabilization and reactants mixture, the performance and efficiency of the stoves are increased compared to other stoves” 13. Similarly why do wood pellets perform better than corn straw? Please describe Response: Thank you for the suggestions. The reason has been included in the “Thermal performances of cooking fuels for gasified cooking stoves” section. 14. Similar descriptions should be provided for all cases presented in Tables 3, 4 and 5 Response: Short description has been provided for all cases presented in Tables 3, 4 and 5" } ] } ]	1	https://f1000research.com/articles/12-38
https://f1000research.com/articles/12-780/v1	05 Jul 23	{ "type": "Research Article", "title": "Effectiveness of half-day interactive continuing medical education workshop in improving oncologists’ knowledge in prescribing opioids", "authors": [ "Nabil A. Almouaalamy", "Mohammed B. Abrar", "Sittelbenat H. Adem", "Abdelmajid Alnatsheh", "Mohammed B. Abrar", "Sittelbenat H. Adem", "Abdelmajid Alnatsheh" ], "abstract": "Background: Patients with cancer commonly experience persistent pain, and opioids have remained the mainstay of pain treatment because of their rapid effectiveness in treating moderate to severe pain. As medicine progresses, we need to establish continuous medical education sessions to educate, update, and establish competency in opioid prescribing in cancer patients. Aim: The objective of this study was to explore whether continuing medical education interventions improve oncologists’ knowledge about pain management when prescribing opioids. Methods: We conducted a cross-sectional prospective pre- post-test study. Continuing medical education workshops lasting three identical half-days was offered in 2019. Training sessions were held at the Princess Noorah Oncology Education Center. A total of 40 participants were recruited from a single discipline (oncology) rather than from multiple disciplines for the workshops. The continuing medical education program included six lectures and case presentations. An assessment of 16 multiple-choice questions (case scenario format) with four options was administered to the participants before the training workshop. Results: The mean scores of the participants’ knowledge increased from 9.48 (pre-test) to 11.93 (post-test). This improvement was statistically significant (p < 0.001). A novel finding of this study is that continuing medical education lasting a half-day is as effective as a one-day workshop and even superior to traditional continuing medical education lasting two days. Conclusions: A half-day continuing medical education program significantly improved physicians’ knowledge of prescribing opioids in cancer patients. This study suggests that a well-designed continuing medical education program is essential for its success.", "keywords": [ "Continuing medical education", "opioids", "workshops." ], "content": "Introduction\n\nPatients with cancer commonly experience persistent pain, on average 30%–50% of patients undergoing active cancer therapy and 75%–90% with advanced disease suffer from chronic pain that necessitates pain management.1,2\n\nCurrently, opioids have remained the mainstay of treatment because of their rapid effectiveness in treating moderate to severe pain.3 However, a systematic review published in 2008 revealed that 43.4% of cancer patients were undertreated according to the Pain Management Index (PMI).4\n\nThe undertreatment of pain is a worldwide phenomenon. In recent years, however, health professionals have identified pain educational efforts as an important step towards making pain management more effective.5 The lack of formal education in medical schools is one reason why continuing medical education (CME) is useful for educating doctors on pain management.5\n\nMedical professionals have a constant need to incorporate new concepts into their practice to remain medically competent. The CMEs program makes it possible for physicians to learn about the ever-evolving body of medical knowledge while maintaining their clinical competencies, but there has never been a study that evaluated whether CME can improve the knowledge of oncology physicians regarding opioid prescribing for patients with cancer.6–11Conducting such studies is critical to ascertain whether a CME workshop is necessary to improve the knowledge deficiency in pain management and prescribing opioids among physicians. To accomplish this, a team of palliative care pain experts developed a CME activity geared towards oncologists to improve their knowledge and attitudes toward chronic cancer pain management and opioid prescription.\n\nThe primary goal of this study was to explore whether CME interventions improve oncologists’ knowledge of pain management and prescribing opioids. The secondary objective was to determine the effectiveness of a half-day workshop with traditional training, which consisted of one or two days.\n\n\nMethods\n\nThis was a cross-sectional, prospective pre- and post-study performed at a single site. In this study, a convenience sample design involving 40 healthcare professionals from our oncology department was used. The study population consisted of staff physicians, residents, assistants, associate consultants, and consultants from our oncology department with varying levels of experience and training. The workshops were conducted three times in 2019 in the education room at the Princess Noorah Oncology Center (PNOC) at King Abdulaziz Medical City, Jeddah. Each workshop accommodated 8–17 participants; with a total of 40 participants. The same presenters and the same material were presented in each workshop. All study participants provided written informed consent, and the study design was approved by the ethics review board of King Abdullah International Medical Research Centre, study number RJ20/171/J.\n\nA team consisting of three pain specialists from our palliative care unit in collaboration with a pharmacist designed the contents of the CME course. This program includes a half-day workshop on pain management and prescribing opioids for cancer patients, geared primarily toward oncologists. The CME workshop was tailored to a small group of specialists within a single field of medicine and designed to provide participants with knowledge and skills. Oncologists should be knowledgeable about the use of opioid therapy while considering their educational needs. The CME activity consisted of six lectures, case presentations, and discussions. The content of this lecture includes cancer pain principles: pathophysiology and assessment; cancer pain management: non-pharmacological and pharmacological; opioids pharmacologically; opioids prescribing in cancer patients: WHO guidelines and pathways, opioid rotation and conversion, and prevention and treatment of opioids’ side effects, and complications also opioids use disorders.\n\nBased on our need our assessment instrument was targeting opioid prescribing in cancer patients and based on a questionnaire from previous studies, a comprehensive questionnaire that fulfills our workshop objectives was drafted.12–15 The content validity of the pre- and post-test was accomplished by the tool that was devised and reviewed by three specialized palliative physicians who were experienced in prescribing opioids to cancer patients and if there’s any issue in understanding the question. At the beginning of the workshop, participant physicians were asked to complete the pre-test assessment which consisted of 16 multiple choice questions (case scenario format) with four options. Each question had one mark. For the correct answer, one mark was awarded. For any wrong answer or any question answered with more than two choices no mark was given. A scoring system based on the correct answers was employed. Since cancer pain assessment, management, and safe opioids prescribing are connected, a total of 16-item multiple-choice questions in the case scenario (Table 1) format were prepared in three parts including pain assessment, opioids prescribing, and opioids side effect assessment and management. The pain assessment domain had three questions, the opioids prescribing domain had eight questions, and the opioids side effects assessment and management domain had five questions. The opioids equianalgesic table (British Columbia opioids equianalgesic table) was included in the question sheet.16\n\n\n\n• To assess cancer pain and its severity.\n\n• To manage cancer pain according to WHO ladder WHO Analgesic Ladder.\n\n• To demonstrate prescribing skills by starting the Appropriate Opioid drug and with appropriate starting dose as per our Saudi national palliative care guidelines.\n\n\n\n• To identify that the patient is having severe pain and have to be started on strong opioids (Morphine).\n\n• To manage her pain first and to complete the assessment after she settles down.\n\n• To discuss side effects with the patients and start preventive measures for those side effects.\n\nAs part of the pre-test questionnaire, data were also collected concerning age, gender, occupation, level of physician (staff physician, resident, clinical fellow, assistant consultant, associate consultant, and consultant), and years of oncology practice. Details of previous pain education (yes/no) were also obtained.\n\nThe mean and standard deviation was used to describe continuous variables and the frequencies and percentages for the categorical variables. The Kolmogorov-Smirnov test and the histograms were used to assess the statistical normality assumption for the physician’s continuous measured variables. The multivariate Generalized Linear Mixed Modelling was used to assess the predictors for the change in the physician’s knowledge score on opiate prescription from before to after the workshop, but the data was restructured from long-to-wide data via the data restructuring feature before the generalized linear mixed analysis was used yielding a data matrix equal to (40 subjects × 2 repeated knowledge score measures = 80 records), the associations between the predictors with the physician’s knowledge on opiates were expressed as a beta coefficient with 95% confidence interval. The Cohen’s D effect size statistic was used to quantify the size of the change in physician’s knowledge from before to after the educational session. Chi-square was used to compare the effectiveness of the workshops. p < 0.05 was used to indicate a statistically significant result.\n\n\nResults\n\nA total of 40 physicians attended the workshop and completed the pre-test and post-test assessments. Half of them were male, and the remaining half were female. The average age of the participants was 38.60 years, and the SD was 6.40 years. However, 65% of the participating physicians were under forty, and 35% were over 41. The mean number of years experience in oncology for the physicians was equal to four years, SD = 2.24 years, and the distribution of their medical level was as follows: 25% of the participating physicians were clinical fellows, most of them 45% were staff physicians and another 17.5% of the physicians were assistant consultants, 7.5% were associate consultants and 5% were indeed oncology consultants. A majority of the doctors, 70%, were juniors and 30% were senior oncology doctors. A descriptive analysis of physicians’ socio-demographic characteristics and professional characteristics appears in Table 2.\n\na Jun-staff Phys and Sen-staff Phys stand for junior and senior staff physicians, respectively.\n\nOn the pre- and post-test, the mean physicians’ knowledge scores on prescribing opiates were 9.48 and 11.93, respectively. Subsequently, the mean physicians’ knowledge score was raised by 2.54 following the post-test which was statistically significant with a p < 0.001 and a 95% confidence interval of (1.157%–3.743%), t = 0.831, df = 39. Based on the Cohen’s D effect size statistic (0.61), the learning session resulted in a substantial (moderate) increase in physicians’ knowledge of opiate prescribing (Table 3).\n\nBased on the marks they received, physicians were categorized into four grades: Grade A, 90% and above, Grade B, 75%–89%, Grade C, 50%–74%, and Grade D, below 50%, as shown in Table 4. The pre-test score distribution was 7.5% grade A, 5% grade B, 67.5% grade C, and 20% grade C, whereas the protest score distribution was 20.0% grade A, 35% grade B, 37.5% grade C, and 7.5% grade C. The workshop results showed that five of the eight participants who scored a D in the pre-test (5/8 = 62.5%) were able to achieve a C or higher.\n\nPre-test results show that only 12.5% of the participating physicians scored 12 or more out of 16 while on post-test 55% scored more than 12 points (Table 4). A significant increase of 42.5% in the number of physicians who scored post-test p < 0.0001 (Figure 1).\n\nNote: A: 90% or above; B: 75%–89%; C: 50%–74%; D: <50%.\n\nTo ascertain our findings from the bivariate analysis the data was transposed from long-to-wide data format yielding a data matrix equal to (40 subjects × 2 repeated knowledge measured scores = 80) and generalized linear mixed methods analysis was used to regress physicians repeated measured knowledge scores against the time (post- versus pre-education) with the physician’s other factors like their experience, level, and gender. The yielded findings from the multivariate analysis (Table 5) showed that the physician’s sex, experience, and seniority did not converge significantly on their knowledge score before and after the educational session was attended, but the analysis model showed that the physician’s knowledge after the educational session was significantly greater than before attending the session on average, beta coefficient = 2.450, p < 0.001, by considering the other predictor variables as accounted for, however, therefore it can be implied that regardless of the oncology physicians sex, age, experience and rank the educational session is effective at enhancing their opiate prescription in the palliative oncology settings (Table 5).\n\n\nDiscussion\n\nWe present some key findings of this study. First, the CME sessions at the three half-day workshops were effective in improving physicians’ knowledge. The average pre-test score was 9.48 and that of the post-test was 11.93. An increase of 20.5% in mean scores from pre-test to post-test. The difference in mean scores between pre-test and post-test was significant, p < 0.001. Literature has shown that the pre- and post-test score technique used in our study is a reliable and valid indicator of knowledge gain among participants.9 Furthermore, several studies have demonstrated an improvement in physician knowledge as an indicator of the effectiveness of CME programs.17–19 Many studies in the literature show that CME and other forms of educational training can improve participants’ knowledge.20–22 Our findings corroborate these findings.\n\nSecond, socio-demographic factors do not predict higher levels of knowledge post-workshop. Our study found that the improvement in mean pre- and post-test scores (gain in knowledge) was achieved regardless of the difference in age, gender, experience, or ranking of oncology physicians. Even though these predictors contributed to higher knowledge post-workshop, the effect was not statistically significant (Table 5). A difference between pre- and post-test scores because of age, gender, type of practice, or the number of years since training commenced was not statistically significant. The findings are similar and confirm the findings of an earlier study conducted by Nazim et al, which indicated no significant differences between pre- and post-scores regardless of demographic factors such as gender, age, or type of practice of the participant.10\n\nThird, in the resent study, post-test scores improved markedly for physicians who obtained lower grades in the pre-test, while those who received higher grades in the pre-test continued to receive higher grades with a significant improvement in their post-test scores. Out of the eight physicians who completed the pre-test with a Grade D, five (62.5%) advanced to Grade C or higher. Among the 27 participants who achieved a Grade C, 12 (80%) advanced to Grade B or higher. Furthermore, 35 (87.5%) physicians scored Grade C or less on the pre-test compared to 18 (45.0%) on the post-test, a 42.5% decrease in the number of physicians scoring <75% in pre-test, p < 0.0001. These findings indicate a significant increase in the number of physicians securing higher grades of marks. Shivaswamy et al. used pre-test and post-test questionnaires to explore improvement in knowledge of acne among medical students and found a similar pattern to ours.21 The study by Chan et al. sought to evaluate the attitude and changes in the clinical knowledge of emergency physicians and nurses through a training course and found significant improvements on the part of the participants.22 Interestingly, they reported similar distributions of scores between pre-test and post-test to those observed in the present study.\n\nFurthermore, several studies have demonstrated an improvement in physician knowledge as an indicator of the effectiveness of CME programs.17–19 However, the effectiveness of various workshops has not yet been examined in a study. To gain some insight into the effectiveness of different CME workshops, we compared workshops lasting three hours, a full day, and two full days. Within the ambulatory setting, Vettese et al. conducted a three-hour interactive workshop that focused on teaching internal medicine residents responsible opioid usage and effective chronic pain management.19 They found that, at the postintervention knowledge test, residents scored 73% correct, higher than 51% at the preintervention test, an increase of 22.0%. There was no significant difference between their and our findings, p = 0.202.\n\nGupta et al. presented a one-day CME workshop on thyroid cancers and their management aimed mainly at the surgical oncologists, otolaryngologists, head-neck surgeons, and other healthcare professionals relevant to the management of thyroid diseases.20 Pre-test scores averaged 24.8 and post-test scores averaged 31.90, an increase of 22.2% compared to the 20.5% difference in the current study, p < 0.699. It follows that a half-day CME is as effective as a full-day CME. Unlike Gupta, Nazim et al.10 evaluated whether a two-day CME program could improve urologists’ clinical and operative knowledge of urology. There was a significant difference between the pre-test mean score of 37.8% and the post-test mean score of 50.3%, suggesting that the workshop improved knowledge. However, their finding differs significantly from that in the present study, p < 0.033. This finding reveals that a two-day workshop is less effective than a half-day CME workshop. Based on the above findings, we conclude that CME lasting a half-day is as effective as a one-day workshop and even superior to traditional CME lasting two days.\n\nThird, our study also found that a half-day CME workshop tailored to a small group of specialists within a single field of medicine is as effective as a one- or two-day program.\n\nTo our understanding, this study is the first to compare half-day workshops with traditional training, which consists of one day or two days. It provides empirical evidence that suggests a CME lasting a half-day may be more effective than the traditional CME lasting two. If this novel finding is substantiated by other studies, it may change the current CME practice and also have potential economic benefits and time savings implications.\n\nThere were a few limitations to our study. First, the present study is a cross-sectional study from a single oncology department, and a small sample size of oncologists, the findings cannot be generalized to all medical professionals or other healthcare professionals or other oncology centers. Second, the present study focused exclusively on short-term knowledge gain and improvement and was unable to follow up on long-term knowledge retention or knowledge improvement. Third, no evaluation of the CME program was undertaken to determine whether it improved clinical practice or patient outcomes. Consequently, the intervention must be evaluated over several months to determine its long-term effectiveness and sustainability.\n\n\nConclusion\n\nOur study demonstrates that a well-designed half-day CME workshop course can improve oncologists’ knowledge on pain management and opioids physicians. In addition, the present study confirmed previous studies that socio-demographic factors contributed to higher knowledge levels post-workshop but not significantly. Age, gender, and years of experience of physicians, or their ranking did not predict higher levels of knowledge after the workshop.\n\nInstitutional Review Board statement: The study was conducted according to the guidelines of the Declaration of Helsinki and approved by King Abdullah International Medical Research Centre ethics review board, study number RJ20/171/J.\n\nInformed consent statement: Informed verbal and written consent was obtained from all subjects involved in the study.", "appendix": "Data availability\n\nFigshare: Effectiveness of half-day interactive continuing medical education workshop in improving oncologists’ knowledge in prescribing opioids, https://doi.org/10.6084/m9.figshare.22776356.v1. 23\n\nThis project contains the following underlying data:\n\n- Opioids Prescribing data Final.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\nVan den Beuken-van Everdingen MHJ, de Rijke JM , Kessels AG, et al.: High prevalence of pain in patients with cancer in a large population-based study in The Netherlands. Pain. 2007; 132: 312–320. PubMed Abstract \| Publisher Full Text\n\nTeunissen SCCM, Wesker W, Kruitwagen C, et al.: Symptom prevalence in patients with incurable cancer: A systematic review. J. Pain Symptom Manag. 2007; 34: 94–104. PubMed Abstract \| Publisher Full Text\n\nWiffen PJ, Wee B, Derry S, et al.: Opioids for cancer pain - an overview of Cochrane reviews. Cochrane Database Syst. Rev. 2017; 2020: CD012592. Publisher Full Text\n\nGreco MT, Roberto A, Corli O, et al.: Quality of cancer pain management: An update of a systematic review of undertreatment of patients with cancer. J. Clin. Oncol. 2014; 32: 4149–4154. PubMed Abstract \| Publisher Full Text\n\nWatt-Watson J, Hunter J, Pennefather P, et al.: An integrated undergraduate pain curriculum, based on IASP curricula, for six health science faculties. Pain. 2004; 110: 140–148. 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PubMed Abstract \| Publisher Full Text\n\nMesseri A, Scollo Abeti M, Guidi G, et al.: Pain knowledge among doctors and nurses: A survey of 4912 healthcare providers in Tuscany. Minerva Anestesiol. 2008; 74: 113–118. PubMed Abstract \| Publisher Full Text\n\nBakshi SG, Jain P, Kannan S: An assessment of basic pain knowledge and impact of pain education on Indian anaesthesiologists - a pre and post questionnaire study. Indian J. Anaesth. 2014; 58: 127–131. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBC Guidelines and Protocols Advisory Committee: Palliative care for the patient with incurable cancer or advanced disease - Part 2: Pain and symptom management. Report. Victoria, BC, Canada: Government of British Columbia; 22 February 2017. Reference Source\n\nGifford DR, Mittman BS, Fink A, et al.: Can a specialty society educate its members to think differently about clinical decisions? Results of a randomized trial. J. Gen. Intern. Med. 1996; 11: 664–672. Publisher Full Text\n\nHarris JM Jr, Kutob RM, Surprenant ZJ, et al.: Can Internet-based education improve physician confidence in dealing with domestic violence? Fam. Med. 2002; 34: 287–292. PubMed Abstract\n\nVettese TE, Thati N, Roxas R: Effective chronic pain management and responsible opioid prescribing: Aligning a resident workshop to a protocol for improved outcomes. MedEdPORTAL. 2018; 14: 10756. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGupta K, Mandlik D, Patel P, et al.: Does continuing medical education (CME) activity contribute to learning gain? An objective evaluation. Indian J. Otolaryngol. Head Neck Surg. 2019; 71: 289–293. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShivaswamy KN, Shyamprasad AL, Sumathy TK, et al.: Knowledge of acne among medical students: Pretest and posttest assessment. ISRN Dermatol. 2014; 2014: 727981. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChan CH, Chan TN, Yuen MC, et al.: Evaluation of a simulation-based workshop on clinical performance for emergency physicians and nurses. World J. Emerg. Med. 2015; 6: 16–22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlmouaalamy N: Effectiveness of half-day interactive continuing medical education workshop in improving oncologists’ knowledge in prescribing opioids data.xlsx. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "239196", "date": "27 Feb 2024", "name": "Hao Zhang", "expertise": [ "Reviewer Expertise Health service research", "health economics", "health policy." ], "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 examines the association between a half-day education workshop on opioids and oncologist's knowledge on pain management and opioids prescribing, I have serious concerns regarding the study design.\nTo begin with, the researchers assessed participants' baseline knowledge through a set of 16 multiple-choice questions. Following this pretest, participants engaged in a half-day workshop, and their knowledge was reevaluated using the same set of questions. It is anticipated that the test scores would show an increase post-workshop due to the participants' exposure to the questions within a relatively short timeframe. However, the more interesting question is the workshop's impact on participants' knowledge over the long term. This could be achieved by measuring post-test knowledge using a different set of questions after a designated period, such as two months.\nSecondly, the study's findings might be influenced by selection bias since the participants were drawn from a convenience sample. The study did not assess how the characteristics of participants differed from those who chose not to participate. It is conceivable that individuals who opted to take part in the study were those who lacked knowledge on opioids and were motivated to enhance their understanding through training.\nFurthermore, the study participants were sourced from a single center, and the workshop was conducted at three distinct times. There is a potential concern that individuals participating in the second and third workshops may have already acquired some information through their colleagues who attended earlier sessions.\nFinally, the authors noted a secondary objective of the study was to assess the effectiveness of a half-day workshop with traditional training. However, this evaluation was conducted by comparing the increase in test scores with those from previous studies, which had differing study designs, sampling frames, and test questions. I doubt if this would yield a valid comparison and question the author's conclusion that the half-day workshop is superior to traditional CME.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "230046", "date": "13 May 2024", "name": "Brian J. Piper", "expertise": [ "Reviewer Expertise Pharmacoepidemiology of opioids", "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 manuscript “Effectiveness of half-day interactive continuing medical education workshop in improving oncologists’ knowledge in prescribing opioids” by Almouaalamy and colleagues addresses a timely and important question, has a sufficient sample, and is reasonably well written.\nGeneral concerns:\nThe abstract contains information about “A novel finding …” but the methods did not describe or compare the one-day workshop. This information should be removed.\n\nSimilarly, the discussion paragraph starting with “Gupta …” attempts to draw sweeping conclusions about different lengths of workshops. However, they have different content/audiences/assessments so this comparison should be trimmed or just deleted. The way the methods are currently written, the current dataset is only from a half-day training. The “To our understanding” paragraph attempts to go way beyond their data and should be trimmed or just deleted.\nMinor points:\nIntro, 2nd paragraph: This should be expanded to include other citations besides the 15 year old systematic review.\nIntro, 3rd paragraph: “The undertreatment of pain is a worldwide phenomenon.” It may not be common knowledge but the US (and Canada too to a lesser extent) was very concerned about over-treatment of pain, particularly with oxycodone. There is world pharmacoepidemiology about how some countries may under-treat pain but this is not homogenous.\nMethods: CME paragraph: side effects, complications, and opioid use disorders.\nMethods: Assessment: avoid contractions such as “there’s” in more formal writing like this.\nTable 1: generic drug names (e.g. morphine) should be in lower-case.\nConsider including some citation(s) for the Saudi national palliative care guidelines.\nStatistics: What software and version was used for the data-analysis? I am more used to seeing the d in Cohen’s d in lower-case.\nStarting a sentence with a lower-case “p” is a bit odd. Consider “A p value of < .05 ...”\nTable 2. Consider reporting all percentages to the tenths place (e.g. 50.0). For Age < 40 years, 26 / 40 is reported as 69 but shouldn’t it be 65.0? For Consultant, 1 / 40 is reported as 5 but shouldn’t this be 2.5%?\nTable 3: A column for N (ideally 40 for both) would be more helpful.\nResults: Knowledge: The term “opiates” is often used for plant based and “opioids” as the broader category including natural, semi-synthetic, and synthetic substances. Consider whether “opioids” would be more appropriate here. Also, please double-check that t value (0.831) as that might be too low to be statistically significant. (Based on the means and SD, this should be a statistically significant finding).\nConsider having a figure or table (but not both) for the grade. The figure (Excel) is ok although somewhat grainy for this reviewer's copy. For future projects, consider professional graphing software (e.g. GraphPad Prism has a free trial).\nLight suggestion: Are there PAs in Saudi Arabia involved in oncology? If so, a future direction might be to include them in the professional development.\nConclusion, first sentence: “and opioids among physicians.”\nConsider deleting the “In addition, … after the workshop” (i.e. last two sentences) as this study was not sufficiently powered to address age, years or experience, etc. type questions.\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/12-780
https://f1000research.com/articles/12-779/v1	05 Jul 23	{ "type": "Research Article", "title": "Upper extremity kinematics of a 3D reach-to-grasp-to-mouth task in sub-acute stroke survivors in comparison with healthy controls", "authors": [ "Sanjukta Sardesai", "John Solomon M", "Ashokan Arumugam", "Elton Dylan Nazareth", "Aparna R Pai", "Senthil Kumaran D", "Sanjukta Sardesai", "John Solomon M", "Ashokan Arumugam", "Elton Dylan Nazareth", "Aparna R Pai" ], "abstract": "Background\nOnly 5-20% of stroke survivors exhibit almost complete motor recovery at six months post-stroke. The Stroke Recovery and Rehabilitation Roundtable (SRRR) Taskforce has recommended the use of performance assays that predict recovery. However, not much is known about the differences across various stroke severity groups. The purpose of this study was to determine whether kinematic parameters of time, average velocity, shoulder angles and elbow angles were able to distinguish upper extremity movement capacity in individuals with varying levels of stroke severity and healthy controls. Methods: This is a cross-sectional study, which is part of a large cohort study. 27 sub-acute stroke survivors (58.8 ± 12.7 years; 18 males, 9 females; categorized into mild (51-66), moderate (25-50) and severe (<25) Fugl Meyer Assessment of Upper Extremity (FM-UE) categories and 10 healthy controls (48.9 ± 13.7 years; 6 males, 4 females) performed 20 trials of a 3D reach-to-grasp-to-mouth task. Kinematic parameters were analyzed using a one-way ANOVA test. Results: Movement time was significantly different between severe and all other stroke groups (mild [p<0.001], moderate [p<0.001]) and healthy controls (p<0.001). Average velocity was significantly different between all three stroke groups (mild [p=0.03], moderate [p<0.001], severe [d= -3.7, p<0.001]) and healthy controls. Elbow flexion was significantly different between moderate and severe stroke groups (p=0.009). Elbow extension showed significant differences between mild and moderate stroke groups (p<0.001). Shoulder extension exhibited significant differences between mild (p<0.001), moderate (p<0.001) and severe (p<0.001) and healthy controls. Conclusions: Kinematic analysis of a reach-to-grasp-to-mouth task helps to differentiate between varying groups of severity post-stroke such as mild, moderate and severe, based on Fugl Meyer for Upper Extremity scores.", "keywords": [ "Hemiparesis", "Kinematics", "Upper limb recovery" ], "content": "Introduction\n\nStroke is the second commonest cause of mortality. In 2019, globally, there were 12.2 million incident strokes and 6.55 million deaths due to stroke.1 Along with being a global phenomenon, stroke is also one of the crucial triggers of early mortality and disability in low as well as low-to-middle income countries. These countries experience demographic changes and an increased prevalence of modifiable risk factors.2\n\nOnly around 5-20% of stroke survivors exhibit almost complete upper extremity (UE) recovery at six months after a stroke and just half of them are able to return to work.3 This primarily could be attributed to persisting UE impairments in approximately two-thirds of stroke survivors.1 Decreased UE capacity in the form of dysfunction of the arm and hand are predominant contributors toward deficits in performing common activities such as reaching for a target and lifting and holding on to objects thus having a negative effect on participation. These maneuvers are important to perform few of the commonest activities of daily living (ADLs).4–6 Consequently, the above mentioned UE impairments could be one of the main factors that could affect an individual’s quality of life (QOL).7 Hence, the majority of neurorehabilitation research studies focus on the effectiveness of interventions targeting UE motor recovery.\n\nHaving said this, post-stroke recovery transpires through a multifaceted combination of recovery mechanisms paired with certain learning-based processes that include spontaneous biological recovery, compensation and behavioral restitution (also known as true recovery). Spontaneous biological recovery refers to betterment in post-stroke UE recovery even in the absence of a precise and goal-oriented treatment. Compensatory strategies include new behavioral approaches by using intact muscles, joints, and effectors in the affected limb, to accomplish the desired task or goal. Behavioral restitution or true recovery on the other hand, has been defined as a return to near normal patterns of motor control with the impaired extremity. It is the return of some or all of the normal behaviors that were available pre-stroke.8 Some amount of neural repair is necessary for recovery to occur in its true form. Although it is incomplete, some degree of true recovery is almost always achieved post-stroke. It could be the result of the contribution from descending inputs arising from bilateral hemispheres, which could also be responsible in shaping the final motor command reaching alpha motor neurons that innervate the UE musculature for optimal movement control.9\n\nIn conjunction with this, certain other factors have also been found to influence post-stroke recovery which include age, stroke severity, lesion volume or lesion location, uncontrolled hypertension, hyper glycaemia, inflammation,10 intensity of therapy, initial motor impairment, degree of injury to Corticospinal Tract (CST),11 mood, neglect and incontinence.12 Numerous techniques exist for subjective as well as objective measurement of the aforementioned factors. Traditionally, UE deficits post-stroke are evaluated using established clinical scales such as Fugl Meyer Assessment of UE and Action Research Arm Test (ARAT). However, a drawback of these assessments is that they are insufficiently sensitive for capturing the quality of sensorimotor performance because of the use of ordinal scales.13\n\nThis shortcoming could be fulfilled by comprehensive neuroimaging techniques such as Computerized Tomography (CT), Magnetic Resonance Imaging (MRI) with diffusion weighted images, Magnetic Resonance angiography and/or neurophysiological measures namely Electroencephalogram (EEG), Motor Evoked Potentials (MEPs) or Somatosensory Evoked Potentials (SSEPs), and lastly biomechanical measures which include kinematic analysis and Electromyography (EMG). These techniques have been shown to discern the pathophysiological basis of an injury and may be better able to gauge a patient’s recovery potential.11 Of these measures, kinematic parameters can be used to assess an individual’s movement quality. They help in providing objective metrics that have the potential to sensitively capture movement quality and enable the monitoring of motor recovery. Several studies incorporating measures such as 3-D kinematics have shown aberrant motor control post-stroke.14–17 Most of these studies explored kinematic variables of movement time, mean velocity, number of velocity peaks and movement smoothness. However, these studies included mild and moderate stroke participants who were given a non-functional task such as the nine-hole peg test18 or a point-to-target task.19\n\nThe previous studies that have incorporated kinematic analysis as an assessment method, display a lack of standardization of assessment tasks, measurement systems and kinematic metrics.13 Consequently, with the aim of bridging this methodological gap, the Stroke Recovery and Rehabilitation Roundtable (SRRR) Taskforce has recommended the use of performance assays such as grip and pinch strength, 2D and 3D kinematic analysis and finger individuation, that predict post-stroke recovery.20 Nevertheless, most kinematic studies that have investigated UE reaching have demonstrated significant differences between healthy controls and stroke survivors in terms of motor task performance as evidenced by kinematic variables. However, there is a gap in literature addressing kinematic analysis of severely affected stroke participants mainly because of task-related feasibility issues. Thus, studies that investigate functional tasks with ecological validity in stroke survivors are warranted. Hence, the purpose of this study was to assess differences in kinematic parameters such as movement time, average velocity and shoulder and elbow angles between stroke survivors (with different levels of stroke severity – mild, moderate and severe) and healthy controls for a reach-to-grasp-to-mouth task.\n\nWe hypothesized that the kinematic parameters of movement time, average velocity and shoulder and elbow range of motion (ROM) may exhibit differences when compared across the three severity levels post-stroke and also with healthy controls.\n\n\nMethods\n\nThis study has been reported using the Strengthening the Reporting of Observational studies in Epidemiology (STROBE) checklist (Table 1).21\n\nThis is a cross-sectional study, which is part of a large prospective longitudinal cohort study that has been carried out from January 2019 to March 2022. The study protocol was approved by the Institutional Research Committee (IRC), University Research Committee and Institutional Ethics Committee (IEC), (IEC/812/2018). The study has been registered under the Clinical Trials Registry (CTRI number: CTRI/2019/04/018774).\n\nThe study was carried out at the Stroke unit, Department of Neurology, and the Neuromotor Control Laboratory, Department of Physiotherapy in a large tertiary care hospital.\n\nThe participants in this study were patients with stroke admitted to the hospital stroke unit as well as healthy controls with no comorbidities who were recruited as a healthy control group.\n\nEligibility criteria\n\nWe included adults with first ever clinically defined stroke of either gender aged between 18 and 85 years. We also recruited a healthy control group of participants who were age- and gender-matched. We excluded individuals who were admitted after 7 days’ post-stroke, those who were unable to comprehend and follow simple commands (Montreal Cognitive Assessment Score <26),22 those who had undergone craniectomy or craniotomy, those with any pre-existing disorders which could affect the UE functions, individuals with other systemic disorders which could affect survival (e.g. malignant diseases, chronic liver or kidney disease, retroviral diseases), uncooperative patients, individuals with bilateral clinical stroke and those with any conditions precluding kinematic analysis.\n\nProcedure\n\nWe screened all patients with stroke admitted to the Neurology unit for the eligibility criteria. A total of 27 people with stroke and 10 age- and gender-matched healthy controls were recruited based on the aforementioned eligibility criteria. A written informed consent was obtained from all participants before commencing the study procedure.\n\nVariables\n\nThe primary investigator assessed variables comprising of demographic characteristics and kinematic parameters for both stroke patients as well as healthy controls. The demographic characteristics for stroke patients included age, sex, affected limb, stroke type, presence of active hand movement, post-stroke duration (days), Shoulder Abduction Finger Extension (SAFE) score and Fugl Meyer Assessment of Upper Extremity (FM-UE) score and were in accordance to the recommendations provided by the SRRR.23 Age and sex were also recorded for healthy controls.\n\nDemographic characteristics:\n\n1. Participants were classified into three categories according to their age: 18-55 years, 56-74 years, and >75 years;\n\n2. Sex was reported as per the categories such as males, females or others;\n\n3. Affected limb was reported as either right side or left side;\n\n4. Stroke subtype was classified based on the Bamford classification24;\n\n5. Presence of active hand movement was observed as the patient’s ability to actively move the hand independently at stroke onset;\n\n6. SAFE score was reported as a score ranging from zero to 10, where a high score implies a better function;\n\n7. The FM-UE scale was assessed as a stroke-specific motor impairment index measured on a three-point ordinal scale. It has a maximum score of 66, where a high score implies a better function.\n\nFollowing the assessment of demographic characteristics, included patients with stroke and healthy controls underwent kinematic assessment. A 3D electromagnetic kinematic analysis tracking system (G4TM Polhemus, Vermont, USA) was used to carry out kinematic analysis for stroke survivors and healthy controls. The kinematic assessment setup included a systems electronic unit (electromagnetic source), two hubs with ports for connecting the sensors, five sensors, namely the sternal, acromion, upper arm, forearm and metacarpophalangeal, a USB (Universal Source Bus), a Bluetooth probe for transferring data from the sensors to the display unit, and a target in the form of a 6 cm diameter cone (Refer to Figure 1 for the equipment used in kinematic analysis and Figure 2 for the kinematic analysis setup).\n\nThis setup was used to kinematically analyse 20 trials of a reach-to-grasp-to-mouth task. While setting up the assessment unit, we first placed four sensors, the sternal, acromion, upper arm and forearm in their respective places. After this, the near and far target distances were marked on the table in front. The far target was set at the point where the participant’s distal wrist crease reached after completely extending the arm, and the near target was considered to be at 2/3rd of the far target distance. The computer and the systems electronic unit were then switched on. We used the PiMgR software (Patriot wellness) for performing kinematic analysis. Once switched on, the fifth sensor namely the metacarpophalangeal sensor was calibrated for both near and far targets. This was followed by measurement of the following distances:\n\na) Sternal to acromion sensor,\n\nb) Acromion sensor to the olecranon process,\n\nc) Upper arm sensor to the olecranon process,\n\nd) Forearm sensor to the ulnar styloid process, and\n\ne) The ulnar styloid process to metacarpophalangeal sensor.\n\nStandardization of distances was done by performing distance calculation and calibration for each individual, so that variability in height and arm length could be accounted for. After measuring these distances, the participants were instructed to carry out the reach-to-grasp-to-mouth task which has been divided into the following 4 phases (refer to Figure 3 for procedure of carrying out the kinematic analysis task):\n\n1. Reach-to-target, where the participant reaches in front to grasp a conical object of 6 cm diameter placed at the target distance (near/far);\n\n2. Reach-to-drink, in which the participant raises the object towards the mouth;\n\n3. Place the object back, where the participant returns the object to its original position and\n\n4. Take UE to the starting position.\n\nEach participant performed 20 trials of the same task, where they were randomly instructed to either reach the near (10 times) or the far target (10 times). After performing kinematic analysis for all stroke participants and healthy controls, the MATLAB © 2020 software was used to calculate the required kinematic parameters, see Table 213,25:\n\n1. Total movement time was defined as the time between the start and end of the reach-to-grasp-to-mouth task.\n\n2. Peak velocity was measured as the overall maximal value of the velocity profile between movement onset and end whereas the average velocity was calculated for the MCP sensor for each phase separately first and then averaged out. The participants were asked to perform the task at a self-paced speed.\n\n3. Shoulder flexion/extension range of motion (angles) between start and end of the task.\n\n4. Elbow flexion/extension range of motion (angles) between start and end of the task.\n\n\n\n1. Total amount of time taken to complete all four phases of the task from start to end\n\n2. Movement initiation was defined as a minimum movement of 2 cm of the metacarpophalangeal sensor\n\n\n\n• Each sensor velocity was determined separately for each phase\n\n• Metacarpophalangeal sensor velocity was considered by averaging it for all four phases (reach-to-target, reach-to-drink, place the object back and taking the UE starting position)\n\nSample size\n\nA convenience sample of 27 patients post-stroke was taken from an ongoing large prospective cohort study. In addition, 10 age- and gender-matched healthy controls were also additionally included in this study.\n\nStatistical methods\n\nThe R studio (commander) (version 1.4.1103) was used for analyzing the data. Data were assessed for normal distribution using the Shapiro-Wilk test. Mean and standard deviation were used to summarize shoulder flexion and average velocity and median and interquartile range were used to summarize skewed data of time, shoulder extension, elbow flexion and elbow extension. One-way ANOVA was used to calculate between-group differences for normally distributed variables such as shoulder flexion and average velocity. Kruskal Wallis test was done to analyse between-group differences for non-normally distributed variables namely, time, shoulder extension, elbow flexion and elbow extension. We also performed the Bonferroni’s post-hoc test to determine individual between group differences. Effect sizes were determined using Cohen’s d. Formula used to calculate effect size was as follows:\n\nWhere, θ is effect size, μ1 and μ2 are the two-group sample means and σ is their pooled standard deviation. Effect sizes were reported by interpreting Cohen’s d as small (0.20-0.50), medium (0.51-0.80) or large (>0.8) effect.26 The level of significance was set at ≤0.05 for all analyses.\n\n\nResults\n\nWe included a total of 27 stroke survivors who were categorized into mild (n=9), moderate (n=10) and severe (n=8) categories based on the FM-UE scale. 10 age and gender matched healthy controls were also included as a control group. Demographic characteristics of all participants such as age, gender, affected limb, stroke type, presence of active hand movement at stroke onset, post-stroke duration and SAFE score are displayed in Table 3.\n\nAs shown in Table 3, out of 27 patients with stroke, 9 had a mild stroke, 10 had a moderate stroke and 8 had a severe stroke. Both, patients with stroke and healthy controls did not differ in the age range (p=0.2). The kinematic characteristics of stroke survivors and healthy controls have been compared and shown in Table 4.\n\nAs seen in Table 5, we observed a significant difference between all assessed kinematic variables, except shoulder flexion, namely time, average velocity, elbow flexion, elbow extension and shoulder extension across all four groups. The variable of time was found to be significantly different between the severe stroke group and all other groups, namely mild (d=-2.37, t=-4.9, p<0.001, df=33), moderate (d=-2.04, t=-4.31, p<0.001, df=33) and healthy controls (d=3.13, t=-6.6, p<0.001, df=33). This depicts maximum magnitude of difference between severe stroke survivors and healthy controls for the parameter of total time taken to complete the task. Participants across all the three stroke groups exhibited a prolonged duration for completing the task.\n\n* ANOVA test of analysis.\n\n# Kruskal Wallis test.\n\na p<0.001 between severe and mild, moderate and healthy controls.\n\nb p<0.001 between mild, moderate, severe and healthy controls.\n\nc p<0.001 between mild and severe stroke groups.\n\nd p<0.01 between moderate and severe stroke groups.\n\ne p<0.001 between severe stroke group and healthy controls.\n\nf p<0.001 between mild and moderate stroke groups.\n\ng p<0.001 between moderate and severe stroke groups.\n\nAverage velocity was also significantly different between all the three stroke groups, namely mild (d=-1.36, t=2.98, p=0.03, df=33), moderate (d=-1.99, t=4.45, p<0.001, df=33), severe (d=-3.7, t=7.81, p<0.001, df=33) and healthy controls. Similar to the parameter of total time, average velocity also exhibited maximum difference between severe stroke group and healthy controls. Additionally, it was found to be significantly different between mild and severe stroke groups (d=2.33, t=4.81 p<0.001, df=33), where the velocity was lower in stroke groups compared to healthy controls. Range of motion deficits were noted across all stroke groups in terms of shoulder and elbow flexion and extension angles, in comparison to healthy controls.\n\nElbow flexion was found to be significantly different between moderate and severe stroke groups (d=1.74, t=3.68, p=0.009, df=33) as well as between severe stroke group and healthy controls (d=-1.83, t=3.86, p<0.001, df=33). The variable of elbow extension showed significant differences between mild and moderate stroke groups (d=0.25, t=0.54, p<0.001, df=33) as well as between healthy controls and all three groups of stroke namely mild (d=0.02, t=-0.05, p<0.001, df=33), moderate (d=-0.22, t=0.5, p<0.001, df=33) and severe (d=2.01, t=-4.24, p<0.001, df=33). The maximum difference in the parameter of elbow extension was observed between severe stroke group and healthy controls. Shoulder extension had significant differences between mild (d=0.1, t=-0.21, p<0.001, df=32), moderate (d=0.27, t=-0.61, p<0.001, df=32) and severe (d=-0.27, t=4.37, p<0.001, df=32) and healthy controls with moderate and severe groups showing equal effect sizes. We also observed significant difference between moderate and severe (d=2.35, t=4.95, p<0.001) stroke groups, where the moderate stroke group had more shoulder extension range compared to severe stroke group. Figure 4 depicts the between- and within-group differences for the kinematic parameters of time, shoulder flexion, average velocity, elbow flexion, elbow extension and shoulder extension across all three groups of stroke and healthy controls.\n\n(The error bars represent confidence intervals).\n\n\nDiscussion\n\nA total of six kinematic variables namely, time, average velocity, elbow flexion, elbow extension, shoulder flexion and shoulder extension were assessed using a 3D kinematic analysis system, while performing a reach-to-grasp-to-mouth task. All kinematic variables except shoulder flexion, exhibited significant differences across all four groups.\n\nThe parameter of time was found to be significantly different between the severe stroke group and all other groups. The participants in the severe stroke group took more time to perform the task compared to mild and moderate stroke groups and healthy controls which either could be because of increased initiation time or due to reduced interjoint coordination. This finding was similar to a study in which mild and moderate stroke survivors (based on FM-UE scores) and healthy controls were recruited. It was reported that participants in the stroke group had slower movement times. This study also made use of 3D motion analysis for a standard drinking task; however, each participant performed only 5 trials as opposed to 20 trials in our study.27 Another study with a task slightly different than ours such as the timed finger-to-nose test also reported that the time required for completing the task was longer in stroke survivors as compared to controls. However, the task given to the participants was a timed finger-to-nose test and the included participants were chronic stroke survivors, which was in contrast to our more functional reach-to-grasp-to-mouth task that was performed by sub-acute stroke survivors.18 Another study with similar findings included a group of chronic stroke survivors and a comparatively less functional task such as the nine-hole peg test. They also reported that the stroke group participants had prolonged timings to complete the task and they attributed it to the significantly reduced dexterity in stroke survivors. As a result of this, the stroke group was observed spending a longer time in the grasping and releasing phases of the nine-hole peg test.28\n\nConsidering the parameter of average velocity to be a derivative of time, we observed that it was significantly different between all three stroke groups and healthy controls as well as between mild and severe stroke groups. Similar findings were exhibited by all three previous studies, in which they reported that stroke survivors demonstrated significantly lower peak speed or peak velocities compared to healthy controls.18,27,28\n\nProlonged task durations and a resulting decrease in velocity, can be attributed to various underlying reasons. Firstly, the stroke survivors find it difficult to initiate a movement. Secondly, as a result of weakness related incoordination and developing synergy patterns, they might take a long duration of time to accurately attempt reaching and grasping the target. Thirdly, the lack of interjoint coordination leads to difficulty in controlling the movement in order to bring the hand back to the starting position. Additionally, we also encounter easy fatigability in stroke survivors while performing a task. Hence, as they progress to more repetitions, they tend to take a comparatively longer duration to complete the task with every recurring movement.29\n\nAlong with kinematic parameters of time and average velocity, we have also reported comparisons of shoulder and elbow range of motion (ROM) between as well as across the four groups. We noted that both shoulder and elbow extension showed significant differences across all stroke groups and healthy controls. Additionally, elbow extension was found to be significantly decreased in the moderate stroke group in comparison to the mild stroke group. The stroke survivors in the severe group were found to exhibit a mean elbow extension angle of 10o throughout the task. The starting position of the task was 0o of elbow extension. Hence, this depicts that the severe group of stroke patients were only able to move the elbow through 10o of flexion. This could be attributed to plausible maximal weakness of both the triceps as well as the biceps in comparison to other stroke groups as well as healthy controls. Similarly, for shoulder extension, we considered a starting neutral position of the shoulder joint at 0o. Thus, shoulder flexion angle increased as the task progressed from the starting position to reaching-to-target and reaching-to-mouth phases. This was followed by a reversal of the movement to bring the UE back to its starting position. As a result of this, we observed a relative shoulder extension to bring the shoulder back to neutral. Thus, healthy control participants were seen to demonstrate maximum shoulder extension when compared to all stroke groups. On the contrary, participants in the mild stroke group demonstrated maximum shoulder flexion, but did not exhibit maximum shoulder extension. This could be because participants with stroke experience difficulty in bringing the shoulder back to its starting position, perhaps, because of poor eccentric control of shoulder flexion in addition to spasticity.\n\nElbow flexion was significantly different in severe versus moderate stroke survivors and healthy controls. Stroke survivors tend to exhibit tonal abnormalities along with weakness, which could result in active ROM deficit especially at the shoulder and elbow joints.\n\nA review article encompassing research in the area of UE kinematic analysis in individuals with stroke also reported that reduced elbow extension and shoulder flexion was frequently described as alterations of movement patterns across numerous studies.30 The same studies, which carried out 3D motion analysis of a drinking task27 and that of the finger-to-nose test18 also reported deficits in elbow flexion and extension angles in stroke survivors.\n\nOut of all the reported kinematic variables in this study, time and average velocity were best able to distinguish between healthy controls and severely affected stroke participants as evidenced by their respective effect sizes. The findings of this study provide us with an objective method of kinematic assessment, which can be used in future longitudinal cohort studies to potentially distinguish between varying groups of stroke survivors with different severity levels such as mild, moderate and severe, based on the FM-UE scores, as well as healthy controls.\n\nOne limitation of this study is that we have not carried out follow-up assessments for the recruited stroke participants. Longitudinal assessments of these kinematic parameters up to 3 and 6 months would be a valuable addition to gaining information regarding post-stroke recovery. However this study is part of an ongoing large longitudinal cohort study in which we have assessed all kinematic parameters at 1 month and outcomes such as FM-UE and ARAT at three months for building prognostic models that can predict post-stroke motor recovery at three months.\n\nWe would also recommend future researchers to plan similar long-term longitudinal cohort studies that would reflect upon the time related responsiveness of kinematic metrics in individuals with stroke. It could further help in distinguishing across the various recovery mechanisms post-stroke by exploring differential movement patterns across different groups of post-stroke recovery. Additionally, spasticity is also known to have a profound effect on the recovery post-stroke. It would hence be beneficial to objectively measure spasticity using well-established methods such as the Montreal spasticity measure that determines the tonic stretch reflex threshold.31 This method can be used as an effective bedside measure of post-stroke spasticity in future studies investigating UE kinematic parameters post-stroke.\n\n\nConclusion\n\nKinematic parameters of time, average velocity, elbow flexion, elbow extension and shoulder extension for a reach-to-grasp-to-mouth task help to differentiate between varying groups of severity post-stroke such as mild, moderate and severe, based on FM-UE scores as well as from healthy controls. This ability to differentiate across stroke severity groups would enable us to objectively quantify post-stroke recovery and help in realistic goal setting and planning rehabilitation.", "appendix": "Data availability\n\nHarvard dataverse. Dataset for kinematic analysis.xlsx. DOI: https://doi.org/10.7910/DVN/EIK0VV 32\n\nThis project contains the following underlying data:\n\nDataset for kinematic analysis.xlsx (This dataset comprises of participant data for 27 stroke patients and 10 healthy control participants. The participants have been analyzed for upper extremity kinematic parameters such as “total movement time, average velocity and shoulder and elbow flexion and extension angles”. The stroke patients have been analyzed against the healthy participants for all of these kinematic parameters.).\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\nMozaffarian D, Benjamin EJ, Go AS, et al.: Executive summary: heart disease and stroke statistics—2016 update: a report from the American Heart Association. Circulation. 2016; 133(4): 447–454. PubMed Abstract \| Publisher Full Text\n\nPandian JD, Sudhan P: Stroke epidemiology and stroke care services in India. J. stroke. 2013; 15(3): 128–134. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLanghorne P, Bernhardt J, Kwakkel G: Stroke rehabilitation. Lancet. 2011; 377(9778): 1693–1702. Publisher Full Text\n\nFaria-Fortini I, Michaelsen SM, Cassiano JG, et al.: Upper extremity function in stroke subjects: Relationships between the international classification of functioning, disability, and health domains. J. Hand Ther. 2011; 24(3): 257–265. PubMed Abstract \| Publisher Full Text\n\nHatem SM, Saussez G, Della Faille M, et al.: Rehabilitation of motor function after stroke: a multiple systematic review focused on techniques to stimulate upper extremity recovery. Front. Hum. Neurosci. 2016; 10: 442.\n\nPark H, Kim S, Winstein CJ, et al.: Short-duration and intensive training improves long-term reaching performance in individuals with chronic stroke. Neurorehabil. Neural Repair. 2016; 30(6): 551–561. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcCrea PH, Eng JJ, Hodgson AJ: Biomechanics of reaching: clinical implications for individuals with acquired brain injury. Disabil. Rehabil. 2002; 24(10): 534–541. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBernhardt J, Hayward KS, Kwakkel G, et al.: Agreed Definitions and a Shared Vision for New Standards in Stroke Recovery Research: The Stroke Recovery and Rehabilitation Roundtable Taskforce. Neurorehabil. Neural Repair. 2017; 31(9): 793–799. PubMed Abstract \| Publisher Full Text\n\nBradnam LV, Stinear CM, Byblow WD: Ipsilateral motor pathways after stroke: implications for non-invasive brain stimulation. Front. Hum. Neurosci. 2013; 7: 184.\n\nChi N-F, Ku H-L, Chen DY-T, et al.: Cerebral motor functional connectivity at the acute stage: an outcome predictor of ischemic stroke. Sci. Rep. 2018; 8(1): 1–11.\n\nFeng W, Wang J, Chhatbar PY, et al.: Corticospinal tract lesion load: an imaging biomarker for stroke motor outcomes. Ann. Neurol. 2015; 78(6): 860–870. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTzvetanov P, Rousseff RT: Predictive value of median-SSEP in early phase of stroke: a comparison in supratentorial infarction and hemorrhage. Clin. Neurol. Neurosurg. 2005; 107(6): 475–481. PubMed Abstract \| Publisher Full Text Reference Source\n\nSchwarz A, Kanzler CM, Lambercy O, et al.: Systematic review on kinematic assessments of upper limb movements after stroke. Stroke. 2019; 50(3): 718–727. PubMed Abstract \| Publisher Full Text\n\nKrebs HI, Krams M, Agrafiotis DK, et al.: Robotic measurement of arm movements after stroke establishes biomarkers of motor recovery. Stroke. 2014; 45(1): 200–204. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMirbagheri MM, Tsao C, Rymer WZ: Changes of elbow kinematics and kinetics during 1 year after stroke. Muscle Nerve Off. J. Am. Assoc. Electrodiagn. Med. 2008; 37(3): 387–395. PubMed Abstract \| Publisher Full Text\n\nThrane G, Murphy MA, Sunnerhagen KS: Recovery of kinematic arm function in well-performing people with subacute stroke: a longitudinal cohort study. J. Neuroeng. Rehabil. 2018; 15: 15. Publisher Full Text Reference Source\n\nvan Dokkum L , Hauret I, Mottet D, et al.: The contribution of kinematics in the assessment of upper limb motor recovery early after stroke. Neurorehabil. Neural Repair. 2014; 28(1): 4–12. PubMed Abstract \| Publisher Full Text\n\nJohansson GM, Grip H, Levin MF, et al.: The added value of kinematic evaluation of the timed finger-to-nose test in persons post-stroke. J. Neuroeng. Rehabil. 2017; 14(1): 1–12.\n\nHussain N, Alt Murphy M, Sunnerhagen KS: Upper limb kinematics in stroke and healthy controls using target-to-target task in virtual reality. Front. Neurol. 2018; 9: 300. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKwakkel G, Van Wegen E , Burridge J, et al.: Standardized measurement of quality of upper limb movement after stroke: Consensus-based core recommendations from the Second Stroke Recovery and Rehabilitation Roundtable. Int. J. Stroke. 2019; 14: 783–791. Publisher Full Text\n\nKnottnerus A, Tugwell P: STROBE--a checklist to Strengthen the Reporting of Observational Studies in Epidemiology. J. Clin. Epidemiol. 2008; 61(4): 323. PubMed Abstract \| Publisher Full Text\n\nYeung PY, Wong LLL, Chan CC, et al.: Montreal cognitive assessment—single cutoff achieves screening purpose. Neuropsychiatr. Dis. Treat. 2020; 16: 2681–2687. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKwakkel G, Lannin NA, Borschmann K, et al.: Standardized measurement of sensorimotor recovery in stroke trials: consensus-based core recommendations from the stroke recovery and rehabilitation roundtable. Neurorehabil. Neural Repair. 2017; 31(9): 784–792. PubMed Abstract \| Publisher Full Text\n\nBamford J, Sandercock P, Dennis M, et al.: Classification and natural history of clinically identifiable subtypes of cerebral infarction. Lancet. 1991; 337(8756): 1521–1526. Publisher Full Text\n\nSardesai S, Nazareth ED; D SK: Kinematic analysis software.2023 May 25 [cited 2023 May 25]. Publisher Full Text\n\nLakens D: Calculating and reporting effect sizes to facilitate cumulative science: a practical primer for t-tests and ANOVAs. Front. Psychol. 2013; 4: 863.\n\nMurphy MA, Willén C, Sunnerhagen KS: Kinematic variables quantifying upper-extremity performance after stroke during reaching and drinking from a glass. Neurorehabil. Neural Repair. 2011; 25(1): 71–80. Publisher Full Text\n\nJohansson GM, Häger CK: A modified standardized nine hole peg test for valid and reliable kinematic assessment of dexterity post-stroke. J. Neuroeng. Rehabil. 2019; 16(1): 1–11.\n\nCollins KC, Kennedy NC, Clark A, et al.: Kinematic components of the reach-to-target movement after stroke for focused rehabilitation interventions: systematic review and meta-analysis. Front. Neurol. 2018; 9: 472. Publisher Full Text\n\nAlt Murphy M, Häger CK: Kinematic analysis of the upper extremity after stroke–how far have we reached and what have we grasped? Phys. Ther. Rev. 2015; 20(3): 137–155. Publisher Full Text\n\nCalota A, Levin MF: Tonic stretch reflex threshold as a measure of spasticity: implications for clinical practice. Top. Stroke Rehabil. 2009; 16(3): 177–188. Publisher Full Text\n\nSardesai S: Dataset for kinematic analysis. V1 ed. Harvard Dataverse. Publisher Full Text\n\nSardesai S: Replication Data for: STROBE Checklist. V1 ed. Harvard Dataverse. Publisher Full Text" }	[ { "id": "225825", "date": "24 Jan 2024", "name": "Sandeep Subramanian", "expertise": [ "Reviewer Expertise stroke rehabilitation", "upper limb", "kinematics" ], "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 have conducted a cross-sectional study on the performance of a reach and grasp and release task in individuals across different severities of stroke as well as healthy controls. Results indicate differences in some measured kinematic variables. The study is overall well-written with sound methods. The results add to the growing literature on better quantification of movement deficits in individuals with stroke. However, there are many issues that need to be addressed.\nComments:\nIntroduction\n\n2nd paragraph: The authors state \"Decreased UE capacity in the form of dysfunction of the arm and hand ....... having a negative effect on participation\". Please provide a reference to support this statement. 3rd paragraph, lines 4-5: The authors mention about use of compensatory strategies. Do these strategies refer to adaptive or substitutive compensations? [3]. 4th paragraph, lines 5-6: Authors state that use of kinematic analyses have revealed differences between healthy controls and individuals with stroke. At which level have these differences been highlighted (in terms of motor performance and movement quality variables?) 4th paragraph, line 8: It needs to be clarified whether feasibility refer to ease of performance or issues with cost and time taken to administer the test? 4th paragraph, last line: What gap in the literature will the availability of data from individuals with more-severe strokes serve? Will they serve as indicators of baseline performance or help provide data to better quantify change over time? Without such information, the utility of the proposed question cannot be fully appreciated.\n\nMethods:\n\nPage 5: Information on the psychometric properties of the FMA and utility of the SAFE score need to be provided. Page 5, last paragraph, line 5: How was upper limb length measured? In addition, the rationale behind the choice of the target distances needs to be provided. Page 7, last line: How were movement onset and offset determined? In addition, what was the recording frequency of the movements? page 8, Statistics part: Generally, effect sizes are calculated using the SD of the pre-assessment. Please provide a reference for using pooled SD.\n\nResults:\nWhat score cut-off points were used for the characterization of FMA into mild, moderate and severe? Please provide a reference to support this. Table 5, Bonferroni values, 2nd column, 1st row: Values provided within the brackets seem to be incorrect. In addition, it needs to be clarified whether these numbers refer to 95% CIs or Quartiles? Figure 4: Please indicate between group differences using asterisk signs. Please provide degrees of freedom for t values.\n\nDiscussion:\n\n1st paragraph, 3rd line: Participants with stroke tend to use more trunk displacement, even for targets placed at the same distance as T1 and T2 in this study. Given the placement of a sensor on the sternum, the non-reporting of trunk displacement values is very surprising. Reasons behind the exclusion of this kinematic variable need to be provided. Page 12, 1st paragraph, last line: Results indicate that individuals with stroke spent a longer time in the grasping and releasing phases of the movement. Previous study results (DeJong et al. 2012, Lamontagne and Fung 2004) have indicated that faster movements are better. Given that you did not place any time constraints on the movement performance, how do you think this factor affected your results? Page 12, 3rd paragraph, 2nd line: Authors mention that stroke survivors face a difficulty in movement initiation. Is this an issue with motor planning or just the ability to execute the movement? How can this be disentangled? Page 12, 3rd paragraph, 4th line: The lack of measurement of inter joint coordination renders the statement on lack of inter joint coordination to be at best speculative. This statement needs to be rewritten. Page 12, 6th paragraph, last line: Given that your finings agree with those found previously, what is the implication of these findings? Limitations paragraph: the use of self-paced movements needs to be accounted for as a limitation.\nReferences:\nLamontagne A, Fung J. Faster is better: implications for speed-intensive gait training after stroke. Stroke. 2004 Nov 1;35(11):2543-8. DeJong SL, Schaefer SY, Lang CE. Need for speed: better movement quality during faster task performance after stroke. Neurorehabilitation and neural repair. 2012 May;26(4):362-73. Levin MF, Kleim JA, Wolf SL. What do motor “recovery” and “compensation” mean in patients following stroke? Neurorehabilitation and neural repair. 2009 May;23(4):313-9.\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": [] }, { "id": "238342", "date": "10 Apr 2024", "name": "Benjamin Michaud", "expertise": [ "Reviewer Expertise Biomechanics", "simulation", "optimal control" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper presents a study on reaching, grasping, moving, and releasing tasks aimed at differentiating stroke severity using kinematic variables. The study is well-structured, with clear methods, sound data collection, reduction, and statistical analyses. The conclusions are well-supported by the data, making the paper straightforward and convincing, with no major flaws. However, I share some comments with the other reviewer (from which I surprinsingly had access?). Here, I focus on points not previously addressed by them:\nMethodology Table 2: The description of range of motion for flexion and extension needs clarification. Range of motion typically refers to the range between peak flexion and peak extension. In the paper, the authors seem to report peak flexion and peak extension angles instead (i.e., providing two values per joint instead of a single one). If the authors meant peaks instead of range of motion, I suggest adjusting the nomenclature accordingly. Results Units in Table 4: While the units are the same as in Table 5, they should still be included in Table 4 for consistency and clarity.\nDiscussion Page 12, paragraph 2: The authors mention that prolonged task durations and a resulting decrease in velocity can be attributed to various underlying reasons. While this is true, it's not clear on what ground these variables (total time and average speed) actually differ (i.e. that the \"various underlying reasons\" are different), and therefore why they both are reported. As far as I am concerned, they actually carry the same information, which would make them fundamentally the same, undermining the benefit of including both. If the authors feel these values should both be included, it should be explained further. The impact of participants moving at a self-paced speed should be discussed more thoroughly. as this choice could (and will) affect time-related results (such as total time and average velocity) both in terms of absolute values and variability. Also I feel this could influence the validity of the test in clinical settings or for replication. Additionally, the implications of participants' awareness (or lack thereof) of time sensitivity on the test's results should also be discussed.\nLastly, discussing the clinical implications of the study would be beneficial. Can this test effectively differentiate stroke severity, or is the difference in time or range of motion too narrow? Unless I missed it, while the authors reported the formula, I haven't found the results for the effect sizes. Effect sizes are a useful way to discuss 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": [] }, { "id": "184647", "date": "14 Sep 2024", "name": "Fayaz Khan", "expertise": [ "Reviewer Expertise Neurorehabilitation", "Rehabilitation of patients with stroke", "balance and falls", "prediction of recovery" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have designed and executed the study well.\nThe importance of objective assessment using kinematic tools has been addressed.\nHowever, a few questions have to be addressed:\n1. The power of the determined sample has not been mentioned, whether the sample is enough to determine the change caused between the groups. And 10 healthy controls is an enough comparable sample?\n2. Figure 4 is replicating the information in Table 5, duplication of the information in table, figure and text is not warranted.\n3. As the authors have assessed all the subjects with FMA and ARAT, an ROC analysis of kinematic variables and FMA/ARAT would give an idea of whether those subjective variables are sensitive and specific to the objective kinematic variables. This would help the clinical therapist where the facilities for performing the kinematic objective analysis are not available.\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/12-779
https://f1000research.com/articles/11-1376/v1	24 Nov 22	{ "type": "Research Article", "title": "Staining ability of herbal tea preparations on a nano-filled composite restorative material – an in-vitro study", "authors": [ "Raj Kumar Narkedamalli", "Vidya Saraswathi Muliya", "Kalyana Chakravarthy Pentapati", "Raj Kumar Narkedamalli", "Kalyana Chakravarthy Pentapati" ], "abstract": "Background: Discoloration of tooth-colored restorations due to various factors is one of the principal causes behind the failure of aesthetics. There has been an surge in the consumption of herbal beverages in recent times and the dietary factors play a potential role in the discoloration tooth-coloured restorations. This study was done to juxtapose the staining ability of green tea (GT), moringa tea (MT), and hibiscus tea (HT) on a nano-filled composite restorative material. Methods: The study was conducted in-vitro on composite samples prepared using moulds. 112 discs were prepared from FiltekTM Z350XT composite using a brass mould lined with mylar strips. Samples were divided into GT, MT, HT, and artificial saliva (AS) groups and immersed in freshly prepared beverages for 15 minutes each day for 45 days. Digital reflectance spectrophotometer was utilized to record color at baseline, 30, and 45 days. Repeated-measures ANOVA with a post-hoc Bonferroni test was used to compare groups within each group. ANOVA with a post-hoc Games Howell test was used to compare mean differences in ΔE among the groups. Results: Maximum discoloration was observed in the GT, followed by HT and MT, with the least being in the AS group at the end of 30 and 45 days (P<0.001 and P<0.001) respectively. Conclusions: The universal nano-filled composite material showed clinically detectable discoloration when exposed to Green Tea, Hibiscus Tea, and Moringa Tea which increased with time. Herbal beverages have the potential to cause discoloration of the composite resin which is often the choice of material for anterior aesthetic restorations.", "keywords": [ "Herbal Tea", "Green Tea", "Hibiscus Tea", "Moringa Tea", "Discoloration", "Spectrophotometer" ], "content": "Introduction\n\nFailure of aesthetics is one of the common causes for replacement of existing restorations.1 Surface or sub-surface changes lead to microleakage resulting in staining of the superficial layer of composite materials contributing to the aesthetic failure of the restoration.2 The discoloration of composites can be due to intrinsic and extrinsic staining.3,4 Foods and beverages that are a part of everyday diet lead to discoloration of composites either by absorption or adsorption of colorants.5 Nano-fillers and nanoclusters enhance the long-term stability of composite resin material. The composites with filler particle <0.4 μm tend to retain surface polish for a more extended period.6\n\nTea is a popular and highly accepted beverage among the Indian population. Various health benefits are claimed by the manufacturers of herbal teas like lowering blood pressure, weight loss, boosting of liver health, immunity, antioxidants, antiageing etc. Due to potential benefits, there is an increasing acceptance among the public for these herbal tea preparations.7 Green tea (GT) is a traditional beverage‚ derived from the Camellia sinensis, loaded with antioxidants and nutrients.7 Moringa tea (MT) is derived from extracts of Moringa oleifera, which has nutrients, vitamins, minerals, proteins, essential amino acids, chlorophyll, omega-3 oils, and many such phytonutrients.8 Hibiscus tea (HT) is abundant in vitamins A and C, and rich in flavonoids and pro-anthocyanins, which are antioxidants.9\n\nThe Z350XT Nanofill Universal Restorative composite resin (3M™ ESPE™ Filtek™) is a nano-filled restorative material with good strength and wear resistance. The manufacturer claims superior polishability and improved fluorescence for excellent aesthetics and a wide variety of shades for natural-looking restorations.\n\nDue to the potential role of dietary factors on the discoloration of composite resin restorations, many studies evaluated the staining potential of various tooth-colored restorations.10 However, there is a dearth of research on the effects of herbal tea preparations on the color stability of nano-filled composite resin. Given this background, the present study aimed to compare the staining potential of GT, HT, and MT on universal nano-filled composite restorative material. The null hypothesis was that there would be no significant difference in the staining ability of these herbal tea preparations.\n\n\nMethods\n\nA total of 112 discs from universal nano-filled composite resin material (3M™ ESPE™ Filtek™ Z350XT) were made using a mould. Each sample had dimensions: 8mm in diameter and 4mm in thickness. The resin material was dispensed into the mould, following which a mylar strip was placed on the resin composite surface. A 1 mm thick glass slab was positioned over the mylar strip to standardize the gap between the curing light and sample. The curing time was adjusted as per the manufacturer’s instructions with an output of 1100mW/cm2 (Blue Phase, Ivoclar). Before the baseline color estimation, all the samples were stored in distilled water at 37°C for 24 hours, following which they were arbitrarily categorized into four study groups (n=28).11\n\nThe control group used artificial saliva (AS) (Department of Biochemistry, Kasturba Medical College, Manipal, Karnataka, India). Herbal tea preparations used were green tea (GT), moringa tea (MT), and hibiscus Tea (HT) (Gtee Botanical Extracts Pvt. Ltd., Chennai, Tamil Nadu, India).\n\nEvery day, new solutions were made by dipping two tea bags (2g X 2) into 300 ml of boiling water for 3 minutes, as directed by the manufacturer. Before immersing the samples, the teabags were disposed, and the solution was cooled down to a temperature between 60 to 650 Celsius\n\nThe samples were dipped in the freshly prepared tea solutions for 15 minutes/day for 45 days. Following the immersion procedure, samples were kept in artificial saliva at room temperature for rest of the day.\n\nA digital reflectance spectrophotometer (X-rite i1 Pro Digital Reflectance Spectrophotometer and ProfileMaker Pro 5.0.10 software) was used to assess the color of the samples at baseline, 30 and 45 days.12 Snapper or Loop could be used as alternative software to fulfill a similar function. After drying the specimen using blotting paper, each sample was placed on a white backdrop, with the spectrophotometer’s active point set at the centre of the sample. The change in color for individual sample after 30 days and 45 days of immersion regimen was calculated using the following equation:\n\nAll analyses were performed using SPSS version 20 (IBM Corp. Released 2011. IBM SPSS Statistics for Windows, Version 20.0. Armonk, NY: IBM Corp). A P-value of <0.05 was considered statistically significant. Repeated-measures ANOVA with a post-hoc Bonferroni test was used to compare groups within each group. ANOVA with a post-hoc Games Howell test was used to compare mean differences in ΔE among the groups at 30 and 45 days. Data can be accessed at Mendeley datasets.38\n\n\nResults\n\nIntra-group comparisons showed that baseline values were the lowest, followed by 30 days, with the highest being at 45 days in GT, MT, HT, and control solutions (Table 1). The inter-group comparison demonstrated significant differences at the end of 30 days (P<0.001) and 45 days (P<0.001), respectively (Table 2). The post-hoc test illustrated that the highest discoloration was seen in GT followed by HT, MT with the least being in the control group. (Figure 1)\n\n\nDiscussion\n\nDiscoloration of dental restorative material in the aesthetic zone has been a matter of concern among clinicians and often requires replacement of the restoration. The current in-vitro study assessed the staining ability of herbal teas on commonly used composite restorative material Filtek™ Z350XT (3M ESPE). Nanocomposites utilize nanofiller incorporation into the resin matrix to amplify the mechanical and aesthetic properties.6 The performance of the nanocomposites is still being investigated in various clinical and in-vitro studies.\n\nSince the use of mylar strips have been proven to produce the smoothest finish, samples were prepared using a brass mould lined by mylar strips.13–15 Researchers proposed numerous techniques of accelerated aging to study the color changes. Various solutions such as tea, coffee, herbal drinks, cola, chlorhexidine, etc., have been advocated over varying time intervals to assess the discoloration on various aesthetic restorative materials.16–18 The herbal tea preparations included in the current study have gained popularity and increased acceptance due to the inclination towards a healthy lifestyle. Due to the brief contact of these preparations with the oral cavity, the specimens were immersed for 15 minutes per day. The samples were kept in artificial saliva to simulate the oral environment. The color changes were assessed using a spectrophotometer which is capable of detecting minute variations.19 The application of CIEL ab* system along with the correlated colour difference metrics have been devised so as to meliorate the visual interpretation of colorimetric data. This system has also been proven to accurate for the analysis of ΔE* values20 alongwith additional advantages of repeatabilty and objectivity.21 The variations in L, a, and b are denoted by ΔL, Δa, and Δb* respectively, where in, L* corresponds to the degree of discoloration of the test samples. The parameter a* stands for red (+a) and green (-a), in the contrary, b* represents yellow (+b) and blue (-b).22 The value of ΔE* is more crucial compared to the individual values of L, a and b*.23\n\nMany factors such as the size of the particle, the form of the organic matrix, percentage of the particle in the matrix, degree of polymerization, finishing and polishing,24 staining material used, etc., have a potential role on the vulnerability of the dental restorative material to staining.25\n\nThe composite restorative material in this study had undergone substantial color change due to the immersion in the tea preparations due to the softening potential of the staining solutions26 The composite resin’s physicochemical characteristics help regulate the harmony of the material in response to extrinsic stains, with water sorption being the most important amongst them.27–29 The hydrophilicity of the resin matrix of the restorative material is associated with the sensitivity of water sorption and solubility behavior of the resin composite materials.30,31 Microcracks, voids, or interfacial gaps result from elevated levels of osmotic pressure at the matrix-filler interphases and are prone to stain initiation.32–34\n\nGT had the maximum potential for discoloration, followed by HT and MT, which may be attributed to the tannin content in GT35 and MT8 and the anthocyanin content in HT.11 The exposure time to the staining solutions determines restorative materials color stability. The results of the present study are in accordance with the previous literature that illustrates the increase in discoloration of composites with an increase in the immersion time.36\n\nColor changes that are imperceptible to the human eye are represented by ΔE values between 0 and 2. In contrast, ΔE values between 2 and 3 represent color changes that are only detectable by the human eye on close inspection. For 50% of qualified observers, values more than or equal to 3.3 are visually apparent at a glance and clinically unacceptable.37 In our study, all the tea preparations showed values of more than 3.3, which was clinically detectable.\n\nOur study highlights the staining potential of these newer herbal teas, affecting dental restorations’ longevity. The patients should be made aware of the aesthetic consequences of these preparations on long-term consumption, and the clinicians should be knowledgeable regarding the staining potential.\n\n\nConclusion\n\nThe universal nano-filled composite material showed clinically detectable discoloration when exposed to green tea, hibiscus tea, and moringa tea which increased with time. The staining potential increased with the duration of exposure to the tea preparations. Dentists should be aware of the patient’s dietary preferences and their implications on the longevity of composite restorations.", "appendix": "Data availability\n\nMendeley Data: Staining ability of herbal tea preparations on a nano-filled composite restorative material. https://doi.org/10.17632/bzx3fhd6hw.1. 38\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgement\n\nNIL\n\n\nReferences\n\nNunn WR, Hembree JH Jr, McKnight JP: The color stability of composite restorative materials. ASDC J Dent Child. 1979; 46: 210–213. PubMed Abstract\n\nAsmussen E, Hansen EK: Surface discoloration of restorative resins in relation to surface softening and oral hygiene. Eur J Oral Sci. 1986; 94: 174–177. Publisher Full Text\n\nSamra APB, Pereira SK, Delgado LC, et al.: Color stability evaluation of aesthetic restorative materials. Braz Oral Res. 2008; 22: 205–210. PubMed Abstract \| Publisher Full Text\n\nChandrasekhar V, Reddy LP, Prakash TJ, et al.: Spectrophotometric and colorimetric evaluation of staining of the light cured composite after exposure with different intensities of light curing units. J Conserv Dent. 2011; 14: 391–394. PubMed Abstract \| Publisher Full Text\n\nBagheri R, Burrow MF, Tyas M: Influence of food-simulating solutions and surface finish on susceptibility to staining of aesthetic restorative materials. J Dent. 2005; 33: 389–398. Publisher Full Text\n\nMitra SB, Wu D, Holmes BN: An application of nanotechnology in advanced dental materials. J Am Dent Assoc. 2003; 134: 1382–1390. Publisher Full Text\n\nCabrera C, Artacho R, Giménez R: Beneficial effects of green tea—a review. J Am Coll Nutr. 2006; 25: 79–99. Publisher Full Text\n\nDevarai L: Moringa Oleifera: a review on nutritive importance. Asian J Plant Sci. 2005; 4: 417–421.\n\nMcKay DL, Chen CO, Saltzman E, et al.: Hibiscus sabdariffa L. tea (tisane) lowers blood pressure in prehypertensive and mildly hypertensive adults. J Nutr. 2010; 140: 298–303. Publisher Full Text\n\nKhokhar ZA, Razzoog ME, Yaman P: Color stability of restorative resins. Quintessence Int. 1991; 22(9): 733–737. PubMed Abstract\n\nTopcu FT, Sahinkesen G, Yamanel K, et al.: Influence of different drinks on the colour stability of dental resin composites. Eur J Dent. 2009; 03: 50–56. Publisher Full Text\n\nJohnston WM: Color measurement in dentistry. J Dent. 2009; 37: e2–e6. Publisher Full Text\n\nHondrum SO, Fernandez R Jr: Contouring, finishing, and polishing Class 5 restorative materials. Oper Dent. 1997; 22: 30–36. PubMed Abstract\n\nYap AUJ, Lye KW, Sau CW: Surface characteristics of tooth-colored restoratives polished utilizing different polishing systems. Oper Dent. 1997; 22: 260–265.\n\nTürkün LS, Türkün M: The effect of one-step polishing system on the surface roughness of three esthetic resin composite materials. Oper Dent. 2004; 29: 203–211. PubMed Abstract\n\nErgün G, Mutlu-Sagesen L, Özkan Y, et al.: In vitro color stability of provisional crown and bridge restoration materials. Dent Mater J. 2005; 24: 342–350. PubMed Abstract \| Publisher Full Text\n\nKhosravi M, Esmaeili B, Nikzad F, et al.: Color stability of nanofilled and microhybrid resin-based composites following exposure to chlorhexidine mouthrinses: an in vitro study. J Dent (Tehran). 2016; 13: 116.\n\nSoares-Geraldo D, Scaramucci T, Steagall-Jr W, et al.: Interaction between staining and degradation of a composite resin in contact with colored foods. Braz Oral Res. 2011; 25: 369–375. PubMed Abstract \| Publisher Full Text\n\nGuler AU, Yilmaz F, Kulunk T, et al.: Effects of different drinks on stainability of resin composite provisional restorative materials. J Prosthet Dent. 2005; 94: 118–124. PubMed Abstract \| Publisher Full Text\n\nMutlu-Sagesen L, Ergün G, Özkan Y, et al.: Color stability of a dental composite after immersion in various media. Dent Mater J. 2005; 24: 382–390. PubMed Abstract \| Publisher Full Text\n\nTaşkınsel E, Özel E, Öztürk E: Effects of sports beverages and polishing systems on color stability of different resin composites. J Conserv Dent. 2014; 17: 325–329. PubMed Abstract \| Publisher Full Text\n\nReis AF, Giannini M, Lovadino JR, et al.: Effects of various finishing systems on the surface roughness and staining susceptibility of packable composite resins. Dent Mater. 2003; 19: 12–18. PubMed Abstract \| Publisher Full Text\n\nSarrett DC, Coletti DP, Peluso A: The effects of alcoholic beverages on composite wear. Dent Mater. 2000; 16: 62–67. PubMed Abstract \| Publisher Full Text\n\nSchroeder T, da Silva PB , Basso GR, et al.: Factors affecting the color stability and staining of esthetic restorations. Odontology. 2019; 107: 507–512. PubMed Abstract \| Publisher Full Text\n\nGarcia PPNS, Rodrigues Neto E, dos Santos PA , et al.: Influence of surface sealant on the translucency of composite resin: effect of immersion time and immersion media. Mater Res. 2008; 11: 193–197. Publisher Full Text\n\nTurssi CP, Hara AT, Serra MC, et al.: Effect of storage media upon the surface micromorphology of resin-based restorative materials. J Oral Rehabil. 2002; 29: 864–871. PubMed Abstract \| Publisher Full Text\n\nLu H, Roeder LB, Lei LEI, et al.: Effect of surface roughness on stain resistance of dental resin composites. J Esthet Restor Dent. 2005; 17: 102–108. PubMed Abstract \| Publisher Full Text\n\nde Gee AJ , ten Harkel-Hagenaar E , Davidson CL: Color dye for identification of incompletely cured composite resins. J Prosthet Dent. 1984; 52: 626–631. PubMed Abstract \| Publisher Full Text\n\nGauthier MA, Stangel I, Ellis TH, et al.: Oxygen inhibition in dental resins. J Dent Res. 2005; 84: 725–729. Publisher Full Text\n\nÖrtengren U, Andersson F, Elgh U, et al.: Influence of pH and storage time on the sorption and solubility behaviour of three composite resin materials. J Dent. 2001; 29: 35–41. Publisher Full Text\n\nOrtengren U: On composite resin materials. Degradation, erosion and possible adverse effects in dentists. Swed Dent J Suppl. 2000; 1–61. PubMed Abstract\n\nMair LH: Surface permeability and degradation of dental composites resulting from oral temperature changes. Dent Mater. 1989; 5: 247–255. PubMed Abstract \| Publisher Full Text\n\nMair LH: Staining of in vivo subsurface degradation in dental composites with silver nitrate. J Dent Res. 1991; 70: 215–220. PubMed Abstract \| Publisher Full Text\n\nSöderholm K-J, Zigan M, Ragan M, et al.: Hydrolytic degradation of dental composites. J Dent Res. 1984; 63: 1248–1254. Publisher Full Text\n\nKhasnabis J, Rai C, Roy A: Determination of tannin content by titrimetric method from different types of tea. J Chem Pharm Res. 2015; 7: 238–241.\n\nAbu-Bakr N, Han L, Okamoto A, et al.: Color stability of compomer after immersion in various media. J Esthet Restor Dent. 2000; 12: 258–263. PubMed Abstract \| Publisher Full Text\n\nRuyter IE, Nilner K, Möller B: Color stability of dental composite resin materials for crown and bridge veneers. Dent Mater. 1987; 3: 246–251. PubMed Abstract \| Publisher Full Text\n\nPentapati K, Muliya VS, Narkedamalli RK:Staining ability of herbal tea preparations on a nano-filled composite restorative material. Dataset. Mendeley Data. 2022; V1. Publisher Full Text" }	[ { "id": "156562", "date": "13 Dec 2022", "name": "Deepshikha Chowdhury", "expertise": [ "Reviewer Expertise Dental materials", "endodontics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 paper is excellent and well written. I really like the conceptualisation of analysing the staining ability of herbal tea preparation that have become a popular beverage in India as well as internationally. It is an important addition to literature. It has been observed that the spectrophotometric analysis has been described in details. Statistical analysis has been done meticulously which is really appreciable. The use of recent citations has increased the credibility of the article. However, I have a few queries that require clearance. They have been mentioned as follows:\nHow was the sample size calculated?\n\nWhy was the 15 mins time of immersion selected as it doesn't simulate the natural intake of beverage? This can lead to a difference in case of an in vivo scenario.\n\nWhy 4 mm thickness of the samples have been selected? The general increment while curing with LED light is 2 mm unless the composite is a bulk fill.\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": "9241", "date": "23 Jan 2023", "name": "Vidya Saraswathi Muliya", "role": "Author Response", "response": "1. How was the sample size calculated? Response: Sample size calculation was done using Gpower software (version 3.1.9.4). The effect size of 0.4 (large effect size) was considered for a priori sample size calculation with maximum power (95%) and alpha of 5% for four groups. The total sample size was estimated to be 112 (n=28 per group) 2. Why was the 15 mins time of immersion selected as it doesn't simulate the natural intake of beverage? This can lead to a difference in case of an in vivo scenario. Response: The average consumption of tea is around 3-4 cups per day. This can however vary from person to person in real life scenario. So, considering the average tea consumption and a time of 5-7 minutes per cup of tea, the immersion time period is considered as 15 minutes per day in the current study (Patil et al., Clinical Cosmetic & Investigational Dentistry, 2020). The conditions however cannot be completely related to real life (in-vivo) scenario since the exact amount and time of tea consumption varies from person to person, in addition to factors like salivary clearance, dietary habits etc. which may have influence of discoloration. 3. Why 4 mm thickness of the samples have been selected? The general increment while curing with LED light is 2 mm unless the composite is a bulk fill. Response: Samples were prepared using 4mm thickness molds. Handling was easier with 4mm thickness. Since a universal composite material was used in the current study, which had a curing depth of 2mm only, samples were cured equally from both the sides as per the manufacturer’s instructions." } ] }, { "id": "167509", "date": "22 May 2023", "name": "Abhishek Parolia", "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\nI have given my suggestions in the attached PDF. This manuscript needs major revision before acceptance 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? 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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "9748", "date": "04 Jul 2023", "name": "Vidya Saraswathi Muliya", "role": "Author Response", "response": "1: Is the institutional ethical clearance taken? That needs to be stated. Response: It has been added in Methods Paragraph 1 2: How was the sample size calculated? Response: Sample size calculation was done using Gpower software (version 3.1.9.4). The effect size of 0.4 (large effect size) was considered for a priori sample size calculation with maximum power (95%) and alpha of 5% for four groups. The total sample size was estimated to be 112 (n=28 per group) 3: How many investigators prepared all samples? Response: One investigator 4: material for the mould? Response: Brass 5: this reference is for what? Response: This reference is to justify the storage of samples in distilled water prior to initiation of the experiment 6: More information of the extract is needed in the methodology Response: Details are mentioned in the discussion 7: How did this simulate the real scenarios? Exposure time of a restored tooth to the tea in mouth may not be continuous for 15 minutes. Response: The average consumption of tea is around 3-4 cups per day. This can however vary from person to person in real life scenario. So, considering the average tea consumption and a time of 5-7 minutes per cup of tea, the immersion time period is considered as 15 minutes per day in the current study (Patil et al., Clinical Cosmetic & Investigational Dentistry, 2020). The conditions however cannot be completely related to real life (in-vivo) scenario since the exact amount and time of tea consumption varies from person to person, in addition to factors like salivary clearance, dietary habits etc. which may have influence of discoloration 8. There is no different in the data when presented in the table or figure so choose either of these two Response: Figure 1 has been deleted 9: Company name and country for Spectrophotometer? Response: Digital reflectance spectrophotometer - ( i1 Pro Digital Reflectance Spectrophotometer, X-Rite Inc. MI, USA) and Profile maker Pro 5.0.10 software 10: Discussion needs to be improved and justify the results in more detail Response: Discussion has been revised 11: It is really important to know the exact composition of this tea and which component affects the outcome Response: This has been mentioned in the discussion as ‘GT had the maximum potential for discoloration, followed by HT and MT, which may be attributed to the tannin content in GT and MT and the anthocyanin content in HT.’ 12: Role of every authors needs to be written Response: Mentioned in page 2 of uploaded manuscript 13: Any funding for this project? Response: No funding received. Mentioned in page 2 of uploaded manuscript" } ] } ]	1	https://f1000research.com/articles/11-1376
https://f1000research.com/articles/11-842/v1	27 Jul 22	{ "type": "Research Article", "title": "A cross-sectional analysis in order to validate the translation of FSFI-6 to Bahasa Indonesia", "authors": [ "Saras Serani Sesari", "Sylvia Detri Elvira", "Tyas Priyatini", "Harrina Erlianti Rahardjo", "Saras Serani Sesari", "Sylvia Detri Elvira", "Tyas Priyatini" ], "abstract": "Background: Numerous tools have been developed to assess female sexual dysfunction. Several of them have also conducted validity tests. Female Sexual Function Index (FSFI) is one of these surveys that has been effectively translated into several different languages. The previous study on the translation and validation of the FSFI-6 questionnaire into Bahasa Indonesia used the original form (FSFI-19), which had many questions. Thus, this study was done to validate and translate a condensed version of the original questionnaire to make it more practicable for individuals to complete in a clinical context. Methods: FSFI-6 was translated into Bahasa Indonesia. Then the data were collected via questionnaires by 72 women in Rumah Sakit Cipto Mangunkusumo (RSCM or Mangunkusumo National Central General Hospital) during the data collection period (January 2018 until April 2018). The data obtained were processed for validity and reliability using the SPSS software program 20. The tests conducted on the data included a normality test, a validity test, descriptive analysis, and reliability testing. The r-value and the value of Cronbach’s Alpha were the parameters used to determine the validity and reliability of the questionnaire. Results: The r-value on each question in the translated FSFI-6 questionnaire was greater than 0.3, while the value of Cronbach's Alpha of the questionnaire FSFI-6 was greater than 0.6, equal to 0.831. Conclusions: The FSFI-6 questionnaire short version that has been translated into Bahasa Indonesia is valid and reliable.", "keywords": [ "Women", "sexual dysfunctions", "surveys and questionnaires", "reproducibility of results" ], "content": "Introduction\n\nSexual dysfunction is a health problem that could potentially degrade quality of life. However, this problem is less discussed and treated, especially in women in Indonesia. This is because of the culture in Indonesia, which considers the topic of sexuality taboo. Therefore, anything that is related to sexuality is rarely discussed. There are only a few pieces of research about sexual dysfunction. Female sexual dysfunction (FSD) is a complex issue in the classification, diagnosis, or treatment. Studies related to the prevalence and incidence of sexual dysfunction in women are scarce. Lack of data and limited research methods make it difficult to interpret the data.\n\nIn recent decades, reproductive health has been a crucial component of quality of life, and it is now a program initiated by the World Health Organization (WHO). WHO defines FSD as the inability of a woman to participate in sexual intercourse. Sexual dysfunction can be grouped into four major groups, they are sexual arousal disorder, sexual desire disorder, pain disorder, and disorders on orgasm.1 Without proper management, sexual dysfunction can potentially influence interpersonal relationships with a spouse, reduce confidence, cause emotional disturbances, and finally affect quality of life.\n\nThe prevalence of FSD in western countries is known to be relatively high. Research has indicated that the numbers are between 43–88% in the US and 22% in Europe.2,3 Based on previous epidemiological research conducted by the Department of Urology of Rumah Sakit Cipto Mangunkusumo (RSCM or Mangunkusumo National Central General Hospital) in 2001, about 15.2% of the 560 female respondents had experienced sexual dysfunction, and its prevalence increased with age.4 Another study in Indonesia stated that the prevalence of FSD is 9.2%.5 The prevalence is relatively high; however, public and health professionals’ awareness is still deficient regarding this issue, especially in Indonesia, which embraces Eastern culture, so sexual problems are taboo topics to talk about. Sexual dysfunction in women is often not explored in high-risk groups.\n\nThere are many instruments designed to evaluate sexual dysfunction in women. Some of them also have tested validity. They are the Brief Index of Sexual Functioning for Women,6 Changes in Sexual Functioning Questionaire,7 Female Sexual Function Index (FSFI),8 and Golombok Rust Inventory of Sexual Satisfaction.9 The FSFI-6 questionnaire is a self-report questionnaire used as an instrument for assessing FSD. It is a short version of the FSFI-19, which has 19 items instead of six. FSFI-19 may be too long for clinical studies, especially in Indonesian women, who do not talk openly about their sexual problems and get embarrassed quickly when talking about sexuality. This questionnaire consists of six questions covering six domains: desire, arousal, lubrication, orgasm, satisfaction, and pain. The FSFI was developed and validated for the first time in 2000.7,10 This questionnaire has been successfully translated into many different languages, ranging from Mandarin, Arabic, Persian, Malay, Turkish, Korean, and Japanese.11–16 Based on a previous study, the FSFI questionnaire is easily understood and can measure all aspects of women’s sexual function.17 A previous study about translation and validation of the FSFI-6 questionnaire into Bahasa Indonesia was conducted on the original version of the FSFI-6, which consisted of many questions. Hence, this study was conducted to validate and translate the simpler version of the initial questionnaire to make it more understandable.\n\n\nMethods\n\nThis was a cross sectional study to understand the validity of the translated FSFI-6 questionnaire. The FSFI-6 questionnaire was translated into Bahasa Indonesia by clinicians (Prof. Rahardjo and Dr Elvira) who are fluent in both English and Bahasa Indonesia. The translation into Bahasa Indonesia aimed to facilitate the respondents in understanding the content of the question. Translation is also needed as one of the steps to test the validity of the translated FSFI-6 questionnaire. Researchers also added a question about the effects on quality of life to assess personal distress.\n\nThe FSFI-6 questionnaire translated into Bahasa Indonesia was translated back into English by Indonesia Medical Education and Research Institute (IMERI) Writing Centre. This back-translation process aimed to compare the new version of the back-translated questionnaire and the original English version of the FSFI-6 questionnaire.\n\nThe Ethics Committee of the Faculty of Medicine, University of Indonesia approved this study (No: 1023/UN2.F1/ETIK/2017) on 13 November 2017, and all participants provided written informed consent.\n\nThe outcome for this study was the FSFI-6 form filled by the respondents. Potential predictors, confounders, and effect modifiers included age, latest education status, occupation, geographical home region, times of marriage, length of marriage, number of children, communication problem with husband, use of contraception, and menopause.\n\nThe target population in this study was all women in RSCM including patients, family members, employees, up to general RSCM visitors during the retrieval of data (January 2018 until April 2018). All women aged >18 years old and married were eligible for this study. The respondents were approached and asked if they wanted to participate in the study. Sampling was conducted with a consecutive sampling method with a total sample of 422 respondents. Respondents data were given serial numbers in order of arrival to maintain confidentiality. Data were kept safely in a password-protected files in the Department of Urology, Faculty of Medicine, Universitas Indonesia. To test the validity of this questionnaire, the researcher used the first 132 samples collected. Sapnas and Zeller (2002) stated that 50 samples are sufficient to test the validity of the psychometric characteristics questionnaire.18 Hence, to make the data more representative, the authors decided to use more than 50 samples.\n\nBefore the data were collected, respondents filled out an informed consent form as part of the questionnaire. They were also provided with information sheets that included information on their right to withdraw. If the respondents wanted to withdraw, they could withdraw at this phase. Furthermore, respondents filled out a questionnaire containing two parts, one part on their background and FSFI-6, without writing their names on the questionnaire. The questionnaire can be found as Extended data.19 Respondents were asked to fill out all questionnaires with honesty. The respondents were asked to leave the question empty if they did not understand to avoid bias. If the respondent could not read or write, the researcher read the questions written in the questionnaire and noted the responses. Once the respondents completed the answers, the questionnaires collected were rechecked to determine whether they could be used as data.\n\nThe data obtained were processed using IBM SPSS Statistics version 20 (RRID:SCR_016479) by testing their validity and reliability. The confidence index used in this study was 0.95.\n\nCorrelation analysis\n\nPearson’s correlation test was used on each question on the questionnaire to ensure its validity. Pearson’s coefficient of correlation quantifies the linear link between two variables. The correlation test was done by correlating each answer score to the overall questionnaire score to check if each answer score correlated strongly with the overall questionnaire score. If an answer score correlated strongly, the question was deemed to be valid. An answer score correlated strongly if the Pearson’s r value was more than 0.3, and an answer score was not considered to correlate strongly if the r value was less than 0.3.\n\nReliability test\n\nAfter determining its validity, the next test performed was the reliability test. A reliability test was used to determine how reliable the questionnaire was in the long term. The parameter used to assess the reliability of this questionnaire was Cronbach’s Alpha value. Cronbach’s alpha is a measure of internal consistency, or how closely a collection of objects is connected to one another as a group. If the Cronbach’s Alpha value obtained was less than 0.6, the questionnaire was considered to be less reliable. However, if the value of Cronbach’s Alpha received was greater than 0.6, the questionnaire was considered to be more reliable. The comparison of FSFI-6 in English and Bahasa Indonesia is provided in Table 1. These questions represent each item, which are desire (question one), arousal (question two), lubrication (question three), orgasm (question four), satisfaction (question five), and pain (question six).\n\n\nResults\n\nThe subjects filling out the questionnaire were categorised based on demographic status. This study’s subject demography data included age, latest education status, occupation, and geographical region. Subject demography data are listed in Table 2.19\n\nTable 2 shows the percentage of each demographic status. Women under 43 years old (70.8%) were the majority subjects in this study. Most of the women who filled this questionnaire graduated with a bachelor’s degree (70.8%). Most of the subjects who filled out this questionnaire worked as employees (61.1%). For geographical region, 79.2% of the subjects lived in an urban area, 5.6% lived in a rural area, and 15.3% did not answer.\n\nThe results of the Pearson’s correlation test in this study, along with the mean and standard deviation, can be seen in Table 3.\n\nTable 3 shows that there were 69 valid data from 72 respondents. The first question had r value 0.837, second 0.676, third 0.808, fourth 0.813, fifth 0.623, and sixth 0.846. The FSFI-6 questionnaire translated into Bahasa Indonesia had a value of Cronbach’s Alpha of 0.889.\n\n\nDiscussion\n\nFSD is a widespread health problem with complex pathogenesis (organic, relational, sociocultural, and psychogenic). In Indonesia, it is often not reported by patients. This problem exists because the topic of sexuality is often avoided. It is embarrassing for people in Indonesia to talk openly about their sexuality because sexuality is a social taboo. This social taboo also means that sexual health education in Indonesia is rarely given. The lack of sexual health education also means that people do not understand FSD and rarely complain about it.20,21 Another reason is that the psychosocial aspect of FSD is overlooked in Indonesia. Public knowledge about mental health in Indonesia is still low, and there are not many schools that implement education about mental health. There is a stigma in Indonesia about going to a psychologist, and because of that, there are not many people who go to a psychologist, even for a consultation. Four factors affect someone’s sexual function according to the biopsychosocial model. The biopsychosocial model states that biology, psychology, sociocultural, and interpersonal factors affect an individual’s sexual function. Any distress in one or more of these factors can cause sexual dysfunction.22 Therefore, the lack of knowledge in mental health and the social taboo about sexuality make FSD undertreated and under-recognized. Because of this, doctors play a big part in discovering and diagnosing FSD with diagnostic tools such as the FSFI.23\n\nThe FSFI-19 has a 19-item self-reported measurement for FSD. Because of this, FSFI-19 is considered to take too much time for routine use in outpatient clinics. Long questionnaires do not work well with overcrowded clinical settings. For this reason, FSFI-6 was made to create a more straightforward diagnostic tool that may help with physical examination and taking a patient’s history in a clinical setting. Isidori et al., validated the English FSFI-6 and concluded that the FSFI-6 is a highly accurate, easy-to-administer, and quick questionnaire to detect FSD.23\n\nThe primary purpose of this study was the translation and validation of the FSFI-6 to Bahasa Indonesia so it may be used in overcrowded clinical practices in Indonesia. The FSFI-6 Bahasa Indonesia was developed through a series of stages, including translation (both forward and back translation), a validation test, and a reliability test.\n\nThis study showed a high reliability of 0.831 using Cronbach’s Alpha coefficient with the six questions of FSFI-6. This means that the sexual function defined by the six domains of FSFI-6 is comprehensible to Indonesian women. The procedure that includes backward and forward translation is aimed to make the questionnaire easily understood by Indonesian women. Issues of anonymity and confidentiality were clarified at the beginning of this study to ensure that women would feel free to express themselves.\n\nTable 1 shows that there were 120 valid data from 132 respondents. The first question had an r value 0.779, second 0.636, third 0.732, fourth 0.738, fifth 0.670, and sixth 0793. Hence it can be concluded that the six FSFI-6 questions that have been translated into Bahasa Indonesia are valid. The FSFI-6 questionnaire translated into Bahasa Indonesia has a Cronbach’s Alpha value of 0.831. Therefore, this questionnaire is reliable and can be used for the assessment of FSD.\n\nCompared to other studies that have validated and translated FSFI to other languages, this study shows a significant correlation in each question (P<0.05) and high reliability (Cronbach’s Alpha >0.7). Validation and translation of FSFI-6 in Japanese, Korean, Philippine, and Malaysian languages shows high reliability with Cronbach Alpha >0.7 in each study.15,17,24,25 The validity and significance values in Malaysian and Korean languages show significant correlation indicated by P<0.05 in each question of the translated questionnaire.15,24 However, the validity in both Japanese and Filipino populations were not significant (P>0.05).17,24 The study conducted by Nuring et al., about the validation and translation of the original version of the FSFI-6 to Bahasa Indonesia, which consists of 19 aspects, show high reliability (Cronbach’s Alpha 0.844) and was valid.26 These findings indicate that the translation of FSFI-6 into Bahasa Indonesia is valid and reliable enough compared to other studies.\n\nThe limitation of this study is that the subjects were mainly healthcare workers who were already well-educated. Hence these subjects are less likely to represent Indonesian women in general. This questionnaire may need to be further evaluated in a group of Indonesian women with other social backgrounds.\n\n\nConclusions\n\nBased on the data analysis that has been performed, it can be concluded that the translated FSFI-6 questionnaire is valid and reliable. Researchers suggest further questionnaire evaluation in a group of Indonesian women with other social backgrounds.\n\n\nData availability\n\nHarvard Dataverse: FSFI Questionnaire Data. https://doi.org/10.7910/DVN/CAZUSL.19\n\nThis project contains the following underlying data:\n\n- FSFI Questionnaire Upload.tab (questionnaire answers; coding schemes: 1, Yes; 2, No)\n\n- STROBE_checklist_cross-sectional.pdf\n\n- FSFI Questionnaire (translated to english).pdf\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).", "appendix": "References\n\nMcCabe MP, Sharlip ID, Atalla E, et al.: Definitions of sexual dysfunctions in women and men: a consensus statement from the fourth international consultation on sexual medicine 2015. J. Sex. Med. 2016; 13(2): 135–143. Publisher Full Text\n\nMcCabe MP, Sharlip ID, Lewis R, et al.: Incidence and prevalence of sexual dysfunction in women and men: a consensus statement from the fourth international consultation on sexual medicine 2015. J. Sex. Med. 2016 Feb; 13(2): 144–152. PubMed Abstract \| Publisher Full Text\n\nClayton AH, Juarez EMV: Female sexual dysfunction. Psychiatr. Clin. North Am. 2017 Jun; 40(2): 267–284. Publisher Full Text\n\nRahardjo H, Nastiti I, Sitanggo L, et al.: Female sexual dysfunction study – Cipto Mangunkusumo Jakarta.2001; 2001.\n\nSatyawan YT, Rahardjo H: Prevalence of sexual dysfunction in medical and non-medical profession women. Indones. J. Urol. 2014; 21(1): 1–7.\n\nTaylor JF, Rosen RC, Leiblum SR: Self-report assessment of female sexual function: psychometric evaluation of the Brief Index of Sexual Functioning for Women. Arch. Sex. Behav. 1994; 23: 627–643. PubMed Abstract \| Publisher Full Text\n\nClayton AH, McGarvey EL, Clavet GJ: The Changes in Sexual Functioning Questionnaire (CSFQ): development, reliability, and validity. Psychopharmacol. Bull. 1997; 33: 731–745.\n\nRosen R, Brown C, Heiman J, et al.: The Female Sexual Function Index (FSFI): a multidimensional self-report instrument for assessing female sexual function. J. Sex Marital Ther. 2000; 26: 191–208. PubMed Abstract \| Publisher Full Text\n\nDerogatis LR: The Derogatis Interview for Sexual Functioning (DISF/DISF-SR): a preliminary report. J. Sex Marital Ther. 1997; 23: 291–304. PubMed Abstract \| Publisher Full Text\n\nSong SH, Jeon H, Kim SW, et al.: The prevalence and risk factors of female sexual dysfunction in young Korean women: an internet-based survey. J. Sex. Med. 2008; 5: 1694–1701. PubMed Abstract \| Publisher Full Text\n\nSun X, Li C, Jin L, et al.: Development and validation of Chinese version of Female Sexual Function Index in a Chinese population—a pilot study. J. Sex. Med. 2011; 8: 1101–1111. PubMed Abstract \| Publisher Full Text\n\nAnis TH, Gheit SA, Saied HS, et al.: Arabic translation of Female Sexual Function Index and validation in an Egyptian population. J. Sex. Med. 2011; 8: 3370–3378. PubMed Abstract \| Publisher Full Text\n\nGhassamia M, Asghari A, Shaeiri MR, et al.: Validation of psychometric properties of the Persian version of the Female Sexual Function Index. Urol. J. 2013; 10: 878, 85.\n\nSidi H, Abdullah N, Puteh SE, et al.: The Female Sexual Function Index (FSFI): validation of the Malay version. J. Sex. Med. 2007; 4: 1642–1654. PubMed Abstract \| Publisher Full Text\n\nBae JH, Han CS, Kang SH, et al.: Development of a Korean version of the Female Sexual Distress Scale. J. Sex. Med. 2006; 3: 1013–1017. PubMed Abstract \| Publisher Full Text\n\nTakahashi M, Inokuchi T, Watanabe C, et al.: The Female Sexual Function Index (FSFI): development of a Japanese version. J. Sex. Med. 2011; 8: 2246–2254. PubMed Abstract \| Publisher Full Text\n\nRyding EL, Blom C: Validation of the Swedish version of the Female Sexual Function Index (FSFI) in women with hypoactive sexual disorder. J. Sex. Med. 2015; 12: 341–349. PubMed Abstract \| Publisher Full Text\n\nSapnas KG, Zeller RA: Minimizing sample size when using exploratory factor analysis for measurement. J. Nurs. Meas. 2002; 12(2): 97–109.\n\nSesari S: FSFI Questionnaire Data.2022. Harvard Dataverse, V3, UNF:6:Xdvsay134XPSWAv4WUktiQ== [fileUNF]. Publisher Full Text\n\nLeerlooijer JN, Ruiter RAC, Damayanti R, et al.: Psychosocial correlates of the motivation to abstain from sexual intercourse among Indonesian adolescents. Tropical Med. Int. Health. 2014 Jan; 19(1): 74–82. PubMed Abstract \| Publisher Full Text\n\nSusanto T, Rahmawati I, Wuryaningsih EW, et al.: Prevalence of factors related to active reproductive health behavior: a cross-sectional study Indonesian adolescent. Epidemiol. Health. 2016 Sep 30; 38: e2016041. PubMed Abstract \| Publisher Full Text\n\nThomas HN, Thurston RC: A biopsychosocial approach to women’s sexual function and dysfunction at midlife: a narrative review. Maturitas. 2016 May; 87: 49–60. PubMed Abstract \| Publisher Full Text\n\nIsidori AM, Pozza C, Esposito K, et al.: Development and validation of a 6-item version of the female sexual function index (FSFI) as a diagnostic tool for female sexual dysfunction. J. Sex. Med. 2010; 7: 1139–1146. PubMed Abstract \| Publisher Full Text\n\nLee Y, Lim MC, Joo J, et al.: Development and validation of the Korean version of the Female Sexual Function Index-6 (FSFI-6K). Yonsei Med. J. 2014; 55(5): 1442–1446. PubMed Abstract \| Publisher Full Text\n\nTabil NR, Malong CL, Vicera JJ, et al.: Translation and validity of the female sexual function index Filipino version (FSFI-Fil). Philipp. J. Intern. Med. 2015; 51(4): 1–11.\n\nNuring P, Iman SB, Denny A, et al.: Validation test of Indonesian female sexual function index (Indonesian FSFI). Bali. Med. J. 2019; 8(1): 164–168." }	[ { "id": "153151", "date": "04 Nov 2022", "name": "Musa Sani Danazumi", "expertise": [ "Reviewer Expertise Musculoskeletal physiotherapy" ], "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\nAlthough the study used a 50+ sample size, it failed to follow established guidelines for cross-cultural validation/adaptation. For instance:\nPermission needs to first be obtained from the original English developers of the FSFI-6 before translation to another language, although we can overlook this.\n\nThe forward and backward translations should be done by expert bilingual translators, not by clinicians.\n\nThe questionnaire was not piloted after translation which is very important to hear feedback from others and then perform peer debriefing.\n\nThere was no mention of measuring content and face validity.\n\nYou should also have measured at least the concurrent validity and test-retest reliability of the questionnaire, not just computing Chronbach's alpha.\n\nWas the normality of the data checked before conducting Pearson’s product‑moment correlation analysis?\n\nYou have not performed responsiveness analysis but have yet to fail to include it in your limitations.\nAddressing the above issues would add value to your study. I am afraid to tell you that your study is flawed but if you can those issues, I will be happy to review it again.\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? Yes", "responses": [ { "c_id": "9828", "date": "04 Jul 2023", "name": "Saras Serani Sesari", "role": "Author Response", "response": "Dear Musa Sani Danazumi, We are pleased to submit the revised draft of our manuscript, “A Cross-Sectional Analysis In Order To Validate The Translation Of FSFI-6 to Bahasa Indonesia”, We appreciate the time and effort dedicated by the editorial staff and reviewers. The comments provided were valuable and helped us refine our paper. As such, we have made several revisions to the manuscript based on the suggestions given. Changes to the manuscript are highlighted. We appreciate your careful review of our paper. Our answers are as follows. 1. The forward and backward translations should be done by expert bilingual translators, not by clinicians. Response: We apologize for this error. The forward translation process was initially done by both clinicians and expert translators to ensure the questionnaire’s grammar and content were correct. However, the final version of the questionnaire was mainly reviewed by the clinicians mentioned in the paper. We have added details regarding the forward translation process on the method section [Page 3, Line 39 – 43], we sincerely apologize for not giving further details on the previous version. 2. The questionnaire was not piloted after translation which is very important to hear feedback from others and then perform peer debriefing. There was no mention of measuring content and face validity. Response: Thank you for this observation. We had done face validation and pilot testing for the questionnaire and has added some more about the details on method section. [Page 4, Line 2 – 4] 3. You should also have measured at least the concurrent validity and test-retest reliability of the questionnaire, not just computing Cronbach's alpha. Response: Thank you for your suggestion. We have added the result of test-retest reliability on Table 4. 4. Was the normality of the data checked before conducting Pearson’s product‑moment correlation analysis? Response: Yes, it was checked using the Kolmogorov-Smirnov test and the result shows normal distribution of the data (p>0.05). 5. You have not performed responsiveness analysis but have yet to fail to include it in your limitations. Response: We apologize for this error. We have added this issue as our study limitations. [Page 11, Line 1 – 2] All authors have read and approved the changes made to the manuscript. We hope that the revised paper is now suitable" } ] }, { "id": "162753", "date": "03 Mar 2023", "name": "Hatta Sidi", "expertise": [ "Reviewer Expertise General psychiatry" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nTitle: A cross-sectional analysis in order to validate the translation of FSFI-6 to Bahasa Indonesia\nOverall comments:\nThis study was brief and does not address the study's objective, i.e., the validity of FSFI-6-Bahasa Indonesia. The study mainly focuses on the reliability of the FSFI-6 Bahasa Indonesia. The study should cover many validation areas, i.e., face, content, concurrent and factorial validity. Nothing was mentioned about this process, i.e., the face value of the questionnaire in Bahasa Indonesia after the translation (validated across the group of women – such as in the group of the high-income and low-income – rural and urban settings – professional (nurses) and non-professional (janitors) and etc., content expert validation of a panel of specialists (their specialty and years of clinical training in the panel group), the cut-off point for the rating scale (concurrent validity) to determine the positive cases [sexual dysfunction] vs. non-cases [no sexual dysfunction], and factorial validity to examine and determine that the factor-structure of the scale is actually similar from the West with the concept of sexual functioning (sexual desire, arousal, orgasm, satisfaction) among the Indonesian population.\n\nRegarding abstract:\nAs per the above comments, the abstract is absent with the validation of the FSFI-6 Bahasa Indonesia.\nRegarding the introduction:\n\nThe statement, “FSFI-19 may be too long for clinical studies, especially in Indonesian women, who do not talk openly about their sexual problems and get embarrassed quickly when talking about sexuality” is very confusing. Is FSFI too long to take for an assessment? Is the content (i.e., face validity) of FSFI intimate and explicit (which other studies, for example, FSFI-19-Malay, were found to be acceptable culturally in Malaysian norm)?\nRegarding methods and results:\nIt is unclear how the respondents were recruited and what validation was performed.\nThe discussion was not addressing the objective of the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "9827", "date": "04 Jul 2023", "name": "Saras Serani Sesari", "role": "Author Response", "response": "Dear Hatta Sidi, We are pleased to submit the revised draft of our manuscript, “A Cross-Sectional Analysis In Order To Validate The Translation Of FSFI-6 to Bahasa Indonesia” , We appreciate the time and effort dedicated by the editorial staff and reviewers. The comments provided were valuable and helped us refine our paper. As such, we have made several revisions to the manuscript based on the suggestions given. Changes to the manuscript are highlighted. Below are our point-by-point responses to the reviewers’ comments. Thank you for your insightful comments and suggestions. Please find the answers to each of your questions below. 1.The study should cover many validation areas, i.e., face, content, concurrent and factorial validity Response: Thank you for this observation. We had done face validation and pilot testing for the questionnaire and has added some more about the details on method section. [Page 4, Line 2 – 4] 2. The abstract is absent with the validation of the FSFI-6 Bahasa Indonesia. Response: We apologize for this error. We have added more details of the validity test on the abstract. 3. The statement, “FSFI-19 may be too long for clinical studies, especially in Indonesian women, who do not talk openly about their sexual problems and get embarrassed quickly when talking about sexuality” is very confusing. Is FSFI too long to take for an assessment? Is the content (i.e., face validity) of FSFI intimate and explicit (which other studies, for example, FSFI-19-Malay, were found to be acceptable culturally in Malaysian norm)? Response: We apologize for the confusing statement. We revised the sentence as follows: “FSFI-19 may took too much time for clinical studies, especially in Indonesian women, who do not talk openly about their sexual problems and get embarrassed quickly when talking about sexuality. It was also considered not suitable to be used in a crowded clinical settings in Indonesia.” [Page 2, Line 23 – 26] 4. It is unclear how the respondents were recruited and what validation was performed Response: Thank you for your close reading of our paper. This is an important point, so we have added more details about the respondent recruitment and face validation on method section. [Page 4, Line 21 – 24] 5. The discussion was not addressing the objective of the study. Response: Thank you for this observation. We have added some highlighted details of the result and its correlation with the study objective. [Page 10, Line 20 – 21, 30 – 35]" } ] } ]	1	https://f1000research.com/articles/11-842
https://f1000research.com/articles/11-1546/v1	21 Dec 22	{ "type": "Research Article", "title": "A cross-sectional study on assessment of spiritual health and its associated factors among undergraduate students in a medical college in Mangalore, Karnataka", "authors": [ "Pracheth Raghuveer", "Ravjot Bhatia", "Rohith Motappa", "Malavika Sachith", "Pracheth Raghuveer", "Ravjot Bhatia", "Malavika Sachith" ], "abstract": "Background: Spirituality and spiritual health are an integral component of an individual’s health and wellbeing. Among medical undergraduates and professionals, spiritual health has positive effects on the individual by decreasing burnout, psychological distress, and rates of substance abuse. Spiritual health is also correlated with increased satisfaction and meaning in life. Spiritual health also influences future patient care, builds patient- provider communication channels, and improves patient outcomes. Methods: A cross-sectional study was conducted to assess the spiritual health levels of medical undergraduates in a medical college, in Karnataka, India, and to identify the factors associated with it. Using a pre-designed, validated semi-structed questionnaire, 600 medical undergraduates were approached and provided the forms. Spiritual health was assessed across the three domains of self-development, self-actualization, and self-realization using the Spiritual Health Assessment Scale (SHAS). Results: A total of 436 medical undergraduates participated. Majority (67.7%) of participants were girls. Most (62%) were found to have fair spiritual health with a large portion of the rest (36%) having good spiritual health and 2% had poor spiritual health. A significant association was found between spiritual health and the father’s (p=0.005) and mother’s (p=0.012) education levels. Spiritual health was also found to be associated with living in a nuclear family (p=0.04). Conclusions: Majority of the medical undergraduates had fair spiritual health. Parents' education levels and nuclear family were significantly associated with spiritual health.", "keywords": [ "Spirituality", "Medical Students", "Dakshina Kannada" ], "content": "Introduction\n\nSpirituality, in its purest form, has been a vital aspect of an individual’s health since time immemorial. Health, often understood as a singular entity, is made up of multiple dimensions, with the WHO defining it as “a state of being where an individual is able to deal with day-to-day life in a manner which leads to the realization of one’s full potential; meaning and purpose of life; and happiness from within.”1 While the three classical dimensions of health are rather extensive, there exists a fourth dimension, namely spiritual health.2,3 Spiritual health, as defined by Dhar et al., is “a state of being where an individual is able to deal with day-to-day life in a manner which leads to the realization of one’s full potential; meaning and purpose of life; and happiness from within.” Under this broad canopy of spiritual health, three aspects have been suggested which are, “Realization of one’s Full Potential”; “Meaning and Purpose of Life”; and “Happiness From Within”.3\n\nOver the last few decades, researchers have explored the relationships that exist between spiritual health Deb et al. c identified a significant positive correlation with finding satisfaction and meaning in life.4 Spirituality has also been associated with a decreased risk for burnout among physicians and trainees.5 A similar correlation has been observed among medical students, with higher levels of spirituality being associated with lower levels of burnout and psychological distress, with spirituality possibly acting as a protective factor.6 Few studies have also found an inverse correlation between substance abuse and spirituality in college and medical students, with higher levels of spirituality correlating with lower rates of substance abuse as well as rates of binge drinking.7,8\n\nBeyond the overall personal wellness of the students, spiritual health also affects physicians and the care and treatment provided by them. In an article by Isaac et al., spiritual health was found to be related to the interpretation of illnesses by patients. They also identified spirituality to have a mixed effect on health behaviour changes, acting both as a positive as well as a negative factor. Spirituality may also act as a bridge, furthering the patient – provider relationship and improving healthcare outcomes for all.9 Geriatric care and palliative care may especially benefit from a physician’s spiritual health, by helping them explore and build a healthy connection with the patient, encouraging open and effective communication. Communication and openness play a vital role in patient centred care, and boost health outcomes.10\n\nThe importance of spirituality for the wellness of a medical student as well as its impact on their care taking abilities cannot be understated. High level of spiritual health will improve the overall wellness of doctors, as well as the quality of care provided by them. While a few studies have been conducted to assess factors associated with spirituality, they are far and few in between, and even fewer exist for this region, and for this demographic that may be disproportionately benefited from spiritual wellness. Therefore, we carried out this study to assess the spiritual health of undergraduate medical students and the factors associated with it.\n\n\nMethods\n\nThe study was conducted on the undergraduate medical students of a medical college in south India. Ethical clearance was taken from the Institutional Ethical committee and all medical students of 4 batches (150×4) i.e. 600 students were approached for the study. Complete enumeration was done to include all medical students of Yenepoya Medical College from First to Third year of Bachelor of Medicine and Bachelor of Surgery (MBBS) course. Each batch has 150 students. So, the total sample size was 600. The study was carried out between December 2020 to January 2021. Those unwilling to give consent, those who did not own a phone or did not understand English were excluded from the study.\n\nA pre-designed, validated, semi-structured proforma was prepared. This proforma was incorporated into a Google form. This was sent to the class representatives of each batch requesting them to distribute among their batchmates. The form had a participant information sheet and informed consent followed by the pre-designed questionnaire. The questionnaire included demographic variables like age, sex, religion, year of study. Spiritual Health Assessment Scale (SHAS) was be used to assess the three domains of spiritual health like self-development, self-actualization and self-realization.11 It involves 21 questions, individual scores in SHAS ranges from 21 to 105 and the level of spiritual health can be further graded as poor (21 to 49), fair (50 to 77) and good (78 to 105). Questions pertaining to the factors associated with it were also included.\n\nThe Google form responses were downloaded in a comma separated value format and the data captured was further cleaned. Descriptive statistics like mean, frequency and proportion were applied. Chi-square test were used to assess the association between level of spiritual health and factors associated with it.\n\nClearance from the Institutional Ethics Committee was obtained. Permission from the Principal of the medical college to carry out the study was obtained. Written informed consent was obtained from all the study participants. Strict confidentiality of the information collected was maintained. All the data was kept confidential.\n\n\nResults\n\nIn the study, a total of 600 students were approached for the study, out of which 436 students responded. The response rate was 72.7%. The sociodemographic data is shown in Table 1. Most of the students (69.7%), belonged to female gender. About half the students (49.1%) students were Muslims while Hindus constituted 41.3% of the participants. Participation from the final year students was the least at 19%. A large majority (85.8%) were in a nuclear family while 14.2% were part of a joint family.\n\nFathers’ education was analysed, and it was found that 46.6% were graduates, 34.9% were postgraduates and above. On the other hand, 47.5% mothers were graduates while 24.8% were postgraduates. Majority of the fathers (37.2%) were self-employed. More than half (52.5%) of the mothers were homemakers.\n\nTable 2 shows the range of spiritual health obtained by the students. Self-development varied from 11 to 34 with a median of 26. Range of self-actualisation score was 7 to 35 and median was 26. Final spiritual health score varied from 40 to 103 with a median of 74.\n\nIt was found that a graphical representation of the findings is displayed in Figure 1.\n\nUsing the chi-square test, association of various demographic factors with spiritual health was analysed and is shown in Table 3. Upon analysis, out of all the variables studied, three of them were found to display significant association. Type of family(p<0.05), father’s education level and mother’s education level were found to be significantly associated with spiritual health. On the other hand, the other studied variables i.e., gender, religion, year of study, occupation of father and mother were not associated with spiritual health.\n\n* Chi-square test.\n\n# Statistically significant.\n\n\nDiscussion\n\nWe studied a variety of demographic factors to identify the ones which share any correlation with spiritual health. A majority of the students were female. Most of the respondents were believers of Hinduism or Islam, with Christians filling in most of the remaining percentage. A roughly equal breakdown of responses were seen across the different years of study. Most of the respondents live in a nuclear family.\n\nOut of all the variables assessed, fathers’ and mother’s education levels were found to be significantly associated with spiritual health. This result is similar to a study conducted by Kalpana et al., among arts and science college students.12 This could indicate and uncover the role a person’s family background plays in the spiritual wellness of an individual. The adage “education begins at home”, could very well be applied here. Parents and families are the first teachers of children. The foundational knowledge of a person is to a large extent influenced by the teachings of their parents and their family environment. Among other things, spiritual wellness and its associated techniques are often taught at home, with parents acting as the conduits of spirituality. Old beliefs, customs and rituals are passed down from generation to generation and play a vital role in the healthy exploration of spirituality.\n\nEducation and it's association with spiritual health should not be ignored. Teaching spiritual health components and techniques could be a possible way to counter and improve upon existing deficits in this aspect. The role of education should be considered and requires further exploration.\n\nA significant association was noted between spirituality and nuclear families. This is unlike the findings of one study conducted by Ahangar et al., which found a higher level of spirituality in adolescents living in joint families, compared to nuclear families.13 This could possibly be due to the fact that the college is located in an urban area, which may have more nuclear families. Another factor is that due to the type of college, most of the students belong to higher socioeconomic stratas, which are often associated with independent nuclear family lifestyles.\n\nIn our study, 36% of the students had good spiritual health while 62% had fair spiritual health. 2% of the students had poor spiritual health. This proportion is somewhat similar to another study, which found a similar breakdown among dental college students, with the majority (74.55%) having fair spiritual health.14 This could be attributed to a similar demographic of the respondents, and supports and strengthens the outcomes of this study.\n\nA few studies have found gender to be a significant variable which we could not identify with significance.14–16 The rest of the variables were not found to have any significant association.\n\nThe lack of a significant association between religion and spirituality could hint towards the general nature of spiritual health regardless of the conforming religion of the respondents. Common approaches could thus possibly be designed and implemented in order to boost spiritual health among the surveyed demographic.\n\nOverall, few studies have been conducted in order to assess the variables associated with this oft neglected domain of spiritual health and wellness. As mentioned previously, the effects of spiritual health reach far and beyond, especially for medical students and future physicians. Further research would be required in order to solidify the associations as well as identify other possible factors influencing and affecting spiritual health.\n\nOur study had several strengths. The large sample size afforded allows us a greater degree of reliability and the ability to generalize the results to other similar demographics. The design of this study also makes it easy to replicate and conduct further assessments across other demographics, as well as solidify the associations.\n\nThe limitations of this study include the fact that spiritual health has different definitions for different respondents, and thus the interpretation of the questions could vary from respondent to respondent, based on their own experiences with it. The second limitation is that this is a cross sectional study, and thus provides possible correlations and associations only. Another limitation that arises is that Yenepoya Medical College, a prestigious medical college in Mangalore, India, is a private college. Private colleges usually have higher fee structures associated with them; thus, the students usually belong to a higher socioeconomic status than government colleges, which have a healthy mix. Therefore, the results, which while useful and suitable for this demographic, cannot be fully generalized to students in all kinds of colleges. Nevertheless, spiritual health, the focus of our study, could play an important role in the overall health of a medical student as well as the outcomes of patient-centred cared that may be provided by the student in future.\n\n\nConclusion\n\nMajority of the undergraduate medical students were found to have spiritual health. We have analyzed a few variables that could have possibly been associated with spiritual health. It was found that parents’ education levels as well as the family type have been identified as possible factors affecting spiritual well-being. These factors can be targeted in order to improve the spiritual health. Early identification of these variables can allow us to develop newer programs and approaches which can be used to improve the students’ spiritual health.", "appendix": "Data availability\n\nFigshare: A cross sectional study on assessment of spiritual health and its associated factors among undergraduate students in a medical college in Mangalore, Karnataka (Responses) (2).xlsx, https://doi.org/10.6084/m9.figshare.21509781.v1. 17\n\nFigshare: A cross-sectional study on assessment of spiritual health and its associated factors among undergraduate students in a medical college in Mangalore, Karnataka. Informed Consent form.docx, https://doi.org/10.6084/m9.figshare.21601029.v1. 18\n\nFigshare: A cross-sectional study on assessment of spiritual health and its associated factors among undergraduate students in a medical college in Mangalore, Karnataka. Participant Information Sheet.docx, https://doi.org/10.6084/m9.figshare.21601023. 19\n\nFigshare: A cross-sectional study on assessment of spiritual health and its associated factors among undergraduate students in a medical college in Mangalore, Karnataka. Questionnaire.docx, https://doi.org/10.6084/m9.figshare.21601005.v1. 20\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nPark K: Park’s Textbook of preventive and social medicine. Banarsidas Bhanot Publishers;2019.\n\nAli SM: Spiritual well-being: the fourth dimension of health. Indian J. Public Health. 2012; 56: 257–258. PubMed Abstract \| Publisher Full Text\n\nDhar N, Chaturvedi S, Nandan D: Spiritual health scale 2011: defining and measuring 4 dimension of health. Indian J. Community Med. Off. Publ. Indian Assoc. Prev. Soc. Med. 2011; 36: 275–282. Publisher Full Text\n\nDeb S, Thomas S, Bose A, et al.: Happiness, Meaning, and Satisfaction in Life as Perceived by Indian University Students and Their Association with Spirituality. J. Relig. Health. 2020; 59: 2469–2485. PubMed Abstract \| Publisher Full Text\n\nCollier KM, James CA, Saint S, et al.: The Role of Spirituality and Religion in Physician and Trainee Wellness. J. Gen. Intern. Med. 2021; 36: 3199–3201. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWachholtz A, Rogoff M: The relationship between spirituality and burnout among medical students. J. Contemp. Med. Educ. 2013; 1: 83–91. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWilliams MK, Greene WM, Leitner SA, et al.: Medical Student Spirituality and Substance Use. J. Addict. Med. 2020; 14: e316–e320. PubMed Abstract \| Publisher Full Text\n\nStewart C: The influence of spirituality on substance use of college students. J. Drug Educ. 2001; 31: 343–351. PubMed Abstract \| Publisher Full Text\n\nIsaac KS, Hay JL, Lubetkin EI: Incorporating Spirituality in Primary Care. J. Relig. Health. 2016; 55: 1065–1077. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBalducci L: Geriatric Oncology, Spirituality, and Palliative Care. J. Pain Symptom Manag. 2019; 57: 171–175. Publisher Full Text\n\nGaur KL, Sharma M: Measuring Spiritual Health: Spiritual Health assessment Scale (SHAS). Int. J. Innov. Res. Dev. 2014; 3: 63–67.\n\nDevi RK, Rajesh NV, Devi MA: Study of Spiritual Intelligence and Adjustment Among Arts and Science College Students. J. Relig. Health. 2017; 56: 828–838. PubMed Abstract \| Publisher Full Text\n\nAhangar M, Khan M: Spiritual Intelligence of Adolescents of Nuclear and Joint Families-A Comparative Study. Int. Res. J. Hum. Resour. Soc. Sci. 2017; 4: 303–313. ISSNO 2349-4085 ISSNP 2394-4218.\n\nDhama K, et al.: An Insight into Spiritual Health and Coping Tactics among Dental Students; A Gain or Blight: A Cross-sectional Study. J. Clin. Diagn. Res. JCDR. 2017; 11: ZC33–ZC38.\n\nPant N, Srivastava SK: The Impact of Spiritual Intelligence, Gender and Educational Background on Mental Health Among College Students. J. Relig. Health. 2019; 58: 87–108. PubMed Abstract \| Publisher Full Text\n\nDeb S, McGirr K, Sun J: Spirituality in Indian University Students and its Associations with Socioeconomic Status, Religious Background, Social Support, and Mental Health. J. Relig. Health. 2016; 55: 1623–1641. PubMed Abstract \| Publisher Full Text\n\nMotappa R:A cross sectional study on assessment of spiritual health and its associated factors among undergraduate students in a medical college in Mangalore, Karnataka. figshare. [Dataset].2022. Publisher Full Text\n\nMotappa R:A cross-sectional study on assessment of spiritual health and its associated factors among undergraduate students in a medical college in Mangalore, Karnataka. Informed Consent form.docx. figshare Extended data.2022. Publisher Full Text\n\nMotappa R:A cross-sectional study on assessment of spiritual health and its associated factors among undergraduate students in a medical college in Mangalore, Karnataka. Participant Information Sheet.docx. figshare. Extended data.2022. Publisher Full Text\n\nMotappa R:A cross-sectional study on assessment of spiritual health and its associated factors among undergraduate students in a medical college in Mangalore, Karnataka. Dataset. Questionnaire.docx. figshare. 2022. Publisher Full Text" }	[ { "id": "158712", "date": "20 Jan 2023", "name": "Vedalaveni Chowdappa Suresh", "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\nAbstract: Conclusion: can be improvised. As both results and conclusion depicts same content.\nKeywords: can consider removing Dakshina Kannada.\nIntroduction\nDefinition of health [reference 1] need to be re-written.\n\nDefinition of Spiritual health defined twice [ two different references]\n\n2nd paragraph: relationship between spiritual health and what?\nMethodology:\nAny specific reason to include only 1st-3rd year students?\n\nEthical committee clearance mentioned twice. Since it is from same institution, need not mention about permission from principal in methods.\n\nStudy proforma had participant information sheet with consent form as mentioned, any reason for obtaining written consent separately?\n\nWhy was the domains like socio-economic status, background [rural/semiurban/urban] was not considered.\nResults: Could mention the variables ie. gender, religion, year of study, occupation did not show any significant correlation with the spirituality.\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": "9693", "date": "04 Jul 2023", "name": "Rohith Motappa", "role": "Author Response", "response": "The definition of health [reference 1] needs to be re-written Response: The definition has been rewritten and incorporated 2nd paragraph: the relationship between spiritual health and what? Response: Thanks we have included it on page 2 of the manuscript in the introduction section, 3rd paragraph Ethical committee clearance mentioned twice. Since it is from same institution, need not mention about permission from principal Response: Thanks we have made the changes as advised. Ethics Committee clearance is mentioned just once. Please find the changes in the methods section, first and third paragraphs. Study proforma had participant information sheet with consent form as mentioned, any reason for obtaining written consent separately? Response: Thanks for the comment. We have removed the written consent part in methods section." } ] }, { "id": "158713", "date": "13 Feb 2023", "name": "Chonnakarn Jatchavala", "expertise": [ "Reviewer Expertise Mental health", "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\nMajor points:\n\nThis study is relatively new, we are talking about spiritual health which is very controversial. And it is a broad range to discuss.\n\nIn the results section of the abstract, please add more findings relevant to the study objectives.\n\nDiscussing empirical implications in medical education, authors need to find other cultures' perspectives on spiritual health that decrease burnout/ mental health issues or increase positive factors in higher education.\n\nCould you modify the conclusion and make it specific to the study objectives?\n\nWhat are the recommendations based on the study findings? Please include them in the discussion.\nMinor points:\nPlease give us the odds ratio for the significantly associated factor if possible\n\nTable 3 is quite enough. Table 2 could be noted: under table 2\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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": "9692", "date": "04 Jul 2023", "name": "Rohith Motappa", "role": "Author Response", "response": "What are the recommendations based on the study findings? Please include them in the discussion Response. Thank you for the comment. Recommendations have been included in the discussion section last paragraph, Page 11. Rest all comments have been addressed in the modified article file" } ] } ]	1	https://f1000research.com/articles/11-1546
https://f1000research.com/articles/11-498/v1	05 May 22	{ "type": "Research Article", "title": "Crisis-management, Anti-stigma, and Mental Health Literacy Program for University Students (CAMPUS): A preliminary evaluation of suicide prevention", "authors": [ "Asumi Takahashi", "Hirokazu Tachikawa", "Ayumi Takayashiki", "Takami Maeno", "Yuki Shiratori", "Asaki Matsuzaki", "Tetsuaki Arai", "Asumi Takahashi", "Ayumi Takayashiki", "Takami Maeno", "Yuki Shiratori", "Asaki Matsuzaki", "Tetsuaki Arai" ], "abstract": "Background: University students have specific risk factors for suicide, necessitating targeted prevention programs. This preliminary study evaluated the efficacy of the Crisis-management, Anti-stigma, Mental health literacy Program for University Students (CAMPUS) for reduction of risk factors and promotion of preventative behaviors. Methods: A total of 136 medical students attended the CAMPUS as a required course at the national university in Japan. The CAMPUS consisted of a lecture and two group sessions covering mental health literacy, self-stigma, and gatekeeper efficacy (e.g., identifying and helping at-risk individuals). The students were asked to role-play based on a movie about gatekeepers and scripts about self-stigma and suicide-related issues. Participants completed questionnaires on suicidal thoughts, depression, help-seeking intentions, self-efficacy as gatekeepers, self-concealment, and self-acceptance. A total of 121 students completed the questionnaires pre- and post-program, and 107 students also responded six months later.\nResults: Students demonstrated significantly reduced overall suicide thoughts six months post-program compared to before the program. In addition, gatekeeper self-efficacy, help-seeking intentions for formal resources, and self-acceptance were improved in the students six month after the program. Conclusions: The CAMPUS suggested effective at reducing suicidal people and promoting preventative psychological tendencies among medial students. This study was a one-group pre post design study without control group. The CAMPUS program was delivered as a mandatory requirement to a group with relatively low suicide risk. Further studies are required to assess its suitability for the general university student population.", "keywords": [ "suicide prevention", "suicide prevention education", "university students" ], "content": "Introduction\n\nSuicide is the leading cause of death among Japanese university students, with about 350 dying by suicide each year. Between 10% and 40% of university students report thoughts of suicide, substantially higher than among the general population (Jain et al., 2012; Osama et al., 2014; Peltzer et al., 2017; Sun et al., 2017). Risk factors for suicide among university students include poor academic performance, pre-existing mental disorders exacerbated by stress, a history of adverse childhood experiences, smoking, alcohol and drug use, and rejection by family or colleagues (Jain et al., 2012; Osama et al., 2014; Zheng & Wang, 2014; Peltzer et al., 2017). Many of these factors are specific to the university environment, so programs tailored to this population are required for suicide prevention.\n\nSome universities already have shown the effectiveness of suicide prevention programs. For example, an online psychoeducational program called ProHelp was shown to improve participants’ help-seeking attitudes and suicide literacy (Han et al., 2018). An online program including multiple technological components, including a website and two social media networking applications, was also reported as useful by a wide spectrum of students (Manning & VanDeusen, 2011). Gatekeeper training has been shown to help students identify colleagues at risk of suicide and provide help such as referral to mental health services (Kibler & Haberyan, 2008; Indelicato et al., 2011). In Japan, Katsumata et al. (2017) reported that a 4-h suicide prevention education program improved attitudes toward suicide and an attitude which was needed in a peer support toward self-destructive behaviors.\n\nHowever, these studies did not evaluate direct effects on mental health and suicidal ideation. Harrod et al. (2014) reviewed eight studies on primary prevention of suicide among university students and concluded that policy interventions including means restriction lowered the suicide incidence compared to universities without such interventions (Joffe, 2008). However, they also concluded that studies examining the effects of classroom instruction on suicidal behavior or long-term outcomes are still required. A suicide prevention education program for high school students, the Youth Aware Mental Health (YAM), was reported to reduce suicidal ideation and suicide attempts at 12 months post-program (although not after 3 months) compared to a control group (Wasserman et al., 2015). As programs may show only transient benefits or not help those at higher risk, it is important to examine the intermediate and longer-term efficacy for prevention of suicidal behaviors and promotion of preventative behaviors.\n\nThe university-targeted mental health education program Crisis management, Anti-stigma, Mental Health Literacy Program for University Students (CAMPUS) consists of a lecture, role-play sessions, and discussion modules focusing on three main components of suicide prevention: 1) mental health literacy, 2) anti-stigma, and (3) crisis management. Mental health literacy is defined by Jorm et al. (1997) as “knowledge and beliefs about mental disorders which aid their recognition, management or prevention.” Mental health literacy can improve mental health among college students (Rafal et al., 2018) and is positively correlated with help-seeking behavior (Gorczynski et al., 2017). The CAMPUS focuses on mental health literacy particularly pertinent to university students and adolescents, including stress, depression, suicidal thoughts, self-care, and support resources. The anti-stigma component aims to combat self-stigma and provide coping methods (Corrigan & Watson, 2002; Goffman, 1990). Several studies have found that people with strong self-stigma regarding mental health issues tend to have low self-esteem, low self-efficacy, and low help-seeking intention (Corrigan & Watson, 2002; Pattyn et al., 2014). The CAMPUS also addresses misunderstandings about suicide and the reasons for acquiring self-stigma such as experiences of discrimination, and aims to mitigate self-stigma through psychological education and exercises. Crisis management concerns gatekeeping for suicide prevention. Students learn about risk assessment, listening to those at risk, and referral to support resources. This content is referred to as gatekeeper training and is a common component of suicide prevention programs in Japan (Hashimoto et al., 2016). Although we completed CAMPUS development in 2019, we have not yet evaluated it mid-term and longer-term efficacy.\n\nThis study aimed to assess the longitudinal efficacy of CAMPUS for reduction of suicide risk factors and promotion of preventative factors and gatekeeper functions among medical students. We speculated that this program would reduce suicidal ideation and enhance preventative psychological factors among all participants.\n\n\nMethods\n\nOne-hundred thirty-six medical students (88 males and 48 females) at the University of Tsukuba, a national university in the Kanto region of Japan, participated in this program as part of a required course. The participants had little knowledge about psychiatry and suicide because they were second-year undergraduates of average age 19.96 years (SD = 1.39; range, 19–29 years).\n\nThe main lecture is composed of three components, mental health literacy, anti-stigma, and crisis management, each lasting about 20 min, and was created using a Power Point presentation (Microsoft Office PowerPoint 2016). A handout with “fill in the blanks” format is distributed to the students. In addition, CAMPUS includes two exercise sessions. In the first gatekeeper training session, students watch a 13-min gatekeeper training film showing student consultation scenes produced by the Ministry of Health, Labour and Welfare of Japan (2016). Next, they are divided into groups of three and perform a close listening exercise and discuss the importance of listening on outcome. This session requires about 30 min and is performed in combination with the second lecture on crisis management. In the second role-playing session, new groups of three perform two role-playing exercises in which they are assigned roles of a student with self-stigma (i.e., problems with mental illness, gender identity, and bullying) or suicide thoughts, a friend who listens to the student, and an observer. After the “student” reads a detailed scenario, he consults about his issues to the friend for a few min. Thereafter, the group discusses how the “student” can resolve these issues, how to proceed with consultation, and the mental issues faced by the “student.” One role-playing session with discussion requires about 30 min. Facilitators trained in the use of CAMPUS monitor and facilitate these sessions. Students also complete various assessment scales before and after the program as detailed below.\n\nPrior to the intervention, we explained the importance of suicide prevention education for undergraduate medical students to the educational coordinator staff. It could be implemented within regular or irregular classes only when the university in Japan agreed with it. We obtained permission from the dean of the medical school to implement the suicide prevention education as a required class.\n\nThe CAMPUS was conducted using three class hours (one frame, 75 min) in July 2019, with mental health literacy and anti-stigma covered in the first hour, crisis management and gatekeeper training in the second hour, and role-play sessions in the third hour. There was the lunch break between the first and second sessions. The main lecture was conducted by one author who is a psychiatrist at the university. The first author (a clinical psychologist) and three other psychiatrists acted as facilitators.\n\nSelf-reported questionnaires were administered before the program (pre-program), immediately after the program (post-program), and six months later (follow-up) in January 2020 to assess CAMPUS efficacy. The follow-up questionnaires were distributed after another class and collected during break time. The participants had no opportunity to participate in classes related to mental health and suicide for the intervening six months.\n\nWe used the following measures to evaluate the general efficacy of the CAMPUS.\n\nSuicide behaviors\n\nThe Suicidal Behaviors Questionnaire-Revised (SBQ-R) is a 4-item self-report measure of suicidal ideation (Osman et al., 2001). The total score ranges from 3 to 18. The cut-off point for non-clinical samples is 7.\n\nDepression\n\nThe Patient Health Questionnaire-9 (PHQ-9) is a 9-item self-report measure in which each item is scored from 0 (Not at all) to 3 (Nearly every day) as a measure of depression severity (Kroenke et al., 2001; Pfizer, 2014). The total score ranges from 0 to 27, and the cut-off point for non-clinical samples is 5.\n\nHelp-seeking intentions\n\nThe General Help-Seeking Questionnaire (GHSQ) is a measure of help-seeking intentions for various resources when facing personal and emotional problems (Wilson et al., 2005). Each item is scored on a 7-point Likert scale ranging from 1 (Extremely unlikely) to 7 (Extremely likely). The help-seeking intentions for informal resources (intimate partner, friends, parents, and other relative/family members) and for formal resources (mental health experts, help lines, doctors, and ministers or religious leaders) were analyzed separately in the present research.\n\nSelf-efficacy as a gatekeeper\n\nThe Gatekeeper Self-Efficacy Scale (GKSES) is a 9-item measure of confidence in gatekeeper skills (Takahashi et al., 2020). The good internal consistency (Cronbach’s α coefficient was.95) and validity were confirmed using data of 875 students. The students answered questions pertaining to gatekeeping skills including their knowledge of suicide prevention using a 7-point Likert scale from 1 (Not at all) to 7 (Extremely).\n\nSelf-stigmatize attitude\n\nThere is no single scale appropriate to measure self-stigma because the target differs markedly among individuals. Therefore, we used two psychological indices that are closely related to self-stigma. The first was a scale measuring self-acceptance of undesirable attributes by Tsukawaki et al. (2009). The scale consists of eight items such as “I accept naturally my weakness.” Each item is scored on a 5-point Likert scale from 1 (Agree) to 5 (Disagree). The second was the Japanese Self-concealment Scale (JSCS) (Larson & Chastain, 1990; Kawano, 2000), a 12-item scale assessing the tendency to actively conceal negative and distressing personal information from others. Each item is scored on a 5-point Likert scale from 1 (Strongly disagree) to 5 (Strongly agree). Self-concealment is related to suicidality (Hogge & Blankenship, 2020), suicidal behavior (Friedlander et al., 2012), and help-seeking attitudes for psychological professional services (Masuda et al., 2012). Positive changes on these two scales are considered indicative of self-stigma mitigation.\n\nThe SBQ-R and PHQ-9 were measured prior to intervention and at the six-month follow-up, while the GKSES, GHSQ, self-acceptance, and JSCS self-concealment scales were measured at all three time points.\n\nWe hypothesized that participants with strong suicidal ideation at baseline would demonstrate reduced ideation as measured by the SBQ-R if the program is effective, while no such change would be observed in those with low baseline ideation. Conversely, most subjects should demonstrate improved attitudes and competence related to suicide prevention.\n\nChanges in the scale scores were evaluated using repeated measures one-way analysis of variance (RT-ANOVA) with main factors time (pre-program, immediately post-program, and six-months post-program) with post hoc Bonferroni correction for multiple comparisons. The significance level of ANOVA was adjusted by Bonferroni’s correction to p < 0.0083 (p < 0.05 divided by six). When the main effect for time was significant, the Bonferroni test was used for post hoc analyses. The effect size is expressed by partial η2 (ηp2). SPSS ver. 25.0 was used for all analyses.\n\nWritten informed consent was obtained from all participants before the program. All students were informed of program aims and required attendance but that the questionnaires were optional. Follow-up e-mails were sent to students if the program SBQ-R or PHQ-9 score indicated cause for concern. The e-mails stated that they could always consult the University Health Center. The study was approved by the Medical Ethics Committee of the University of Tsukuba (No. 1402-1).\n\n\nResults\n\nAmong the 136 medical students attending the CAMPUS program as required, 121 (79 males and 42 females, 89.0%) completed all questionnaires before and immediately after the program. In addition, 107 students (67 males and 40 females, 78.7%) answered the follow-up questionnaires at six months post-program.\n\nThe correlations between pre- and post-program test scores are shown in Table 1. Pre-program suicidal ideation as measured by the SBQ-R was positively but weakly correlated with depression severity as measured by the PHQ-9 (r = 0.25). Despite greater depression severity among participants at higher scores (showing greater suicidal ideation), SBQ-R was negatively correlated with help-seeking intention for informal resources as assessed by the GHSQ (r = −0.25). Also, SBQ-R was positively correlated with greater self-concealment score (r = 0.37). Poor self-acceptance was more strongly correlated with depression (r = −0.34) than with suicidal ideation (r = −0.19). Self-efficacy as a gatekeeper was correlated with help-seeking intentions for formal resources both pre-program (r = 0.33) and post-program (r = 0.39). Self-efficacy as a gatekeeper and self-acceptance were unrelated pre-program (r =0.04), but significantly correlated post-program (r =0.40).\n\n* p < 0.05,\n\n p < 0.01,\n\n* p < 0.001.\n\nThe numbers of participants according to SBQ-R scores pre- and post-program are shown in Table 2. Among 107 participants who completed all follow-up tests, 59 scored 3 (lowest limit) on the SBQ-R pre-program while 48 scored 4 or more (44.9%). Of those, eight people had more than the cut-off points (7). At six-months follow-up, a greater number of participants scored 3 (n = 70) and fewer scored 4 or more (n = 37, (34.6%; p = 0.04 by McNemar’s test). Of those, six people had more than 7 cut-off points. The highest score was 9 points pre-program, but it was 11 points after six months.\n\nNext, average scores for all pre-program, post-program, and follow-up tests as well as the results of one-way RT-ANOVA are shown in Table 3.\n\n p < 0.01,\n\n* p < 0.001.\n\nDepression scores were below the clinical cut-off point pre-program and at follow-up. The PHQ-9 depression severity scores were reduced at follow-up compared to pre-program baseline, but main effects of time were not significant (F(1, 105) = 0.26, p = 0.61, ηp2 = 0.00).\n\nHelp-seeking intentions for informal resources were greater in the post-program than in the pre-program, but the main effect of time was not significant (F(1.68, 163.08) = 3.76, p = 0.03, ηp2 = 0.04). There was a significant main effect of time on help-seeking intention for formal resources (F(1.57, 157.33) = 14.88, p < 0.001, ηp2 = 0.13). Scores were higher post-program, but decreased significantly at follow-up.\n\nThere was a significant main effect of time on gatekeeper self-efficacy (F(2, 208) = 142.45, p < 0.001, ηp2 = 0.58). Participants demonstrated higher scores post-program, but scores decreased significantly from post-program to follow-up. Nonetheless, the score at follow-up was still higher than pre-program, indicating a long-term enhancement of gatekeeper self-efficacy.\n\nThere was also a main effect of time on self-acceptance score (F(2, 210) = 7.55, p < 0.001, ηp2 = 0.07), and the participants demonstrated significantly improved scores post-program as well as at follow-up. Alternatively, self-concealment was not changed significantly (F(1.74, 182.80) = 1.25, p = 0.29, ηp2 = 0.01).\n\n\nDiscussion\n\nThe purpose of this study was to examine the immediate and longer-term benefits of the CAMPUS for reducing suicidal risk factors and promoting preventative psychological factors among university students. The proportion of participants at higher SBQ-R score was significantly lower at six months post-program compared to baseline. Further, participants demonstrated improved self-acceptance and gatekeeper self-efficacy, two important suicide mitigation factors. Other suicide educational programs for university students have been shown to improve literacy and attitudes toward suicide, but have not been demonstrated to reduce suicidal ideation or behavior (Han et al., 2018; Katsumata et al., 2017; Indelicato et al., 2011; Kibler & Haberyan, 2008). In contrast, this relatively brief and easily delivered program tailored to the special needs of university students reduced suicidal ideation (as revealed by the SBQ-R) at follow-up. Thus, CAMPUS can be effectively implemented on a smaller scale to reduce suicidal ideation, warranting studies on broader application throughout this and other institutions.\n\nHowever, a few students had higher SBQ-R scores after six months, so CAMPUS as a primary suicide prevention program was not effective for all subjects, particularly those at highest risk at baseline in this study. Other programs may share this limitation. For example, students with severe suicidal ideation and suicide attempts were immediately taken for clinical assessment and provided treatment; hence, they were excluded from the analysis of the YAM (Wasserman et al., 2015). It is thus critical to underscore that the CAMPUS is a primary preventative measure and cannot replace targeted medical interventions. In our study, the number of students with SBQ-R ≥ 7 cut-off points was small; hence, further research is needed on the effects of CAMPUS on high-risk students.\n\nEducational contents and role-playing appeared to facilitate gatekeeper skills and self-acceptance, even after six months. Thus, the CAMPUS achieved one of its central aims, to enhance awareness of suicide risk in others, thereby increasing the likelihood that high-risk individuals are listened to and referred to mental health services.\n\nSurprisingly, this reduction in suicidal ideation was not accompanied by marked changes in depression severity scores, possibly due to the relatively low baseline depression scores among the participants. Indeed, depression scores were significantly lower than in a previous study of medical students in Serbia (Miletic et al., 2015). However, the correlation between depression and suicide risk pre-program was weak. Mild depression may be relatively common among university students due to academic pressures and in some cases distance from family. These results suggest that the CAMPUS directly targets theme of suicide rather than theme of depression.\n\nImportantly, CAMPUS also increased help-seeking intention for formal resources. Recognition of need and confidence in treatment benefits are important factors promoting help-seeking (Czyz et al., 2013; Downs & Eisenberg, 2012). Considering the positive correlation between help-seeking intention and gatekeeper self-efficacy, the students with high gatekeeper self-efficacy are more likely to consult formal resources for themselves and to refer others to these resources.\n\nOn the other hand, the CAMPUS did not improve self-concealment, implying that many participants were still reticent to discuss suicidal thoughts. Even though some participants role-played a suicidal person, the role-playing friends likely did not include anyone that the participant would actually consult. Those who can seek help from informal resources report greater well-being (Goodwin et al., 2016), so it is important to consult familiar people. Self-concealment may hinder help-seeking intentions for informal resources as low help-seeking intention for informal resources was associated with higher self-concealment in the present study. Surprisingly, self-concealment rating tended to increase immediately after the program. They may have found that “it was surprisingly difficult or uncomfortable to tell people about suicidal ideation” during the role-playing session, resulting in greater self-concealment. However, the variance in self-concealment scores was larger than other measures, indicating large inherent differences and responses to the role-playing exercise. Knowing a close friend or relation who has sought help can facilitate help-seeking behavior (Disabato et al., 2018), so help-seeking intention to informal resources may be improved by discussing experience of consulting close people in the CAMPUS exercises. Lindow et al. (2020) reported that teenage peers and school personnel did not promote help-seeking intention by YAM participants despite the program improving mental health knowledge and reducing the stigma surrounding mental illness; however, it did promote help-seeking behaviors. This suggests that students may reach out to informal resources even if they do not intend to seek help for themselves. For example, university students may seek or offer help for family members and friends in the flow of irrelevant conversation. Therefore, it is necessary to measure help-seeking behaviors among CAMPUS participants in the future.\n\nThis study has several limitations. First, this study was a one-group pre-post design; hence, it was not possible to randomize or establish a control group due to conflicts with university’s regular courses and educational ethical consideration. The psychological scale scores confirmed after six months should be influenced by a variety of factors that affect the individual during the six months of student life. However, applying for suicide prevention education in Japanese universities is a hurdle due to the framework in which the classes are conducted. Realistically, it would be desirable to be able to compare the results with those of the control group, preferably by means of a crossover study in which the timing of the education is shifted. Second, this study looked at the effects of self-reported selective questionnaires alone. It is necessary to examine the changes in students’ attitudes and actions, which do not appear in the questionnaire, through qualitative methods, such as interviews. Third, although the questionnaire responses were voluntary, attending the CAMPUS was compulsory. Required participation may have raised gatekeeper self-efficacy and knowledge of suicide, but coercion in education can induce psychological reactance (Brehm, 1966). However, suicide prevention programs for elementary and junior high schools are similarly required, and required classes do not always have a negative impact on students. Nonetheless, it is necessary to consider how the form of education affects the program.\n\n\nData availability\n\nThe raw data supporting the results of this article cannot be shared as stated by the ethical committee that approved this study. Researchers interested in accessing the data will need to require to be approved by the Ethical Committee of University of Tsukuba. Requests to access these datasets should be directed to First author, Asumi Takahashi, a-takahashi@hokusei.ac.jp.", "appendix": "References\n\nBrehm JW: A Theory of Psychological Reactance. New York: Academic Press; 1966.\n\nCorrigan PW, Watson AC: The paradox of self-stigma and mental illness. Clinical Psychology (New York). 2002; 9: 35–53. Publisher Full Text\n\nCzyz EK, Horwitz AG, Eisenberg D, et al.: Self-reported barriers to professional help seeking among college students at elevated risk for suicide. J. Am. Coll. Heal. 2013; 61: 398–406. PubMed Abstract \| Publisher Full Text\n\nDisabato DJ, Short JL, Lameira DM, et al.: Predicting help-seeking behavior: the impact of knowing someone close who has sought help. J. Am. Coll. Heal. 2018; 66: 731–738. PubMed Abstract \| Publisher Full Text\n\nDowns MF, Eisenberg D: Help seeking and treatment use among suicidal college students. J. Am. Coll. Heal. 2012; 60: 104–114. Publisher Full Text\n\nFriedlander A, Nazem S, Fiske A, et al.: Self-concealment and suicidal behaviors. Suicide Life Threat. Behav. 2012; 42: 332–340. PubMed Abstract \| Publisher Full Text\n\nGoffman E: Stigma: Notes on the Management of Spoiled Identity. London: Penguin; 1990. [Ishigro, T., 2001. Tokyo: Serica syobo].\n\nGoodwin J, Behan L, Kelly P, et al.: Help-seeking behaviors and mental well-being of first year undergraduate university students. Psychiatry Res. 2016; 246: 129–135. Publisher Full Text\n\nGorczynski P, Sims-Schouten W, Hill D, et al.: Examining mental health literacy, help seeking behaviours, and mental health outcomes in UK university students. J. Ment. Health Train. Educ. Pract. 2017; 12: 111–120. Publisher Full Text\n\nHan J, Batterham PJ, Calear AL, et al.: Development and pilot evaluation of an online psychoeducational program for suicide prevention among university students: a randomised controlled trial. Internet Interv. 2018; 12: 111–120. PubMed Abstract \| Publisher Full Text\n\nHarrod CS, Goss CW, Stallones L, et al.: Interventions for primary prevention of suicide in university and other post-secondary educational settings. The. Cochrane Database Syst. Rev. 2014; 10: CD009439. PubMed Abstract \| Publisher Full Text\n\nHashimoto N, Suzuki Y, Kato TA, et al.: Effectiveness of suicide prevention gatekeeper-training for university administrative staff in Japan. Psychiatry Clin. Neurosci. 2016; 70: 62–70. PubMed Abstract \| Publisher Full Text\n\nHogge I, Blankenship P: Self-concealment and suicidality: mediating roles of unmet interpersonal needs and attitudes toward help-seeking. J. Clin. Psychol. 2020; 76: 1893–1903. PubMed Abstract \| Publisher Full Text\n\nIndelicato NA, Mirsu-Paun A, Griffin WD: Outcomes of a suicide prevention gatekeeper training on a university campus. J. Coll. Stud. Dev. 2011; 52: 350–361. Publisher Full Text\n\nJain A, Jain R, Menezes RG, et al.: Suicide ideation among medical students: a cross sectional study from South India. Inj. Prev. 2012; 18: A166.2–A1A166. Publisher Full Text\n\nJoffe P: An empirically supported program to prevent suicide in a college student population. Suicide Life Threat. Behav. 2008; 38: 87–103. PubMed Abstract \| Publisher Full Text\n\nJorm AF, Korten AE, Jacomb PA, et al.: Mental health literacy: a survey of the public's ability to recognise mental disorders and their beliefs about the effectiveness of treatment. Med. J. Aust. 1997; 166: 182–186. PubMed Abstract \| Publisher Full Text\n\nKatsumata Y, Narita T, Nakagawa T: Development of a suicide prevention education program for university students: a single-arm pilot study. Asian J. Psychiatr. 2017; 30: 190–191. PubMed Abstract \| Publisher Full Text\n\nKawano K: Correlational analysis among Japanese self-concealment scale, Kida’s stimulus-seeking scale and self-reported physical symptoms. J. Exp. Soc. Psychol. 2000; 40: 115–121.\n\nKibler J, Haberyan A: Suicide prevention training for resident assistants: Results of the Northwest training model. Based on a program presented at the ACA Annual Conference & Exhibition, Honolulu, HI. 2008. (Accessed 27 June 2020). Reference Source\n\nKroenke K, Spitzer RL, Williams JBW: The PHQ-9: Validity of a brief depression severity measure. J. Gen. Intern. Med. 2001; 16: 606–613. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLarson DG, Chastain RL: Self-concealment: conceptualization, measurement, and health implications. J. Soc. Clin. Psychol. 1990; 9: 439–455. Publisher Full Text\n\nLindow JC, Hughes JL, South C, et al.: The Youth Aware of Mental Health Intervention: impact on help seeking, mental health knowledge, and stigma in U.S. adolescents. J. Adolesc. Health. 2020; 67: 101–107. PubMed Abstract \| Publisher Full Text\n\nManning J, VanDeusen K: Suicide prevention in the dot com era: technological aspects of a university suicide prevention program. J. Am. Coll. Heal. 2011; 59: 431–433. PubMed Abstract \| Publisher Full Text\n\nMasuda A, Anderson PL, Edmonds J: Help-seeking attitudes, mental health stigma, and self-concealment among African American college students. J. Black Stud. 2012; 43: 773–786. Publisher Full Text\n\nMiletic V, Lukovic JA, Ratkovic N, et al.: Demographic risk factors for suicide and depression among Serbian medical school students. Soc. Psychiatry Psychiatr. Epidemiol. 2015; 50: 633–638. PubMed Abstract \| Publisher Full Text\n\nMinistry of Health, Labour and Welfare of Japan: Kokoro no sign ni kiduitara: gakusei sodan hen [If you aware the mental sign: student consultation version].2016. (Accessed 4 August 2020). Reference Source\n\nOsama M, Islam MY, Hussain SA, et al.: Suicidal ideation among medical students of Pakistan: a cross-sectional study. J. Forensic Legal Med. 2014; 27: 65–68. PubMed Abstract \| Publisher Full Text\n\nOsman A, Bagge CL, Gutierrez PM, et al.: The suicidal behaviors questionnaire-revised (SBQ-R): validation with clinical and nonclinical samples. Assessment. 2001; 8: 443–454. PubMed Abstract \| Publisher Full Text\n\nPattyn E, Verhaeghe M, Sercu C, et al.: Public stigma and self-stigma: differential association with attitudes toward formal and informal help seeking. Psychiatr. Serv. 2014; 65: 232–238. PubMed Abstract \| Publisher Full Text\n\nPeltzer K, Yi S, Pengpid S: Suicidal behaviors and associated factors among university students in six countries in the Association of Southeast Asian Nations (ASEAN). Asian J. Psychiatr. 2017; 26: 32–38. PubMed Abstract \| Publisher Full Text\n\nPfizer: Welcome to the Patient HealthQuestionnaire (PHQ) Screeners: Screener overview. 2014. (Accessed 30 November 2020). Reference Source\n\nRafal G, Gatto A, DeBate R: Mental health literacy, stigma, and help-seeking behaviors among male college students. J. Am. Coll. Heal. 2018; 66: 284–291. Publisher Full Text\n\nSun L, Zhou C, Xu L, et al.: Suicidal ideation, plans and attempts among medical college students in china: the effect of their parental characteristics. Psychiatry Res. 2017; 247: 139–143. PubMed Abstract \| Publisher Full Text\n\nTakahashi A, Tachikawa H, Morita N, et al.: Suicide prevention gatekeeper self-efficacy scale (GKSES). Crisis. 2020; 42: 128–135. Publisher Full Text\n\nTsukawaki R, Higuchi M, Fukada H: Relationships between humor expression and self-acceptance, aggression, and altruism. The Japanese Journal of Psychology. 2009; 80: 339–344. Publisher Full Text\n\nWasserman D, Hoven CW, Wasserman C, et al.: School-based suicide prevention programmes: the SEYLE cluster-randomized controlled trial. Lancet. 2015; 385: 1536–1544. PubMed Abstract \| Publisher Full Text\n\nWilson CJ, Deane FP, Ciarrochi J: Can hopelessness and adolescents’ beliefs and attitudes about seeking help account for help negation?. J. Clin. Psychol. 2005; 61: 1525–1539. PubMed Abstract \| Publisher Full Text\n\nZheng A, Wang Z: Social and psychological factors of the suicidal tendencies of Chinese medical students. BioPsychoSocial Medicine. 2014; 8: 23. PubMed Abstract \| Publisher Full Text" }	[ { "id": "161741", "date": "17 Feb 2023", "name": "Kate Wolitzky-Taylor", "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 paper presents data from a gatekeeper program in Japan with undergraduate medical students. There are many strengths of the paper, including that it is well-written, with clear methodology and presentation of results. It also includes several key outcome variables, including suicide risk, depression, and changes in stigma, attitudes, and awareness, encompassing many of the critical outcomes in this type of work. Other prior studies have not examined all of these interesting outcomes. However, there are a few minor issues that could strengthen the paper.\nFirst, for an international audience, it may be helpful to describe the “undergraduate medical student” sample, as medical school is a professional school that comes after an undergraduate education in many Western countries.\nSecond, there are some minor concerns about the interpretation of the results that should be addressed. Specifically, the changes in the suicide measure are presented in a way that is either confusing or may distort the magnitude of the change. I would suggest reporting a dichotomous cutoff of high risk v low risk, in which the authors put people into two categories pre-intervention and follow-up, and then do a chi-square test so there can be an actual inferential statistic there. Also, the description of the depression scores improving though non-statistically significantly should be changed to “no significant improvement” – the change was very small and the effect size was 0, so it is misleading to say there was any change.\nOtherwise, I think this is a nice paper that makes a contribution to the 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?\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": "9743", "date": "03 Jul 2023", "name": "Asumi Takahashi", "role": "Author Response", "response": "Thank you for providing these insights. We have responded to the reviewers' comments below. In addition, we have underlined any additions and have struck out any deletions. We hope that the manuscript will now be ready for indexing. First, for an international audience, it may be helpful to describe the “undergraduate medical student” sample, as medical school is a professional school that comes after an undergraduate education in many Western countries. Answer: Thank you for bringing this to our attention. We have added the information about Japanese medical students as follows: Most Japanese medical students enter medical school straight out of high school, so the participants were second-year undergraduates averaging 19.96 years (SD = 1.39; range, 19–29 years) in age and had little knowledge of psychiatry and suicide. In a survey of Japanese students on their understanding of suicide (Takahashi et al., 2020), the average percentage of correct answers by students in health majors such as medicine and nursing was 56.9%, which was lower than that of Australian National University students (63.4% ) (Calear, Batterham, Trias & Christensen, 2021). (in Methods - Participants) Second, there are some minor concerns about the interpretation of the results that should be addressed. Specifically, the changes in the suicide measure are presented in a way that is either confusing or may distort the magnitude of the change. I would suggest reporting a dichotomous cutoff of high risk v low risk, in which the authors put people into two categories pre-intervention and follow-up, and then do a chi-square test so there can be an actual inferential statistic there. Answer: Thank you for the suggestions. We have added the results of the chi-square test to ensure that the effect on high-risk students is not misinterpreted as follows: A chi-square test with Yates’ continuity correction before and six months after the program, dividing the participants into two groups by the cutoff score, showed no significant difference (x2(1)=0.076, n.s.). (in Results - Longitudinal effects of the CAMPUS) However, a few students had higher SBQ-R scores after six months and no decrease in students above the cutoff score, so CAMPUS as a primary suicide prevention program was not effective for all participants, particularly those at highest risk at baseline in this study. (in Discussion) Also, the description of the depression scores improving though non-statistically significantly should be changed to “no significant improvement” – the change was very small and the effect size was 0, so it is misleading to say there was any change. Answer: Thank you, we agree with your assessment and have changed the sentence describing the depression scores as follows: Depression scores were below the clinical cutoff point pre-program and at follow-up. The main effects of time were not significant (F(1, 105) = 0.26, p = 0.61, ηp2 = 0.00), and depression severity showed no significant improvement. (in Results - Longitudinal effects of the CAMPUS)" } ] }, { "id": "161748", "date": "28 Feb 2023", "name": "Erminia Colucci", "expertise": [ "Reviewer Expertise Suicide prevention" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a valuable piece of work considering the high prevalence of suicidal behaviour in this population, however there are a few issues that I suggest to address:\nPlease support this statement 'the participants had little knowledge about psychiatry and suicide because they were second-year undergraduates'.\n\nI have great concerns about labelling an intervention as 'suicide prevention' when the training materials are about mental health literacy as it is based on the (north-European/American) biomedical model of suicide that sees suicide fundamentally as caused by mental illness. This belief is contested by cultural/global mental health and critical suicidology scholars and the authors must justify their decision to develop a training based on the English speaking countries MHFA, when they also had the option, for instance, to use the tool that was specifically developed for Japan but is not even mentioned in the article, i.e. Colucci et al., 20111.\n\nSimilarly measuring depression as distal measurement for suicide is based on the same assumption indicated above and the authors should show first of all awareness of this belief and second justify it (and paper contains many of these assumptions as demonstrated by this statement 'Surprisingly, this reduction in suicidal ideation was not accompanied by marked changes in depression severity scores').\n\nThe limitations section should include the limitations stated above, namely that the authors used MH literacy instead of suicide literacy specifically.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "9744", "date": "03 Jul 2023", "name": "Asumi Takahashi", "role": "Author Response", "response": "Thank you for your comments and suggestions. We have underlined any additions and struck out deletions. We have responded to the reviewers' comments below. We appreciate your re-review. Please support this statement 'the participants had little knowledge about psychiatry and suicide because they were second-year undergraduates'. Answer: We have added the information about Japanese medical students as follows: Most Japanese medical students enter medical school straight out of high school, so the participants were second-year undergraduates averaging 19.96 years (SD = 1.39; range, 19–29 years) in age and had little knowledge of psychiatry and suicide. In a survey of Japanese students on their understanding of suicide (Takahashi et al., 2020), the average percentage of correct answers by students in health majors such as medicine and nursing was 56.9%, which was lower than that of Australian National University students (63.4% ) (Calear, Batterham, Trias & Christensen, 2021). (in Methods-Participants) I have great concerns about labelling an intervention as 'suicide prevention' when the training materials are about mental health literacy as it is based on the (north-European/American) biomedical model of suicide that sees suicide fundamentally as caused by mental illness. This belief is contested by cultural/global mental health and critical suicidology scholars and the authors must justify their decision to develop a training based on the English speaking countries MHFA, when they also had the option, for instance, to use the tool that was specifically developed for Japan but is not even mentioned in the article, i.e. Colucci et al., 20111. Similarly measuring depression as distal measurement for suicide is based on the same assumption indicated above and the authors should show first of all awareness of this belief and second justify it (and paper contains many of these assumptions as demonstrated by this statement 'Surprisingly, this reduction in suicidal ideation was not accompanied by marked changes in depression severity scores'). Answer: Thank you for this insightful comment. Some parts of this program indeed treat mental illness as strongly related to suicide, and many parts are based on the medical model. On the other hand, we would like to confirm that mental health literacy is only one element of this program: The crisis-management component deals with suicide literacy, and the anti-stigma component deals with the difficulty in seeking help specific to Japanese adolescents and does not focus solely on mental health. As Colucci et al. (2011) point out, the discourse that \"talking about suicide increases anxiety\" is believed in Japan, and thus education that does not even use the word \"suicide\" is recommended (Motohashi et al., 2019) even when the goal of the teaching is suicide prevention for adolescents. In such a situation, the word \"suicide\" is clearly used in our program. Therefore, we believe that the fact that \"suicide\" is not explicitly taught about in Japan and that the purpose of this intervention is suicide prevention justifies labeling this program as suicide prevention education. The elements of mental health literacy are based on YAM, for which there is evidence. This is important because the program has been validated as suicide prevention education. Considering the above, the following changes have been made to support the justification for addressing mental health literacy and the fact that this intervention can be said to be suicide prevention. Depression is a major causative factor for suicide among Japanese university students. We have added the following to the introduction: Although the background of student suicides in Japan is often unclear in the reports from individual universities, when combined with national suicide statistics, it is estimated that poor academic performance, worries about career paths, and mental health issues are often behind the suicides. In a large survey involving 80% of Japanese universities and colleges for the 2020-2021 biennium, 52.8% (n=662) of the deceased students reported by each university (2-year total N=1,254) were suicides or suspected suicides. The presumed history was mostly unknown (n=470), but the most common reasons tended to be related to poor academic performance (n=77), worries about career paths (n=60), feelings of isolation and loneliness (n=48), and worries about illness (n=35) (Ministry of Education, Culture, Sports, Science and Technology of Japan, 2021; 2022). National suicide statistics also show that male students are more likely to suffer from poor academic performance (18.4%), worries about career paths other than entrance exams (15.3%), and depression (10.9%). In comparison, female college students are more likely to suffer from depression (21.7%), worries about career paths (12.0%), and poor academic performance (10.1%) (Ministry of Health, Labour and Welfare of Japan, 2022). In accordance with the WHO (2014) report that mental illness is likely to be behind suicides, universities are required to implement preventative mental health care and to detect students with mental health concerns early. (in Introduction) 1. We added (to the introduction) that the program incorporates an element of anti-stigma by acknowledging that Japanese students find it difficult to seek help. Only 10-20% of students who died by suicide in Japan were connected to on-campus resources such as student counseling (Ministry of Education, Culture, Sports, Science and Technology, 2021; 2022). Therefore, there is a need to specifically address the stigma of mental health issues and suicide and facilitate help-seeking behavior. (in Introduction) 2. We have also added a comment regarding YAM, for which there is ample evidence. CAMPUS began development in 2017 and referred to YAM, an evidence-based education program. (in Introduction) 3. We have added a comment that Japan is challenged to explicitly use the WORD \"suicide\" in a culture that typically avoids it. One of the features of CAMPUS is its explicit treatment of the word \"suicide.\" As noted by Colucci et al. (2011), even experts in Japan acknowledge that there is more avoidance of the topic of suicide in Japan than in other countries. Perhaps for this reason, suicide prevention education in Japan is encompassed by \"education on how to give SOS\" and \"stress management education,\" and the terms suicide and suicide prevention are not actively used (Motohashi et al., 2019). CAMPUS, however, has at its core, a fearless dialogue around suicide. (in Introduction) 4. We have added the following to the Methods section to indicate that the lesson is positioned at the beginning of the education program as a story about suicide. At the beginning of the class, it was clearly explained that the class was about suicide and positioned as a lesson that is part of suicide prevention. (in Method - Contents of CAMPUS) 5. We have added a note about the issues raised in the scenario to indicate that the content covered in the role play is diverse. After the “student” reads a detailed scenario, they consult with their friends about the issues for a few min. The background information leading to the issue of suicide is set in the context of poor academic performance, career path concerns, relationships among college students, and so on. (in Method - Contents of CAMPUS) The limitations section should include the limitations stated above, namely that the authors used MH literacy instead of suicide literacy specifically. Answer: We have added to the limitations section as follows: Finally, CAMPUS was more concerned with mental health literacy than suicide literacy, which might have resulted in a possible lack of information about suicide. When aiming for direct prevention of suicide rather than mental health issues, one approach would be to address the difficulties of student life, such as studying and finances, that underlie student suicide or to address their knowledge of suicide, such as how to limit the means of suicide (cf. lethal means counseling) and safety planning. It remains to be seen what theoretical model should be followed in structuring the content that can educate students in a limited time. (in Limitations)" } ] } ]	1	https://f1000research.com/articles/11-498
https://f1000research.com/articles/11-326/v1	17 Mar 22	{ "type": "Software Tool Article", "title": "Estimation of Covid-19 lungs damage based on computer tomography images analysis", "authors": [ "Martin Schätz", "Olga Rubešová", "Jan Mareš", "David Girsa", "Alan Spark", "Olga Rubešová", "Jan Mareš", "David Girsa", "Alan Spark" ], "abstract": "Modern treatment is based on reproducible quantitative analysis of available data. The Covid-19 pandemic did accelerate development and research in several multidisciplinary areas. One of them is the use of software tools for faster and reproducible patient data evaluation. A CT scan can be invaluable for a search of details, but it is not always easy to see the big picture in 3D data. Even in the visual analysis of CT slice by slice can inter and intra variability makes a big difference. We present an ImageJ tool developed together with the radiology center of Faculty hospital Královské Vinohrady for CT evaluation of patients with COVID-19. The tool was developed to help estimate the percentage of lungs affected by the infection. The patients can be divided into five groups based on percentage score and proper treatment can be applied", "keywords": [ "Computed Tomography", "Image Analysis", "ImageJ", "Covid-19", "Lungs" ], "content": "Introduction\n\nThe covid pandemic that has affected in recent months has revealed a number of strengths and weaknesses in health systems around the world.\n\nOne of the key ideas is a quick and accurate diagnosis of the patient, which was problematic in congested hospitals. Software engineering and image processing methods could be helpful in speeding up and refining patient diagnosis. Especially in radiological and radiodiagnostic workplaces, where a large part of diagnostic processes take place over image data (CT, NMR, X-ray). Various software tools have been used for this purpose for years. In general, it is possible to divide them into two groups:\n\n• universal software packages: used for general analysis of image data such as filtering, smoothing or image registration\n\n• software tools “made to measure”: very specific software tools for analysis of rare diseases\n\nThe first group of tools is represented mostly by software integrated into packages supplied by the tomograph developer. It is possible to mention a software tool for CT image preprocessing and automated analysis of three standard phantoms1 or software tool for metal artifacts reduction in dental care.2\n\nThe second group of tools is from both the research and application point of view much more interesting. It is necessary to state that only a small part of them is applied in a real clinical environment. It is possible to mention a tool for analysis of GPA disease using image registration and self-organizing maps,3 or a tool for analysis of peripheral bypass grafts.4 Many research groups focused on precise measurement of pathological findings, 3D analysis, or volumetric analysis.5,6\n\nMoreover, some papers deal with image fusions from different scanners e.g. combination of data from CT, PET/CT, SPECT/CT, or MR.7,8 Thus, the topic of CT image analysis of “covid lungs” is important from both the research point of view (there is still room for further research in precise semi-automatic analysis) and the clinical point of view. Therefore, the aim of this study is to develop a semi-automatic software for “covid lungs” CT image analysis, based on knowledge presented in Ref. 9. The authors present the idea based on the correlation between the degree of lung involvement and the course of the disease. The global score (0–25) of lung involvement is calculated based on the extent of each lobar involvement score (0: 0%, 1: <5%, 2: 5-25%, 3:26 – 50%, 4:51–75%, 5, > 75%). The authors then introduce the role of CT score for predicting the outcome of SARS-CoV-2 patients. The scoring is highly correlated with laboratory findings, disease severity and mortality. Moreover, it might speed up diagnostic workflow in symptomatic cases.\n\n\nMethods\n\nThe Covid CT estimation tool is based on standard image processing techniques. Our interest is in volume, so the same voxel size is critical for good enough estimation. But it is also important to go through the different types of data we can encounter. In general, the Hounsfield Units (HU) make up the grayscale in medical CT imaging. It is a scale from black to white of 4096 values (12 bit) and ranges from -1024 HU to 3071 HU (zero is also a value). It is defined by the following:\n\n-1024 HU is black and represents air (in the lungs). 0 HU represents water (since we consist mostly out of the water, there is a large peak here). 3071 HU is white and represents the densest tissue in a human body, such as tooth enamel. All other tissues are somewhere within this scale; fat is around -100 HU, muscle around 100 HU, and bone spans from 200 HU (trabecular/spongeous bone) to about 2000 HU (cortical bone).\n\nDICOM files are usually saved in signed 16 bit, with original HU, usually with 3 mm slicing or 0.6 mm slicing CT images. TIFF, however, may have reshaped histogram values to cover the whole range and can preferable be in unsigned 16 bit or 8bit with some loss due to conversion. TIFF values usually lose Z voxel size metadata in conversion (resulting in Z voxel size value of 1), so it is important to reset voxel values. The XY voxel size can be different with each data set, even from the same CT machine. The distribution of intensity values may change with different CT protocols, so some of the processing steps need to be done manually.\n\nThe workflow follows the Croney Ethical guidelines for the appropriate use and manipulation of scientific digital images.10\n\nThe plugin tool is developed in ImageJ macro language, it needs Bio Format plugin to import DICOM files, which comes installed in FIJI. The macro language uses standard image processing techniques and morphological operations to estimate the volume ratio of lungs and pneumonia caused by COVID-19. It allows users to subsequently set up a threshold for pneumonia and lungs, and go through the whole data-set slice by slice and interactively tweak the threshold values. The tool was developed based on demand and with coordination from the Department of Radiology from the Faculty hospital Královské Vinohrady. It is challenging to do any kind of percentage estimate of pneumonia in the lungs just by visually inspecting CT scans stack by stack. Available hardware equipment and local account restrictions had to be taken into account for development tool selection. The ImageJ plugin is a compromise in accuracy and requirements. The workflow is following:\n\n1. DICOM or Tiff stack is imported, the user is prompted to select sub-volume containing only lungs. This step is necessary for the exclusion of other body cavities, which would be otherwise counted as lungs.\n\n2. User manually thresholds background and inside of lungs (air).\n\n3. A lung mask is created by excluding mask components touching the edge of images and by excluding other objects based on size and roundness.\n\n4. User is prompted to select by threshold all areas containing pneumonia (possible parts outside lungs will be excluded).\n\n5. A clean pneumonia mask is created by element-wise multiplication of lung and pneumonia mask.\n\n6. A volume fraction is estimated by voxel count in each mask.\n\n7. Numeric result and coloured visual representation of original data, lung and pneumonia mask is shown to the user as illustrated on Figure 1.\n\n8. A detailed log with tool version, original folder path, score, percentage results, threshold values, and all masks is saved in a folder next to the original image set. Log contains all information needed to do analysis again with same results.\n\nThe numeric results in percent is then corrected by subtracting of 3% (median of tissue present in healthy lungs, estimated from 10 patients) and CT is scored based on severity ranged (0:0%; 1, < 5%; 2:5–25%; 3:26–50%; 4:51–75%; 5, > 75%; range 0–5) defined by Ref. 9.\n\nThere are several steps during the tool runtime which require user inputs:\n\n1. Select the CT lung data (Figure 2, TIFF or DICOM file based on the script version) - the CT sequence is opened and user can go through loaded stack in image sequence with a slider or as a video with a play button.\n\n2. “Please find the start of lungs in stack” - user has an option to select the first image with lungs with a slider and confirm the selection with “Ok” button.\n\n3. “Please find the end of lungs in stack” - user has an option to select the last image of lungs selection with the slider and confirm with “Ok” button. The tool works with the images only in between the chosen interval of the lungs stack to minimize the computational effort.\n\n4. “Setup threshold for all but body” - the whole image- exclude the body, shall be highlighted with red colour. The tool makes automatic estimation, and the user can adjust the threshold with the sliders on the histogram. Confirm with the “Ok” button.\n\n5. “Setup threshold of Covid” - the covid threshold shall be highlighted with red colour. The tool makes automatic estimation, and the user can adjust the threshold with the sliders on the histogram. It is not a problem if part of the body (not lungs!) will be chosen together with Covid. The tool automatically subtracts the body threshold from the chosen Covid threshold. Confirm with the “Ok” button.\n\n• After each calculation the tool is adding information to the log window. The log file is automatically saved to the CT data directory. The output lungs and covid masks are saved in TIFF format into an additional folder in the CT data location.\n\n• The tool provides % estimation of Covid damage in the lungs and a semi-quantitative CT score. The score is calculated based on the extent of lobar involvement (0:0%; 1, < 5%; 2:5–25%; 3:26–50%; 4:51–75%; 5, > 75%; range 0–5 based on the medical research “Chest CT score in COVID-19 patients: correlation with the disease severity and short-term prognosis.9\n\nThe tool has been tested both 3 mm slicing and 0.6 mm slicing CT images. The results were similar in percentage and the final CT score was the same.\n\nIn order to use the tool, the user needs to prepare CT images exported as DICOM or TIFF in preferred view mode and preferably 16-bit representation. The CT images have usually a 12-bit gray-scale representation and an 8-bit conversion would lead to loss of potentially important information or shift of brightness values. The thickness of the CT slice can also contribute to numerical errors in the process, but there was no significant difference in results when processing the same data-set with 3 mm and 0.6 slicing.\n\nThe ImageJ software tool available from Zenodo needs an ImageJ installed with Bio-Formats (preferably with version 6.8.0 which we tested) plugin (or FIJI which is a version of ImageJ with an already integrated Bio-Formats plugin).\n\nMinimal requirements for both are Windows XP or later with Java installed, Mac OS X 10.8 or later with Java installed, Ubuntu Linux 12.04 LTS, or later with Java installed. Minimal RAM is based on the size of processed images, in this case, there are multiple images opened at once.\n\n\nUse cases\n\nA usability of introduced tools is presented in next sections. A use case for comparison for a CT measured with different slicing setup is presented. Results for a set of 5 CTs evaluated by different users is discussed. Since we were restricted by hardware, two versions of tool were created. One that is working with 8-bit version of images and needs less RAM, and one that works with 16-bit signed images and can load HU units.\n\nThe international standard for saving DICOM files defines 3 mm slicing of CT data as the default way. However resaving data as TIFF (losing voxel information) or using different slice thicknesses (like 0.6 mm slicing) may result in a different result. In theory, 0.6 slicing would provide 5 times more detailed sampling in the Z-axis, however, in practice it is different.\n\nThe same CT dataset exported with 0.6 and 3 mm slices (XZ view for comparison is in Figure 3) was analyzed with our tool with a lung threshold of 0-155 and a pneumonia threshold of 47-115. The results can be found in Table 1. The error from a comparison of 3 mm and 0.6 mm slicing is estimated at 0.58 %. The used CT is available in the attached published dataset as CT1_1 (0.6 mm slicing) and CT1_2 (3 mm slicing).\n\nThe biggest challenge in using this tool is an individual perception of images, as each person may see image data fundamentally the same - despite different appearances. Based on this a user can add the biggest bias even though the underlying data analysis is done correctly. The Table 2 contains a comparison of analysis results on 5 different CT datasets provided by the Faculty hospital of Královské Vinohrady. All of the CTs are analysed by users with various experience, the first CT exported with different slicing (also used in Table 1) is analysed by a radiologist (an expert user). The score aims to divide the percentage into groups based on previous research done,9 and should be the deciding factor of future care for patients.\n\n\nDiscussion\n\nThe ImageJ/FIJI tool can import various DICOM or TIFF files. Users should be always aware of whenever the saved data are using signed or unsigned bit depth, as unsigned data will shift pixel brightness. The same will happen when exporting data in different bit depth or with a specific CT view. The slicing of the CT dataset also matters, however, the analysis in Table 1 showed that it won’t significantly affect neither the percentage or the score (other CT machines might have different settings). A small case study for user inter and intra variability was made (Table 2) to evaluate the usability of the proposed tool. Some expected variability in results occur, interesting is inter variability in evaluating CT1 which is 3-5%. The intra variability is more extensive, up to 20%, and points out the fact that users should have at least some training in how to recognize pneumonia in CT images.\n\n\nConclusions\n\nThe tool was developed on demand from the Department of Radiology from the Faculty hospital Královské Vinohrady, as it was difficult for them to estimate the percentage and score of pneumonia in the lungs just by visually inspecting CT scans. Available hardware equipment and local account restrictions had to be taken into account for development tool selection. The ImageJ plugin is a compromise in accuracy and requirements. It logs all the user inputs for reproducibility and saves the results of all the steps as TIFF stacks. These masks and images can be used for visual inspection or possibly in the future for more advanced machine learning tools.\n\nThis software tool is the first step of a longer journey to create a tool that would be both easy to use for radiologists to diagnose COVID-19 based on CTs and include an advanced image analysis tool for percentage estimation of pneumonia in lungs. The use of open software promises ease of future development, however, it might be beneficial to move from ImageJ to 3D Slicer11 or Napari12 as they offer better tools for 3D visualization and integration of machine learning tools, which we aim to develop and integrate in our future works.\n\nThe biggest limitation of this approach is human error, and inter and intra variation of manual selection. The percentage estimation might also be affected by other body cavities filled with air. There might also be a variance in results based on slice thickness, in worst case scenario 20%, but our experiment shows that there is only about 0.58% difference in result between 0.6 and 3mm CT slice thickness. The scoring should also be improved so it is not dependent only on one value (volume percentage), but normalized SHU distribution in the pneumonia area should be also considered.\n\n\nData availability\n\nZenodo: CT scans of COVID-19 patients, https://doi.org/10.5281/zenodo.5805939.13\n\nThis project contains the following underlying data:\n\n• CT1_1\n\n– CT1_1_TIFF_06_MM (Single stack 8-bit TIFF data)\n\n• CT1_2\n\n– CT1_2_TIFF_3_MM (Single stack 8-bit TIFF data)\n\n• CT2\n\n– CT2_DICOM\n\n– CT2_TIFF (Single stack 8-bit TIFF data)\n\n• CT3\n\n– CT3_DICOM\n\n– CT3_TIFF (Single stack 8-bit TIFF data)\n\n• CT4\n\n– CT4_DICOM\n\n– CT4_TIFF (Single stack 8-bit TIFF data)\n\n• CT5\n\n– CT5_DICOM\n\n– CT5_TIFF (Single stack 8-bit TIFF data)\n\n• overview.csv (Detailed overview of each CT set.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International (CC-BY 4.0).\n\n\nSoftware availability\n\nZenodo: ImageJ tool for percentage estimation of pneumonia in lungs, https://doi.org/10.5281/zenodo.5805989.14\n\nThis project contains the following underlying data:\n\n• SEQUENCE_Est_Percentage_CT_16bit_V03_clean.ijm (16bit version)\n\n• SEQUENCE_Est_Percentage_CT_u8bit_V03_clean.ijm (8bit version)\n\n• results.csv (More detailed results of the dataset analysis)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Acknowledgements\n\nComputational resources were supplied by the project “e-Infrastruktura CZ” (e-INFRA LM2018140) provided within the program Projects of Large Research, Development and Innovations Infrastructures. Special acknowledgment goes to the Department of Radiology of Faculty hospital Královské Vinohrady, who provided the data, for medical support.\n\n\nReferences\n\nTorfeh T, Beaumont S, Guédon J, et al.: Software tools dedicated for an automatic analysis of the ct scanner quality control’s images. Progress in Biomedical Optics and Imaging - Proceedings of SPIE. 2007; volume 6510. Cited By:4. Reference Source\n\nCha J, Kim ST, Kim YK, et al.: Dual-energy ct with virtual monochromatic images and metal artifact reduction software for reducing metallic dental artifacts. Acta Radiol. 2017; 58(11): 1312–1319. Cited By:34. PubMed Abstract \| Publisher Full Text Reference Source\n\nGrajciarová L, Mareš J, Dvǒrák P, et al.: Software for diagnosis of the gpa disease using ct image analysis. International Conference on Applied Electronics. 2013. Reference Source\n\nKeller D, Wildermuth S, Boehm T, et al.: Ct angiography of peripheral arterial bypass grafts: Accuracy and time-effectiveness of quantitative image analysis with an automated software tool. Acad. Radiol. 2006; 13(5): 610–620. Cited By:3. PubMed Abstract \| Publisher Full Text Reference Source\n\nEbersberger U, Marcus RP, Schoepf UJ, et al.: Dynamic ct myocardial perfusion imaging: Performance of 3d semi-automated evaluation software. Eur. Radiol. 2014; 24(1): 191–199. Cited By: 34. PubMed Abstract \| Publisher Full Text Reference Source\n\nBehnaz AS, Snider J, Chibuzor E, et al.: Quantitative ct for volumetric analysis of medical images: Initial results for liver tumors. Progress in Biomedical Optics and Imaging - Proceedings of SPIE. 2010; volume 7623. Cited By:8. Reference Source\n\nPfluger T, La Fougère C, Stauss J, et al.: Combined scanners (pet/ct, spect/ct) versus multimodality imaging with separated systems. Radiologe. 2004; 44(11): 1105–1112. Cited By:2. PubMed Abstract \| Publisher Full Text Reference Source\n\nJuergens KU, Grude M, Maintz D, et al.: Multi-detector row ct of left ventricular function with dedicated analysis software versus mr imaging: Initial experience. Radiology. 2004; 230(2): 403–410. Cited By:234. PubMed Abstract \| Publisher Full Text Reference Source\n\nFrancone M, Iafrate F, Masci GM, et al.: Chest CT score in COVID19 patients: correlation with disease severity and short-term prognosis.July 2020; 30(12): 6808–6817. Publisher Full Text\n\nCromey DW: Avoiding twisted pixels: Ethical guidelines for the appropriate use and manipulation of scientific digital images.2010; 16(4): 639–667 June. Publisher Full Text\n\nKikinis R, Pieper SD, Vosburgh KG:3d slicer: A platform for subject-specific image analysis, visualization, and clinical support. In Intraoperative Imaging and Image-Guided Therapy. New York: Springer; November 2013; pages 277–289. Publisher Full Text\n\nSofroniew N, Lambert T, Evans K, et al.: napari/napari: 0.4.12rc2.2021. Reference Source\n\nSchätz M, Rubešová O, Girsa D, et al.: CT scans of COVID-19 patients (Version V0) [Data set]. Zenodo. 2022. Publisher Full Text\n\nSchätz M, Rubešová O, Mareš J, et al.: ImageJ tool for percentage estimation of pneumonia in lungs (Version V0). Zenodo. 2022. Publisher Full Text" }	[ { "id": "146294", "date": "10 Aug 2022", "name": "Tamas Dolinay", "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\nDr. Schätz and colleagues describe a new image analysis modality to quickly review and score lung CT scan images. The image analysis was applied to patients with COVID-19 pneumonia to aid with diagnostic accuracy. It is increasingly recognized that viral pneumonias, including COVID-19-associated pneumonia, may have a specific radiographic pattern. Automated modalities, including the one described by the authors can help with the rapid identification viral pneumonias and with measurement of the extent of the disease.\nThe manuscript is interesting and covers an important topic, but its current format suffers from a few weaknesses.\nMajor comments:\nThe abstract describes 5 different pattern of radiographic findings, but I do not find these in the manuscript. A novelty of the article would be the stratification of pneumonias based on the imaging.\n\nPlease describe, if you had success implementing the image analysis in your clinical practice. What are the benefits and/or barriers of using the analysis in the real world?\nMinor comments: Please write out the abbreviation when used for the first time to help the reader, who is not necessarily familiar with the specific language used.\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": "9641", "date": "03 Jul 2023", "name": "Martin Schätz", "role": "Author Response", "response": "Dear Dr. Tamas Dolinay, I want to express my sincere gratitude for taking the time to review our work and providing us with such thoughtful feedback. Your comments have helped us to strengthen our work significantly, and I appreciate your efforts. Our replies to your major comments: 1) The abstract describes 5 different pattern of radiographic findings, but I do not find these in the manuscript. A novelty of the article would be the stratification of pneumonia based on the imaging. We appreciate your comments and would like to address your concern about the radiographic findings described in the abstract. The 5 groups are distinguished based on the percentage coverage in the lungs. We appologize for the confusion. We will revise the abstract to more accurately reflect your comment. The 5 different scores are originally based on paper „Chest CT score in COVID-19 patients: correlation with disease severity and short-term prognosis“ (https://doi.org/10.1007/s00330-020-07033-y) where the lungs are divided and the result of each part is summed up to the score. It would be possible to do the same with 3D Slicer and the „Lung CT Analyzer“ (https://github.com/rbumm/SlicerLungCTAnalyzer) deep learning tool, however, it would require installing it and having more powerful hardware available. The software tool paper aims to present software tool that was made per request of Faculty Hospital, however analysis of different pattern of radiographic findings would be quite an interesting suggestion for a full research article. 2) Please describe, if you had success implementing the image analysis in your clinical practice. What are the benefits and/or barriers of using the analysis in the real world? The ImageJ software tool was developed on request by the Facultypital of Královské Vinohrady, and it has been used by the Radiology center since September 2021. The score was mainly used for additional estimation to help doctors estimate the severity of COVID-19 disease in hospitalized patients. The first benefit is having a quick estimation of lung coverage by disease, which can be challenging to estimate by visual inspection. The second benefit is that the ImageJ and this specific SW Tool do not need installation (which can be challenging at the hospital IT infrastructure) and works on a average office computer. The challenge is mentioned inter and intra variability per user, but logging the whole process helps with that. In meantime we did optimization and some correction of reported issues of our ImageJ scripts, you are able to find them in the linked GitHub repository. It involves time and result robustness tests , inter and intra variance overview from reported parameters used, a new version including updated log protocols to help users troubleshoot possible issues with the version of ImageJ. New logs from both 8 and 16-bit versions of scripts now contain both the ImageJ version used and Bio-Image version used. We will welcome any issue reports or enhancement suggestions in the GitHub repository. Thank you again for your valuable feedback. Martin Schätz" } ] }, { "id": "153263", "date": "25 Oct 2022", "name": "Hamid A. Jalab", "expertise": [ "Reviewer Expertise image processing" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study describes a novel image tool developed for CT assessment of COVID-19 patients. The tool was created to assist in estimating the percentage of lungs infected by the virus.\nThe manuscript is interesting and addresses an important issue. Major comments:\n1. The Introduction should provide a strong argument for why the software tool is important.\n2. It is of importance to have sufficient results to justify the novelty of the proposed software tool.\n3. The robustness of the proposed software tool has not been addressed; this should be emphasized in the discussion section.\n4. What are the benefits of the proposed approach above other current the new software tool?\n\nIs the rationale for developing the new software tool clearly explained? No\n\nIs the description of the software tool technically sound? No\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? No\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? No\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? No", "responses": [ { "c_id": "9642", "date": "03 Jul 2023", "name": "Martin Schätz", "role": "Author Response", "response": "Dear Dr. Hamid A. Jalab, I am extremely grateful for the time and effort you have dedicated to reviewing our Software Tool Article. Your constructive comments have been instrumental in shaping our manuscript, and I truly appreciate your contributions to the peer review process. Our replies to your comments: 1. The Introduction should provide a strong argument for why the software tool is important. Thank you for your valuable feedback. We agree that the Introduction should provide a strong argument for the software tool's importance. As we highlighted in the new paragraph, there is a need for a open source, user-friendly software tool for reproducible quantitative analysis of CT scans to estimate COVID lung pneumonia. Current software tools such as ImageJ and 3D Slicer may not be user-friendly for end-users who are not familiar with creating analysis workflows. Our software tool aims to fill this gap by providing a user-friendly solution for reproducible quantitative analysis, with available code, training data, tutorial and GitHub repository. 2. It is of importance to have sufficient results to justify the novelty of the proposed software tool. The main motivation for the software tool was that no other similar software tool was available for use on the computer infrastructure of Faculty Hospital of Královské Vinohrady. The main obstacles were in internal network policy, the unavailability of any high performance computing hardware, and need of specific tool. Since more hospitals might be challenged in similar ways, the highest motivation was to share our work openly and freely to help innovate and enable them. 3. The robustness of the proposed software tool has not been addressed; this should be emphasized in the discussion section. Since the software tool is user operated, there is high inter and intra variability of results – which we addressed in text. The robustness of whole workflow is now addressed in terms of repeatability. 4. What are the benefits of the proposed approach above other current the new software tool? The only other open-source software tool adressing similar medical analysis is plugin SlicerLungCTAnalyzer for 3D Slicer software (available on GitHub: https://github.com/rbumm/SlicerLungCTAnalyzer). Of course there also exists commercially available software like Thoracic VCAR and others, but the money and hardware requirements might render these software unreachable for a lot of facilities, and since the tools are closed it might be enough for diagnosis but not for other research. The benefits of our Software tool are that it is developed open-source, in its very low hardware requirements and its ease of use with low technical requirements for installation. These were also the requirements of the faculty hospital where it was requested. Is the rationale for developing the new software tool clearly explained? We added a comparison to other freely available open source software tool as requested. Is the description of the software tool technically sound? We improved the pseudo-code on top of the available source code, which should improve the description overview of the whole tool. Are sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? The whole original code and its update is available through a linked (now updated) repository and on GitHub with a small tutorial. The data and software availability parts were extended. We added pseudocode for a better overview, but best option is to go through the code. Any encountered problems with the macro on specific machines and/or ImageJ version can be reported through an issue on GitHub repository. Is sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? The output of the software tool is a log of whole process and partial results, it is a necessary step for reproducibility, good data management and interpretation. If you encountered any issues with the tool or prepared protocols please report them in GitHub repositories so we can properly address them. We are happy to help, sustainability is important part of our project. Are the conclusions about the tool and its performance adequately supported by the findings presented in the article? We included more analysis about performance of the tool and also inter and intra variability overview (also available on GitHub). Scripts are included in linked materials with both new version of Software Tool. In the meantime we did optimization and some correction of reported issues of our ImageJ scripts, you are able to find them in the linked GitHub repository. It involves time and result-robustness tests , inter and intra variance overview from reported parameters used, a new version including updated log protocols to help users troubleshoot possible issues with the version of ImageJ. New logs from both 8 and 16-bit versions of scripts now contain both the ImageJ version used and Bio-Image version used. We will welcome any issue reports or enhancement suggestions in the GitHub repository. Thank you again for your valuable feedback. Martin Schätz" } ] } ]	1	https://f1000research.com/articles/11-326
https://f1000research.com/articles/12-771/v1	03 Jul 23	{ "type": "Research Article", "title": "Fatalism and knowledge associated to diabetes mellitus type 2 risk perception in Mexican population during COVID-19 confinement", "authors": [ "Geu Mendoza-Catalán", "Alicia Álvarez Aguirre", "Claudia Jennifer Domínguez Chávez", "María del Rosario Tolentino Ferrel", "Alma Angélica Villa Rueda", "Elizabeth Guzmán Ortiz", "Geu Mendoza-Catalán", "Alicia Álvarez Aguirre", "Claudia Jennifer Domínguez Chávez", "María del Rosario Tolentino Ferrel", "Alma Angélica Villa Rueda" ], "abstract": "Background: People with fatalistic beliefs and lack of knowledge of healthy lifestyles tend to show conformism and resignation due to their state of health. Even people with fatalism consider that contracting a disease is divine punishment, and this is reflected when they perform in unhealthy behaviours. The relationship between fatalistic beliefs, knowledge about diabetes risk factors, and perception of diabetes risk in Mexican adults during the COVID-19 pandemic were evaluated. Methods: The study design was cross-sectional and correlational. The study included individuals between 30 and 70 years of age, from a rural community in Guanajuato, Mexico. The data collection was done electronically. Results: The average age was 29.2 years (SD = 10.5), 55% were women, 52.3% were single, 36.2% had university studies and 57.3% were working. Perceived DMT2 risk was inversely related to fatalistic beliefs. Knowledge level was positively correlated to DMT2 risk perception. In multiple linear regression, pessimism and divine control dimensions were the only predictors of DMT2 risk perception. Conclusions: In young adults, knowledge increases regarding DMT2 risk perception. But the higher the fatalistic beliefs the lower the level of knowledge and the lower the perception of DMT2 risk.", "keywords": [ "Perception", "diabetes mellitus type 2", "fatalistic beliefs", "knowledge" ], "content": "Introduction\n\nPeople with chronic diseases such as type 2 diabetes mellitus (T2DM) are the most vulnerable group of people for hospital incidence and mortality during the COVID-19 pandemic (coronavirus disease 2019).1,2 Recent studies reported that during emergency care, people with COVID-19 were diagnosed as new cases of T2DM,3,4 suggesting that people were unaware of their disease until admission to the hospital. Therefore, this situation may have generated concern in the general population about their health status and their perceived risk of T2DM.\n\nThe perceived risk of T2DM is the individual’s appreciation of the probability of developing the disease in the future. People who perceive a higher T2DM have more intention and adopt healthier lifestyles to prevent the disease.5 This type of risk perception increases in women, those who are older, have a family history of diabetes, are overweight/obese, consume sugary drinks, do not consume fruits and vegetables, have a previous diagnosis of hypertension, have knowledge about the risk factors for T2DM and have a poor perception of their health status.6–10 However, a study conducted in Alemannia, reports that people with prediabetes and undiagnosed T2DM report low risk perception,11 the same as in the Mexican population.12 The low risk perception of T2DM may be due to different factors such as beliefs that diseases are unpredictable, or fatalistic beliefs.13 Fatalistic beliefs are considered as the idea that there is a force superior to the human being that determines the facts of life; this belief is referred to as external locus, luck, fate, destiny, or divine control.14 People with fatalistic beliefs adopt pessimistic or despair behaviors, whose behavior results in thoughts that death and disease are inevitable.15 This type of belief is considered an important coping factor when faced with the diagnosis of a chronic disease,16 that is to say people with higher fatalistic beliefs use health services less, abandon treatments, and show higher mortality rates.17,18\n\nOther studies report that fatalistic beliefs minimize and underestimate health risk because people do not comply with preventive behaviors,19–21 for example, preventive measures to avoid infection by COVID-19, therefore people with fatalistic beliefs may underestimate the risk of chronic diseases such as T2DM. So far, the association between fatalistic beliefs, knowledge, and perceived risk of T2DM has not been demonstrated. How people perceive themselves and feel vulnerable to developing chronic diseases is a predictor for lifestyle change and disease prevention. However, fatalistic beliefs may be a factor that underestimates knowledge of risk factors and perceived risk of T2DM. Therefore, the aim of this research was to assess the relationship between fatalistic beliefs, knowledge regarding the risk factors of diabetes, and the perception of T2DM in Mexican adults during the COVID-19 pandemic.\n\n\nMethods\n\nThe study followed the guidelines of declaration of Helsinki and the General Health Law on health research in Mexico, and it was approved by the Ethics and Research Committee of the University of Guanajuato, Mexico with permit number DCSI-CI 20190308-3. Written informed consent was obtained from participants before their data was collected. Ethics approval was granted in 2019.\n\nThe study design was cross-sectional and correlational. We had included adult men and women aged 30 to 70 years, residents of San Miguel Eménguaro, Salvatierra, Guanajuato, Mexico. We had excluded persons with a diagnosis of type 1, type 2, and gestational diabetes. The sample was estimated using the statistical program Gpower 3.1.4, with 95% reliability, 90% power and effect size of.08, which gave a sample of 218 people.\n\nParticipants were invited through online social networks (Facebook, WhatsApp and Instagram). The access link for the survey (hosted on Google Forms) was electronically shared through social networks. The invitation stated the objective of the survey, the declaration of respect for the confidentiality and anonymity of information, as well as that the survey was aimed at residents of San Miguel Eménguaro, Salvatierra, Guanajuato. When the link was opened, the informed consent form with the option to agree to participate in the study was displayed first. Subsequently, information on sociodemographic data was requested and ended with the completion of the questionnaires. We restricted to survey to only allow one entry per person. Data collection was carried out from August to November 2020. The study followed the guidelines of declaration of Helsinki and the General Health Law on health research in Mexico.\n\nIndependent variables: fatalism and knowledge.\n\nDependent variable: Perceived risk of Type 2 Diabetes Mellitus.\n\nA sociodemographic data card was used to collect information such as age, sex, marital status, schooling, and occupation.\n\nTo evaluate fatalism, the Multidimensional Fatalism Scale in Spanish15 was used, with 30 statements grouped into five factors: fatalism, pessimism/hopelessness, internal locus, luck, and divine control with a response from 1 to 5, where 1 means frequently disagree and 5 means frequently agree, with a maximum score of 150 points and a minimum of 30 points. The higher the score, the greater the fatalism. Cronbach’s alpha in this study was .88.\n\nIn addition, we used of Risk Perception Survey for Developing Diabetes (RPS-DD), which contains 43 items that measures beliefs about one’s risk for developing diabetes. This scale has six subscales: personal control (4 items), worry (2 items), optimistic bias (2 items), personal disease risk (15 items), comparative environment risk (9 items), and knowledge of diabetes risk factors (11 items). The higher the score the higher the perceived risk of T2DM.22,23 To evaluate knowledge of risk factors, a subscale of the same instrument with 11 questions was used. Each question has 4 answers (increases the risk, has no effect on risk, decreases the risk and don’t know). The items are dichotomously scored, correct/incorrect and the total sum of the subscale is from 0 to 11, the higher the score, the greater the knowledge.23 Cronbach’s alpha in this study was .76.\n\nSPSS version 25 was used to capture and assess data. Descriptive statistics were used for the characteristics of the participants, frequencies and percentages for categorical variables and measures of central tendency and dispersion for continuous variables. The variables of fatalistic beliefs (low 30 to 90; high 91 to 150), knowledge (low 0 to 4; high 5 to 9) and perceived risk of T2DM (low 8 to 20; high 21 to 32) were categorized according to the mean of the total score of the questionnaires. For the correlation analysis, Spearman’s coefficient and multiple linear regression were used to explain the perceived risk of T2DM.\n\n\nResults\n\nIn total 222 people participated in the survey, and 218 participants provided complete data. The average age was 29.2 years (SD=10.5), the sample was characterized by being mostly women (55%), single (52.3%), having a university education (36.2%) and having a job (53.7%), see Table 1.\n\nRegarding fatalism, 27.5% report high fatalistic belief scores, 83.5% have high knowledge about T2DM risk factors and 66.1% have high perceived risk of developing T2DM; the measures of central tendency and dispersion of the variables are seen in Table 2.\n\nAccording to the correlation analysis, the perceived risk of T2DM was inversely related to fatalism and its dimensions - see Table 3. The level of knowledge was positively correlated with perceived risk of T2DM (r=.178, p<.01). Subsequently, multiple linear regression was performed for perceived risk of T2DM, with fatalism dimensions and knowledge as predictor variables, but only pessimism (β=-.194, p<.01) and divine control (β=-.164, p<.05) were the only predictors, they explained 7.6% of the variance.\n\n p<.05.\n\n** p<.01.\n\n\nDiscussion\n\nThe purpose of this research was to analyze the relationship between fatalistic beliefs, knowledge of T2DM risk factors, and the perceived risk of T2DM in Mexican adults during the COVID-19 pandemic. In Mexico there is a large percentage of the adult population at risk of developing T2DM; according to the results of the 2018 National Health and Nutrition Survey most adults aged 20 years or older have a high prevalence of overweight/obesity, as well as being involved in risky behaviors such as alcohol consumption, smoking, sedentary lifestyle, and food insecurity.24\n\nIn this study, it was identified that the perceived risk of T2DM was high in comparison with other studies in the Asian population.25 This may be since the most vulnerable population to complications, hospitalization and death from SARS-Cov-2 was people with chronic diseases.1,2,26 This situation may have generated concern in the population about feeling at risk of developing T2DM and therefore, also feeling vulnerable to the COVID-19 virus. Likewise, even though people with a higher perceived risk of T2DM can make lifestyle changes, it has been reported that during the pandemic, people report an increase in the consumption of alcohol, tobacco and processed foods, emotional problems, and less physical activity.27,28\n\nOur results identified that a quarter of the respondents had above-average scores on fatalistic beliefs. Cultural beliefs are a key element in health care seeking and chronic disease prevention.29 In several studies it has been reported that people who believe that illness is a result of a supernatural phenomenon do not seek allopathic medical care, but instead seek help from healers or shamans who can help alleviate bad luck, witchcraft or perform prayers.30,31 This is due firstly because of the distrust they have about the negative beliefs held about treatments such as insulin or peritoneal dialysis, and secondly, because they think that allopathic medicine cannot cure or alleviate diseases that are caused by superhuman forces.\n\nThe level of knowledge was related to a greater perceived risk of T2DM. These results are consistent with previous studies, in which it has been reported that people who have information on the main risk factors and who have family members with a history of T2DM perceive a greater probability of becoming ill.7 In these studies, differences have been found between men and women with the level of knowledge and perceived risk of T2DM. Men have lower level of knowledge about risk factors and lower risk perception but have higher risk of developing T2DM compared to women. Health literacy has been considered as a relevant factor to face health problems and to know that chronic diseases are preventable,13 but studies in Latin America have indicated that although people have knowledge about T2DM risk factors, they consider that the disease cannot be prevented, that it is the responsibility of the health professional to prevent it and not of oneself.32\n\nFinally, we found that people who have high fatalistic beliefs have low perceived risk of developing T2DM. One of the dimensions of fatalistic beliefs that was related to low-risk perception was pessimism. Pessimism has been considered as a negative view, attitude, or idea regarding life events. People with pessimistic ideas have fewer coping strategies, lower self-efficacy, and are carefree33 considering that positive changes in health cannot be achieved. Thus, people with a pessimistic view have greater problems in making a healthy lifestyle change when they develop chronic diseases.34 Some authors report that these ideas are since they consider disease as something fatal and that death is inevitable, so that any action they take cannot change it.31 Another important factor in the perceived risk of T2DM is the belief in divine control. From a religious point of view, beliefs about God are a key element that influences people’s behaviors. On the one hand, people with fatalistic religious beliefs allow them to cope better with health problems.35–37But, on the other hand, they may consider that diseases are tests or punishments from God, and that only God can cure the disease.38–40 This set of beliefs influences people to consider that it does not matter if they make changes in their way of living, because illness cannot be prevented if God does not want it. Also, people may self-perceive themselves to be at lower risk of developing T2DM by self-evaluating themselves without conflict with God.\n\nThe weaknesses of the study include data collection conducted through electronic means and social media on the internet, which resulted in a majority of young adult participants. It is necessary for future studies to collect data through face-to-face interactions in order to include participants from older age groups. The research design was cross-sectional; therefore a cause-and-effect relationship cannot be established. As a result, the findings should be interpreted with caution and extrapolated to similar populations to those in this study.\n\nOn the other hand, the strengths of the study include being one of the first investigations to link fatalistic beliefs with knowledge and perceived risk of T2DM. Additionally, it is a study conducted on a population of young adults from a rural community in Mexico, which highlights the relevance of these beliefs and their implications in identifying knowledge and health risks.\n\n\nConclusions\n\nIn young adults, knowledge increases the perceived risk of T2DM. But fatalistic beliefs decrease knowledge and perceived risk of T2DM. Fatalistic beliefs should be considered a variable that has to be dealt with by health professionals. It is necessary that health professionals consider fatalistic beliefs for the prevention of chronic diseases and improve through educational programs health literacy about the risk factors of T2DM and the benefit of lifestyle, mainly in young adult populations. It is important to provide more education in those who have low knowledge about T2DM risk factors, so that people become more aware of their risk.", "appendix": "Data availability\n\nfigshare: Data.sav. https://doi.org/10.6084/m9.figshare.22773977.v3. 41\n\nThis project contains the raw questionnaire responses.\n\nfigshare: Data.sav. https://doi.org/10.6084/m9.figshare.22773977.v3. 41\n\nThis project contains the demographics questionnaire.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nCarrillo-Vega MF, Salinas-Escudero G, García-Peña C, et al.: Early estimation of the risk factors for hospitalization and mortality by COVID-19 in Mexico. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBachem R, Tsur N, Levin Y, et al.: Negative Affect, Fatalism, and Perceived Institutional Betrayal in Times of the Coronavirus Pandemic: A Cross-Cultural Investigation of Control Beliefs. Front. Psychol. 2020 Oct [cited 2022 Feb 18]; 11(1): 40–51. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNordfjaern T, Mehdizadeh M, Fallah ZM: Social Psychology of Coronavirus Disease 2019: Do Fatalism and Comparative Optimism Affect Attitudes and Adherence to Sanitary Protocols? Front. Psychol. 2021 May [cited 2022 Feb 20]; 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWalker EA, Mertz CK, Kalten MR, et al.: Risk perception for developing diabetes: comparative risk judgments of physicians. Diabetes Care. 2003 Sep [cited 2022 Feb 20]; 26(9): 2543–2548. 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Publisher Full Text Reference Source\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 May [cited 2022 Feb 20]; 12(6). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKumar A, Arora A, Sharma P, et al.: Is diabetes mellitus associated with mortality and severity of COVID-19? A meta-analysis. Diabetes Metab. Syndr. 2020 Jul-Aug [cited 2022 Feb 20]; 14(4): 535–545. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKeith KD: Cross-cultural psychology: Contemporary themes and perspectives. 2nd ed.John Wiley & Sons; 2019.\n\nZakiawati D, Setiadhi R: Oral manifestations of acute leukemia in children: family supernatural beliefs and its contribution to the prognosis of the disease. Int. J. Med. Dent. Case Rep. 2021 Jul [cited 2022 Oct 20]; 12(6): 1–4. Publisher Full Text\n\nArabiat D, Whitehead L, Al Jabery M, et al.: Beliefs About Illness and Treatment Decision Modelling During Ill-Health in Arabic Fami-lies. J. Multidiscip. Healthc. 2021 Jul [cited 2022 Aug 20]; 14: 1755–1768. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVicente Sánchez B, Bonilla Romero J, Vicente Peña E, et al.: Percepción de riesgo de desarrollar diabetes mellitus en personas no diabéticas. Re-vista Finlay. 2016 [cited 2022 Aug 20]; 6(2): 81–92. Reference Source\n\nFink G: Stress: Concepts, Cognition, Emotion, and Behavior: Handbook of Stress Series. Academic Press; 2016.\n\nHelgeson VS, Zajdel M: Adjusting to Chronic Health Conditions. Annu. Rev. Psychol. 2017 Jan [cited 2022 Aug 20]; 68: 545–571. Publisher Full Text Reference Source\n\nHan J, Zhou X, Meng Y: The impact of religious beliefs on the health of the resi-dents-Evidence from China. Int. J. Health Plann. Manag. 2020 Jan [cited 2022 Feb 19]; 35(1): 378–393. PubMed Abstract \| Publisher Full Text\n\nHill TD, Saenz JL, Rote SM: Religious Participation and Mortality Risk in Mexico. J. Gerontol. B Psychol. Sci. Soc. Sci. 2020 Apr [cited 2022 Feb 19]; 75(5): 1053–1061. PubMed Abstract \| Publisher Full Text\n\nBorges M, Lucchetti G, Leão FC, et al.: Religious Affiliations Influ-ence Health-Related and General Decision Making: A Brazilian Nationwide Survey. Int. J. Environ. Res. Public Health. 2021 Mar [cited 2022 Feb 19; 18(6): 2873. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJalal Z, Antoniou S, Taylor D, et al.: South Asians living in the UK and adherence to coronary heart disease medication: a mixed- method study. Int. J. Clin. Pharm. 2019 Feb [cited 2022 Apr 19]; 41(1): 122–130. Publisher Full Text Reference Source\n\nAhmedani BK, Peterson EL, Wells KE, et al.: Asthma medication adherence: the role of God and other health locus of control factors. Ann. Allergy Asthma Immunol. 2013 Feb [cited 2022 Apr 19]; 110(2): 75–79.e2. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKilshaw S, Omar N, Major S, et al.: Causal ex-planations of miscarriage amongst Qataris. BMC Pregnancy Childbirth. 2017 Jul [cited 2022 Apr 19]; 17(1): 250. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMendoza Catalan G: Fatalism and risk perception T2DM. [Dataset]. figshare.2023. Publisher Full Text" }	[ { "id": "196704", "date": "04 Sep 2023", "name": "Ola Sukkarieh", "expertise": [ "Reviewer Expertise My areas of expertise is diabetes self-management", "fatalism in diabetes", "social determinants of health" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe purpose of this study was to analyze the relationship between fatalistic beliefs, knowledge of T2DM risk factors, and the perceived risk of T2DM in Mexican adults during the COVID-19 pandemic. The authors could not present clearly the relationship between the three variables of interest. It was hard to follow.\nAbstract: missing aim, statistical analyses, sample size and questionnaires used\nManuscript:\nIntroduction: the focus of the introduction is not clear specifically with context of COVID 19. If the main goal is to study fatalism, why is COVID 19 introduced and how does it matter or affect the relationship?\nMethods:\ninclusion criteria: what about excluding pre-diabetes since it's a major risk factor to develop T2DM and might affect participants' perceptions. what about criteria related to COVID 19 since the time frame seems to be influenced with COVID pandemic.\nResults:\nWhy were the scores categorized instead of being used as continuous variables when the latter yields stronger data analyses?\nDescriptive data can be combined in one table for ease of following (T1and T2)\nThere needs to be T4 for multiple linear regression.\nDiscussion:\nneeds to start with brief summary of the findings\n\nin 1st paragraph, authors cannot introduce new concepts of risky behaviors when it is out of the scope of the paper.\n\npresentation of findings are not aligned with T3, i.e. there is no reflection on negative or positive existing relationships.\n\nAdditionally, the variables are not well identified in the discussion as to what is the outcome of interest which is according to the methods section: Dependent variable: Perceived risk of Type 2 Diabetes Mellitus.\n\nregression analysis is missed from the discussion.\n\nWeakness: need to acknowledge limitations of self-report which affects biases in responses and lack of generalizability due to research 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? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "335082", "date": "28 Oct 2024", "name": "Sanisah Binti Saidi", "expertise": [ "Reviewer Expertise Diabetes self-care/self-management", "fatalism", "spiritual care", "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\nAbstract: The problem statement is missing within the abstract. Furthermore, methods of analysis and the total number of samples are missing. Introduction: The concept of fatalism, i.e., the fatalistic perception of diabetes vs. fatalism due to COVID-19, is not clearly discussed. Fatalism might be viewed differently based on these situations, which would affect patients' perceptions of diabetes and the perceived risk that they may have. Furthermore, further discussion on the hypothesised relationship between knowledge about diabetes, fatalistic behaviour related to diabetes and perceived risk of Type 2 diabetes is required to justify the current study. Methods: Did the authors exclude people with type 2 diabetes? Have the samples been infected with and recovered from COVID-19? This might affect their fatalistic beliefs. Findings: Further interpretation of the statistical findings is needed. Discussion: In the first paragraph, the authors do not have to repeat the prevalence of obesity/diabetes but brief the reader about the research objectives and summarize the findings. The primary variable introduced to the reader was fatalism; therefore, it would be more apparent if the authors discussed the findings of fatalism in more detail and provided a clear view to the reader about the fatalistic beliefs of the samples within this study. The influence of culture on fatalistic beliefs was not discussed earlier; therefore, it would be more beneficial if the authors could inform the reader how they have included this aspect within the questionnaires or if it is a new component that has been identified, as it was contained within the discussion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-771
https://f1000research.com/articles/11-402/v1	08 Apr 22	{ "type": "Systematic Review", "title": "Brain-based learning in design and visual arts education: a bibliometric assessment of Scopus indexed literature", "authors": [ "Hala A. El-Wakeel", "Reham Abdellatif", "Dalia Hussain Eldardiry", "Deema F. Al-Saleh", "Mai I. Shukri", "Khadeeja M N Ansari", "Reham Abdellatif", "Dalia Hussain Eldardiry", "Deema F. Al-Saleh", "Mai I. Shukri", "Khadeeja M N Ansari" ], "abstract": "Background: This study aims to critically review, quantify, and assess research outcomes on brain-based learning with an evidence-based study on Scopus indexed literature, with a focus to understand the evolution structure and growth, detect trends, subject development, and most importantly, identify the gaps in the published body of literature that relates brain-based learning to design and visual arts education. Methods: Various scientometric tools were used to map, visualize, and analyze 186 research publications, indexed in Scopus in a twenty-year timespan ‘2001-2021’. Annual publication trends, relevant sources, prolific authors, authorship patterns, productive organizations and countries, funding agencies, keyword co-occurrence analysis, and thematic evolution mapping on brain-based learning publications were examined in this study. Results: Despite the significance to apply brain-based learning strategies in design and visual arts education to boost students’ knowledge and creative skills, the findings show a decline in quantities and growth patterns in brain-based learning research directed towards design disciplines in the past twenty years. Among the identified (186) documents published in (128) sources, with (1013) citations, the study detected only (57) research (30%) that were related to ‘design education,’ including those focusing on ‘instructional design, ‘and ‘syllabus design’ whereas only (3) articles were in ‘design and visual arts’ disciplines. Conclusion: These rather small numbers reflect the big gap in the current body of literature that associates brain-based learning with creativity-based disciplines, specifically in design and visual arts education. This infers the necessity to direct the attention of academics, researchers, and educationalists in the fields of design and arts towards brain-based learning applications, research and pedagogy.", "keywords": [ "Brain-based learning", "Design Education", "Creativity", "Visual Arts", "Bibliometric assessment", "Scopus indexed journals", "Scientometric analysis." ], "content": "Introduction\n\nBrain-based learning (BBL) is perceived as a core theory; it represents a learning paradigm that takes a holistic approach, looking at teaching and learning developmentally, socio-culturally, and in other broader ways (Caine & Caine, 1995). It involves accepting the rules of the human brain processes and functions and then designing instruction, accordingly, achieving meaningful learning (Duman, 2010). BBL includes specific learning processes based on how pupils are motivated, how attention works, how memories are created, how conceptual knowledge is acquired, how information is presented and other essential components of teaching and learning (Shukla, 2019). Teaching and learning have always been based on what students, teachers, and policymakers believe. Their perspectives, experiences, logical arguments, and quasi-experiments enlighten the teaching and learning process. However, when teaching and learning are applied based on the faculties of the brain, they facilitate more effective and comprehensive student learning (Shukla, 2019).\n\nSeveral researchers examined the brain and its functions as ‘the primary learning organ.’ As a result, BBL emerged as one of the most effective learning methods, providing learners with excellent opportunities. According to the BBL theory, the brain’s plasticity (the ability to remodel itself for improved functionality) is maintained throughout life. El-Wakeel (2008) has confirmed that the structure and function of the brain are the foundations of this learning theory. In this sense, it can be stated that ‘learning will occur if the brain is not prevented from carrying out its usual functions.’\n\nA massive shift has been achieved in neuroscience during the last three decades; the discovery of neuroplasticity, ‘the brain’s ability to selectively modify itself in response to specific repeated actions and experiences,’ proved that the brain retains its flexibility throughout life (Cramer et al., 2011). Thus, neuroscientists have gathered reliable data through designing clinical studies that use double-blind, extensive, diverse, multi-age, multicultural groups of people to determine how humans learn (Spears & Wilson, 2021). The way the brain functions has been identified to have a substantial impact on the most successful learning activities (Wilson, 2013).\n\nThe last two decades witnessed several successful examples of practicing BBL in all levels of education in numerous subject areas. Academics from prominent universities worldwide have incorporated this knowledge in their classrooms and research, based explicitly on conclusions from neuroscience research (Spears & Wilson, 2021).\n\nDisciplines that are based on creativity and visual creation, such as design and visual arts, maybe served most by BBL methods and strategies. Caine and Caine (1995) stated that BBL stresses the importance of ‘patterning,’ which is that the brain easily learns logic and creates meaning because it relates, integrates and connect information and builds upon it, as humans resist learning unrelated information, this may be seen in design and visual arts education. Another point that relates BBL to design and visual arts education is that BBL stresses the principle that the brain is a ‘parallel processor,’ which performs complex cognitive and creative functions simultaneously and in a nonlinear way.\n\nLearning design and art requires exceptional capabilities and skills; students must manipulate knowledge, information, and experiences they gain, relate, connect and convert them into creative, aesthetical, and functional ideas and meaningful outcomes to solve a design problem. This manipulation is the core of creativity, and it takes varying lengths of time. It also requires concentration and effort, leaving the student emotionally involved and stressed.\n\nBBL can help design and visual art students understand how their brains work, think, and perceive; it can also facilitate the development of creative skills with reduced frustration (El-Wakeel, 2020). Therefore, BBL provides a biologically based framework for teaching and learning in the context of design and visual arts that explains to students the concepts behind learning; essentially learning how to learn. This meta-concept encompasses a diverse range of strategies that reduce the amount of stress in the classrooms and achieve educational goals easier and faster. Yet, educationalists, especially in the field of design and visual arts, have not fully utilized results from neuroscience studies into BBL methodologies.\n\nEdwards (2002) discussed the increasing number of research and activities related to creativity throughout the next century, where the concept of creativity evolves from simply a process of solving problems (that continually arise in human life) into a meta-process of generating new ideas about the process of searching and identifying the issues to solve where no one else has perceived.\n\nDespite the relevance of BBL to design and arts education as creativity-inspired disciplines, yet there is scarcity in published research that has made the proper connection between them.\n\nA very few studies were found that incorporated BBL principles into learning in the field of ‘Arts’ in general but not particularly in design and visual arts. For example, Betty Edwards from California State University and Howard Gardner from Harvard University are among the very few authors who incorporated BBL into the design and visual arts. Edwards’s book “The New, drawing on the Right Side of the Brain” (2002) is a brilliant approach to recent developments in brain-based research that relate to developing drawing skills. In addition, Gardner’s book “Art Education and Human Development” (1991) is another pioneering work that links art education with several brain capabilities.\n\nA more recent pioneering study focusing on ‘Design’ applied BBL in studio-based design courses for three years, aiming to support, develop, and improve teaching strategies and learning processes (El-Wakeel, 2008). The study applied 12 principles of BBL in designing courses and observing students’ performance to modify pedagogical strategies accordingly. The result isolated six BBL principles directed towards enhancing the creativity progress stages in ‘Arts and Design’ and enhancing the students’ creative capabilities in a much shorter time and less stressful way. In 2020, El-Wakeel argued that creativity is an exceptional brain progressive capability that needs a direct simultaneous response from the brain towards the body. The study added that BBL offers design and art educators a perfect chance to understand the human brain’s physiology and performance and then convert this knowledge into educational tools and principles. This was a new integrated view of the learning process for the learner. The study claimed that students could develop their skills, activate their creative brain capabilities, and control the stages of their creative process by applying this instructional approach to design freshmen students (El-Wakeel, 2020).\n\nThe necessity for more specialized studies and application of BBL in design and visual arts motived the authors to perform a bibliometric analysis to identify the gaps, trends, subject development, and growth in the published body of literature on BBL in design, visual arts, and creativity-based subjects. Identifying such gaps will help direct more focused and applicable future research.\n\nAiming to identify the gaps in the current literature that relates brain-based learning to creative subjects such as design and visual arts. This research therefore carries out the following objectives:\n\n1. Map and visualize Scopus indexed BBL literature published in the past twenty years, using bibliometric methods and scientometric analysis tools to evaluate yearly research growth and trends, citation structure, topics of the most productive publication sources, prolific authors and their disciplines, authorship patterns, contributing organizations and countries, and collaborating funding bodies.\n\n2. To critically analyze patterns of progression and evolution of research in BBL according to their keywords, topics, themes and titles in the studied time span.\n\n3. To detect the actual gaps and decline in BBL research in disciplines related to creativity, design and visual arts based on the aforementioned analysis.\n\n\nMethods\n\nThe bibliometric method (a quantitative evaluation for analyzing bibliographic data) was employed to assess the research performances of brain-based learning in terms of creativity-based subjects such as design and visual arts. Although this methodology of determining published research literature has been around for a long time, however, it became more prevalent with the introduction of large-scale bibliographic databases (e.g., Scopus, Web of Science, PubMed). The method used in this research presents the scientific landscape of annual growth trends, productive authors, actively participating countries, organizations, and collaborative contributors to the global scientific literature, with stress on investigating the evolution of themes and area topics studied in BBL research. Data was collected on 13th June 2021 at Imam Abdulrahman bin Faisal University in Dammam, Saudi Arabia, from the Scopus database. The topics ‘design’ and ‘creativity’ were used in the initial search and then refined by the term ‘brain-based learning,’ this allowed the retrieval of records used in this study, the following search strategy was applied:\n\n(TITLE-ABS-KEY (“Design”) OR TITLE-ABS-KEY (“Creativity”) AND (“brain-based learning”)\n\nThe data was downloaded in BibTex, RIS format, and CSV format. Microsoft Excel, scientometric and bibliometric tools, such as Bibexcel (Persson et al., 2009), Biblioshiny (Massimo & Corrado, 2019), and VOSviewer (van Eck & Waltman, 2010), were used to analyze the data and visualize the results.\n\n\nResults\n\nFor the topics ‘design’ and ‘creativity,’ 5,980,330 records were retrieved; when refined by ‘brain-based learning,’ only 186 documents were retrieved. Those were the bases of this study; the results included 175 research papers that mentioned the word ‘design,’ however, the term ‘design’ is a vast word that yields several interpretations and relates to processes within many disciplines covering several aspects of the term, e.g., ‘syllabus design’ and ‘instructional design.’ Narrowing the search down, just 57 papers focused on ‘design education.’ Among those, only 3 research articles were directly related to ‘design and visual arts.’ These numbers reflect the huge gap in the BBL research that is directed towards topics in creativity, design and visual arts education.\n\nAccording to the overall results, 454 authors transcribed the identified 186 research, spread in 128 sources during 2001-2021 (see Table 1). As shown, 8745 papers were cited to produce the 186 publications. The average number of publications was 5.39, while the average number of citations per document was 0.6875, and 5.446 was the average number of citations per document observed. The authors used 466 keywords in 186 publications. Single-author documents were 50, with averages of an author per document 2.44, co-authors per document 2.67, and a collaboration index of 3.01.\n\nThe first research paper published in 2001 did not receive any citations; similarly, there were no publications in 2002. Remarkably, one paper was published in the year 2003 that received 66 citations. The average annual growth rate for the twenty years is about 9.3 publications. The literature production from 2001 to 2016 was below 15 publications; later an impressive research growth rate was observed in the recent five years (2017-2021). The year 2019 recorded the highest in research outcomes (29 publications, 35 citations), followed by 2020 (26 publications, 16 citations) 2018 (21 publications, 44 citations). The year 2021 recorded 11 publications with zero citations until 13th June 2021. Table 2 displays the impact of citations over the twenty years (2001-2021), a total of 1013 citations were recorded for the 186 publications. The average yearly citation growth is stated as 50.65 citations. The highest number of citations were recorded in 2015 (128 citations) for only 14 publications, followed by 2016, 100 citations for nine publications. The analysis indicates a slow growth of publications in the first ten years, resulting in a higher citation rate per publication. The interest in the subject began to grow rapidly in the next ten years, with some fluctuations in the annual growth of publications and the impact of citations on BBL research.\n\n* NP=Number of papers.\n\n** TC=Total citation.\n\nTable 3 shows that the forms of publications most favored by authors in BBL research were journaled articles (96 papers, 649 citations), followed by conference paper (56 publications, 38 citations), then books (11 publications, 115 citations), book chapter (11 publications, 13 citations), and then review (with 7 publications and 115 citations). The short survey, note, and letter were the least preferred form for BBL research, with one paper each. The authors preferred form of publications agrees with the results found by Ansari et al. (2021) and Rahaman et al. (2021), where journal papers have a higher reach rate and ensure dissemination of results.\n\nThe top ten sources of BBL research are listed in Table 4; looking closely at the results, it was pointed out that only three sources have more than five publications. Journal of physics: conference series (Q4) was acknowledged as the most relevant source for published BBL research with 22 publications and 17 citations, followed by the European Journal of Social Sciences (Q4) and then Lecture Notes in Computer Science (Q3) with three publications each and 11, and 2 citations, respectively. International Journal of Advanced Computer Science and Applications (Q3), Journal on Mathematics Education (Q2), ACM International Conference Proceeding Series, and Procedia - Social and Behavioural Sciences with three publications each having 5, 26, 3, and 15 citations, respectively. Energy Education Science and Technology Part B: Social and Educational Studies, Journal of Cardiothoracic and Vascular Anesthesia and Proceedings - IEEE Symposium on Computers and Communications came tenth in the top ten list with two publications each. Half of the leading sources belonged to the UK, followed by the USA (2), Germany, Indonesia, and Turkey each had only 1 source. It is observed from this result that none of the sources identified in the top ten for BBL research relate to design or visual arts specialties, so the authors had a closer look at all of the 186 publications, this revealed that most sources were within the fields of physics, computer science, education, behavioural sciences, etc., while there were only 3 sources that were directly related to design and visual arts studies and/or education, and they were not detected in the top ten results. This shows that there is a very slim opportunity for researchers to publish in platforms dedicated to this field which explains the extended literature gap in this area.\n\nThe top ten most prolific authors of BBL research are listed in Table 5. Chaijaroen, S. (Khon Kaen University) is the highest publishing author with 22 publications and 7 citations. Howard-Jones, P.A. (University of Bristol), Yelamarthi, K. (Central Michigan University), and Abidin, SRZ. (University of Technology Mara), each has three publications and 32, 51, and 4 citations, respectively. Ashaari, N.S., Ausburn, L.J., Bose, R., Drake, E., Hendriana, H., and Hess, P.E. ranked tenth of the list, with two publications each and 4, 5, 28, 50, 19, and 28 citations, respectively. Yelamarthi, K. was identified as the most impactful author with 51 citations for three publications, followed by Drake, E. with 50 citations for two publications, and Howard-Jones, P.A. with 32 citations for three publications. The table also reveals that 50% of the top ten published authors are from the USA, followed by Malaysia (two authors), Thailand, Indonesia, and the UK are home to one author each.\n\nWhen looking at the specialties of authors with high citations, they happened to be specialized in the fields of engineering and technology education, neuroeducation, neuropsychological concepts, computer science, and medicine; these publications appear to have more acceptable and useable results. On the other hand, the low impact of authors specialized in design and visual arts education raises the question on why researchers, academics, and educationalists in design disciplines are not directed towards liking BBL to design education despite the significance of this topic and its high relevance to enhancing design students’ knowledge acquisition and creativity.\n\nThe authorship pattern is visualized in Figure 2, which shows that out of 186 publications, only 50 papers represent single authorship, and these 50 received 273 citations. Double authorship produced 49 papers and received 319 citations, followed by triple authorship, which contributed to 42 papers, with 211 citations, and four-authored research yielded 22 papers with 124 citations. A much smaller number of publications, 23, included five or more authors with 86 citations in total. The visualization infers that the more authors contribute to a research, the more general it may be, hence it is cited less. Another inference is that there is a lower chance of collaboration due to the scarcity of researchers specialized in this topic. A similar result on the authorship pattern was reported by Rahaman et al. (2021).\n\nThe top ten most beneficial organizations of BBL research are displayed in Table 6. Khon Kaen University in Thailand produced 13 papers, followed by Universitas Pendidikan Indonesia with eight papers. Central Michigan University in the United States produced 7 papers, Universitas Sultan Ageng Tirtayasa in Indonesia, and Universiti Kebangsaan Malaysia with 5 papers each. The Harvard Medical School, Universitas Negeri Yogyakarta, University of Bristol, and the University of Oklahoma contributed to 4 publications each. Imam Abdulrahman Bin Faisal University ranked last in the top ten, contributing to 2 papers of BBL research. When investigating the titles of these organizations’ publications, it was found that research from the highest-ranking organizations focused on mathematics, physics, and computer education, while the less-ranking organizations produced research on neuroscience, engineering, mathematics, and design education. Therefore, there is more room for contribution in the topics related to creative disciplines.\n\nIndonesia was acknowledged as the most productive country in BBL research in Table 7, producing 48 papers and receiving 61 citations, followed by the United States (39 papers and 405 citations), Turkey (16 publications and 44 citations), Thailand (14 publications and 17 citations), and Malaysia (10 and 17 citations). China and Saudi Arabia ranked tenth on the list with 4 publications each, having 5 and 3 citations, respectively. In terms of order of citations, the United States scored the highest number of citations (405), followed by the United Kingdom (229 citations) and Indonesia (61 citations).\n\nThe keywords set by authors in their published work are considered to be more precise and better express the research’s scope than those set by the publisher. The co-occurrences of authors’ keywords are assessed in this paper to identify BBL research trends; therefore, a minimum of two co-occurrences are considered; this is similar to the type of analysis done by Rahaman et al. (2021). Thus, from the total of 466 keywords, only 49 met the thresholds. The total strength of the co-occurrence links with other keywords was calculated for each of the 49 keywords where the total link strength were selected. Hence 47 keywords, 10 clusters, 102 links, and 139 total link strengths were observed. The 10 clusters are differentiated through a colour code shown in Figure 3, where authors’ keywords are visualized using VOSviewer software.\n\nThe authors’ keywords that appeared the most in the studied BBL research were; Brain-Based Learning, Education, Instructional Design, Learning, Creativity, Brain, Neuroscience, Achievement, Brain-Based Learning, and Collaborative Learning. Keywords are grouped in the following clusters:\n\nCluster 1 consists of seven author keywords: Active Learning, Collaborative Learning, Critical Thinking, Flipped Classroom, Mathematics Education, Problem-Based Learning, and Students. The most common (n = 4) author keywords in this cluster are Collaborative Learning and Flipped Classrooms.\n\nCluster 2 consists of seven author keywords: Brain, Constructivism, Design, EEG, Motivation, Neuroscience, and Visual Arts. The keywords Brain and Neuroscience were found to be the most occurring (five times each) author keywords in this group.\n\nCluster 3 includes the five author keywords: Anxiety, Behaviors, Learning, Scaffolding, and Simulation. Learning (n=7) was found as a highly occurring author keyword in this group.\n\nCluster 4 includes five author keywords: Achievement, Brain-Based Learning, Creative Thinking, Creativity, and Retention. Creativity (n=6) was noted as the highest occurring author keyword in this cluster.\n\nCluster 5 comprises four author keywords: Chemistry Education, Constructivist Learning Environment, Multimedia Learning Environment, and Scientific Thinking. All of the author’s keywords appeared at least twice in this cluster.\n\nCluster 6 consists of four author keywords: Co-Creation, Online Learning, Student Engagement, and Virtual Reality. Online learning appeared the most in this cluster (n=3).\n\nCluster 7 includes four author keywords: Artificial Neural Networks, Face-To-Face Tutoring, Learning-Environment, and Mental Stimulation. All the chosen keywords appear at least twice.\n\nCluster 8 includes the following keywords: education, game design, multiple intelligence, and serious games. Education (n=10) pointed out as the most occurred author keyword in cluster 8.\n\nCluster 9 consists of four author keywords: Brain-Based Learning, Elementary School, Serious Game, and Slow-Reading. The phrase Brain-based Learning (n = 14) highly appeared keyword in the cluster.\n\nCluster 10 includes the keywords: Instructional Design, Pedagogy, and Problem-Solving. Instructional design (n=8) was found as the highest-appearing keyword in the cluster.\n\nThe previous mapping shows that the authors’ keywords used to search for BBL research may not include the subject area related to brain-based learning, but rather they mostly include pedagogical aspects teaching strategies, instructional design. Searching for keywords such as Design and Visual arts may not yield many results; however, the keyword Neuroscience was found in the same cluster as Design and Visual Arts. The occurrences were very low, but there is a direct association between these fields researchers must relate to. Creativity and Creative thinking are keywords that find somewhat relevant literature related to design disciplines.\n\nFor all keywords’ analysis, a minimum of four occurrences of all keywords were considered in this research; therefore, out of 1018 keywords, only 59 meet the thresholds. The total strength of the co-occurrence links with the other keywords was calculated for each of the 59 keywords, and the greatest total link strength was also calculated. Hence 59 keywords, 4 clusters, 527 links, and 1082 total link strength were observed. All 4 clusters were then differentiated into four different colours, as seen in Figure 4.\n\nCluster 1 comprises 20 keywords: article, controlled study, curriculum, female, human, human experiment, humans, learning, male, motivation, nursing student, online learning, priority journal, problem-based learning, scientist, simulation, skill, student, united states and virtual reality. Among the 20 keywords, the most occurred keywords were human and article with 15 and 14 frequency, respectively.\n\nCluster 2 consists of 14 keywords: achievement, brain, brain-based learning, brain-based learning, creative thinking, creativity, design, educational environment, learning achievement, learning process, learning systems, neuroscience, research, and scaffolds. Among the 14 keywords, the highest occurred keywords were brain-based learning and learning systems occurring 14 times each.\n\nCluster 3 included 13 keywords: control groups, critical thinking, critical thinking skills, education computing, junior high schools, learning models, physics, problem-solving, quasi-experiments, research and development, research methods, students, and surveys. The most occurred keywords in this group were students and education computing with 42 and 14 respectively.\n\nCluster 4 represented 12 keywords: active learning, collaborative learning, computer-aided instruction, curricula, e-learning, education, engineering education, flipped classroom, instructional design, learning environments, and teaching. Education and teaching were the most occurring keywords in this cluster, with 24 and 23 occurrences, respectively.\n\nIt is observed in Figure 4 that ‘creativity’ and ‘design’ in Cluster 2 occurred scarcely in the studied publications; the term ‘art’ and ‘visual art’ did not appear to occur in the all-keywords categories.\n\nA comparison between the highly accruing ‘all-keywords’ and ‘authors’ keywords’ are listed in Table 8. It is noticed that the authors’ keywords are more precise than all keywords. It is also found that the appearance of the keywords such as ‘Brain-Based Learning’ is the same in all keywords and author keywords; however, it is on the top of the top-ten list of ‘authors’ keywords’ and the sixth in the list of ‘all keywords’ top-ten list. The keyword ‘Creativity’ appears fifth in the authors’ keywords list, whereas it does not appear in the all-keywords list’s top ten occurrences.\n\nThe thematic evolution analysis by topic was considered to investigate the stability, progression and/or regression in BBL research topics. For this type of analysis, a topic-model unigram was developed from 250 words with a minimum cluster frequency (5), and a time slice (4) with cutting years for each slice: 2006, 2011, 2016, and 2020 respectively, see Figure 5.\n\nThe unigram shows the most frequent topics, where it can be seen that the period 2001-2006 includes BBL research related merely to two topics which are ‘creativity’ and ‘learning’, these topics remain in the focus of BBL research until 2007. The development in the subject area can be noticed starting from 2007 up to 2012, where combinations of topics are noticed relating the initial titles ‘creativity’ and ‘learning’ to ‘students’ and ‘education’. While there are a number of emerging topics such as ‘solving-problems’, ‘constructivist’, ‘brain’ and ‘approach’ with consistent development. By 2012, research relating those topics to ‘approach’, ‘learning’, ‘teaching’, ‘education’ and ‘engineering’ were published.\n\nThe topic ‘framework’ emerged during the period 2012-2016, which mostly contributed to the development of research related to the topic ‘design’ in 2017-2020. However, this does not relate directly to ‘design and creativity’ or ‘design and art’, but rather to educational frameworks, engineering and curricula design, as shown in the Figure 5.\n\nMore interestingly, this unigram shows that several topics such as ‘thinking’, ‘designing’, ‘model’, ‘effect’ and ‘skills’ are not showing any relationship with the topic ‘design’, contrary to what may be assumed. The visualization also reveals that in 2017-2020, a few new topics have emerged such as ‘thinking’, and ‘skills’ which are strongly related to ‘mathematics’ and ‘education’. It is also worth mentioning that the topic ‘visual arts’ is missing from the unigram, meaning its frequency was not detected. The thematic evolution analysis substantiates that there is decline in the development of BBL research relating to the topics of design, visual arts, creativity and design education. Table 9 presents the number of occurrences\n\nThe top ten highly cited publications of BBL research are sorted in Table 10. The 2010 article entitled “Using a games console in the primary classroom: Effects of ‘Brain Training’ programme on computation and self-esteem” by Miller, D.J. and Robertson, D. P. was the most cited publication with 81 citations, followed by “The practical and principled problems with educational neuroscience” by Bowers, J.S. with 70 citations (2016), “Participatory Action Research: creating an effective prevention curriculum for adolescents in the Southwestern US” by Gosin et al. (2003) with 66 citations came afterward. “Linking Architecture and Education: Sustainable Design for Learning Environments” (2009) by Taylor, A. (2009) with 60 citations and “A review of empirical evidence on scaffolding for science education” by Lin et al., (2012) with 44 citations followed. The paper entitled “Variables Affecting Learning in a Simulation Experience: A Mixed Methods Study” by Beischel, K.P. (2013) ranked tenth in the list with 29 citations. Table 9 also shows that most of the top ten cited papers were published between 2003 and 2016. The highest total citations per year (T.C./Year =11.67), as well as the highest normalized total citations (NTC=6.30), were reported in the article entitled “The practical and principled problems with educational neuroscience” (Bowers, 2016). From the titles of the publications, it is revealed that the most cited publications are directed towards using pedagogical strategies of BBL as well as applying different technological methods to enhance students’ knowledge acquisition and skills attainment in several disciplines. While one publication by Taylor (2009) focused on designing the learning environment to develop learning senses and perceptions of students, where the built environment becomes a teaching tool.\n\nFigure 6 demonstrates the country collaboration patterns in producing research on BBL during 2001-2021. Surprisingly, all the listed 13 countries contributed to single partnerships each, i.e., Australia with Norway, Austria with Belgium, Indonesia with China, Indonesia with Malaysia, Indonesia with Pakistan, Malaysia with Nigeria, Malaysia with the UK, the UK with Canada, the USA with Brazil, the USA with Korea, the USA with Mexico and the USA with Thailand. The figure also shows that the United States collaborated the most with other countries (four collaborations). These results indicate that there is no particular direction or pattern of collaborative and joint research across countries.\n\nAs visualized in Figure 7, between 2001 and 2021, the top ten funding agencies that supported the highest number of researches in BBL were Khon Kaen University in Thailand and National Science in the United States with four funded publications each, followed by the Indonesian Riset Teknologi Dan Pendidikan Tinggi Republik Indonesia and the National Research Council of Thailand, each funding two publications. The American Psychological Association Foundation, the Federal Aviation Administration, the Hand in Hand Institute, the Health Resources and Services Administration, the Horizon 2020 framework program, and Isfahan University of Medical Sciences each agency financed only one publication. These results give insight into the active funding bodies interested in supporting BBL-related research, so researchers willing to develop outcomes and practical results can approach them. Another inference is made; the low number of funding agencies contributing to BBL research explains the low numbers of publications in this field which require developing instructional technology, apparatus, and setting up experiments and quasy-experiments, moreover, need high numbers of participants/learners to produce publishable and applicable outcomes.\n\n\nConclusion\n\nThis research identified the relevance of brain-based learning in the field of design and arts education as it carefully considers how the brain learns, especially in creativity-based subjects.\n\nHowever, the initial literature review indicated the absence of publications relating BBL pedagogical methodologies to design and visual arts education despite the associated relevance regarding these vital topics. The authors saw it as an opportunity to conduct an evidence-based bibliometric analysis for critical review and assessment of Scopus indexed published literature on brain-based learning during the past twenty years. The results demonstrated the growth trends in research, identified the productive authors, institutions, sources, authorship patterns, and visualized subject variation and keyword mapping, etc. The discussion of the analysed results revealed that there was a slow literature growth in the first ten years of the millennia; however, the topic received attention in the latter ten years. There was an interruption in the publication growth during 2013 and 2014 but was followed by rapid development until 2020. It was also evident that collaborative authorship was preferred over single authorship, while double authorship received more citations.\n\nComparison of authors’ keywords with all keywords indicated that the subject approach of author keywords is direct, more precise, and relatable to the topic. However, the keywords that appeared the most in the studied publications mainly focused on learning and education in general, instructional design and collaborative learning, neuroscience, and creativity. No keywords related to ‘design’ and ‘arts’ as a topic were found. This indicates that there is a large gap in the current body of literature that relates BBL to creativity-based disciplines such as design and visual arts despite the apparent relevance between them. In addition, the thematic evolution analysis carried out in this research substantiates that there is clear regression in the development of BBL research relating to the topics of design, visual arts, creativity and design education.\n\nTherefore, to contribute to the development of BBL research in design and arts education, several stakeholders may play active roles in recognizing and incorporating BBL techniques in design education. Decision-makers and funding agencies should implement policies and direct their support to apply strategies that empower the role of BBL in academia and research. Academics, researchers, and educationalists in design and visual arts institutes are advised to direct their attention to BBL pedagogical activities and funded action research to benefit from neurosciences research on how the brain learns. This will increase students’ conscious learning, expand their imagination, and improve creativity and support multiple intelligences that develop their learning experience. This will also contribute to increasing the number of studies aiming at improving BBL methods to keep pace with the global challenges in education that we are currently facing.\n\n\nData availability\n\nZenodo: Brain-based learning, https://doi.org/10.5281/zenodo.6298928 (El-Wakeel et al., 2022a).\n\nThis project contains the following underlying data:\n\n• Data for brainbased Bibliometrix.xlsx\n\nZenodo: Brain-based learning in design and visual arts education, https://doi.org/10.5281/zenodo.6386705 (El-Wakeel et al., 2022b).\n\nThis project contains the following extended data:\n\n• PRISMA flow diagram.pdf\n\n• PRISMA Checklist.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nAnsari KMN, Khan NBN, Omar NFBM, et al.: Assessment of literature growth in Anthropometric measurement research: A bibliometric analyses of Scopus indexed publications. Libr. Philos. Pract. 2021; 1–27. Reference Source\n\nBeischel KP: Variables affecting learning in a simulation experience: a mixed methods study. West. J. Nurs. Res. 2013; 35(2): 226–247. Publisher Full Text\n\nBowers JS: The practical and principled problems with educational neuroscience. Psychol. Rev. 2016; 123(5): 600–612. PubMed Abstract \| Publisher Full Text\n\nCaine RN, Caine G: Reinventing schools through brain-based learning. Educ. Leadersh. 1995; 52: 43–47.\n\nCramer SC, Sur M, Dobkin BH, et al.: Harnessing neuroplasticity for clinical applications. Brain. 2011; 134(6): 1591–1609. PubMed Abstract \| Publisher Full Text\n\nDuman B: The Effects of Brain-Based Learning on the Academic Achievement of Students with Different Learning Styles. Educ. Sci.: Theory Pract. 2010; 10(4): 2077–2103.\n\nEdwards B: The New- Drawing on the Right Side of the Brain- Guided Practice in the Five Basic Skills of Drawing. Tarcher; 2002.\n\nEl-Wakeel H: Creating Minds, an Analytical Study of Using Brain Based Learning in Visual Arts and Design Education. Scientific Journal of Faculty of Fine Arts-Alexandria University. 2008; 1: 131–148.\n\nEl-Wakeel H: Design Studio: Creativity, Neuroscience, and Brain-Based Learning. The International Journal of Design Education. 2020; 15(1): 43–55. Publisher Full Text\n\nEl-Wakeel HA, Abdellatif RA, Eldardiry DH, et al.: Brain-based learning.2022a. Publisher Full Text\n\nEl-Wakeel HA, Abdellatif RA, Eldardiry DH, et al.: Brain-based learning in design and visual arts education.2022b. Publisher Full Text\n\nGardner H: Art Education and Human Development (Occasional Papers, Series 3). Getty Trust Publications: Getty Education Institute for the Arts; 1991.\n\nGosin MN, Dustman PA, Drapeau AE, et al.: Participatory Action Research: creating an effective prevention curriculum for adolescents in the Southwestern US. Health Educ. Res. 2003; 18(3): 363–379. PubMed Abstract \| Publisher Full Text\n\nHardiman M, Rinne L, Gregory E, et al.: Neuroethics, Neuroeducation, and Classroom Teaching: Where the Brain Sciences Meet Pedagogy. Neuroethics. 2012; 5(2): 135–143. Publisher Full Text\n\nLin T-C, Hsu Y-S, Lin S-S, et al.: A review of empirical evidence on scaffolding for science education. Int. J. Sci. Math. Educ. 2012; 10(2): 437–455. Publisher Full Text\n\nMassimo A, Cuccurullo C: bibliometrix 3.0. 2019. Reference SourceReference Source\n\nMiller DJ, Robertson DP: Using a games console in the primary classroom: Effects of ‘Brain Training’ programme on computation and self-esteem. Br. J. Educ. Technol. 2010; 41(2): 242–255. Publisher Full Text\n\nPersky AM, Pollack GM: A modified team-based learning physiology course. Am. J. Pharm. Educ. 2011; 75(10): 204. PubMed Abstract \| Publisher Full Text\n\nPersson O, Danell R, Schneider J: How to use Bibexcel for various types of bibliometric analysis. In Celebrating scholarly communication studies: A Festschrift for Olle Persson at his 60th Birthday. International Society for Scientometrics and Informetrics; 2009; (pp. p9–24).\n\nRahaman MS, Ansari KMN, Kumar H, et al. ( Mapping and Visualizing Research Output on Global Solid Waste Management: A Bibliometric Review of Literature. Sci. Technol. Libr. 2021a; 00(00): 1–29. Publisher Full Text\n\nRahaman MS, Kumar S, Ansari KMN, et al.: Twenty-five years of global research publications trends of novel coronavirus: A scientometrics assessment. Libr. Philos. Pract. 2021b; 1–17. Reference Source\n\nRahaman MS, Kumar S, Shah K: A scientometric assessment of global research productivity in traditional knowledge: Evidence from scopus database. Kelpro Bulletin. 2021c; 25(June): 15–29.\n\nSerin O: The effects of the computer-based instruction on the achievement and problem solving skills of the science and technology students. Turkish Online J. Educ. Technol. 2011; 10(1): 183–201.\n\nShukla A: 2019. Brain-Based Learning: Theory, Strategies, And Concepts. Reference Source\n\nSpears A, Wilson L: Brain-Based Learning Highlights. The CELT Center; 2021. Reference Source\n\nTaylor A: Linking Architecture and Education: Sustainable Design for Learning Environments. Linking Architecture and Education: Sustainable Design for Learning Environments. University of Cincinnati; 2009. Publisher Full Text\n\nvan Eck NJ , Waltman L: Software survey: VOSviewer, a computer program for bibliometric mapping. Scientometrics. 2010; 84(2): 523–538. PubMed Abstract \| Publisher Full Text\n\nWilson LO: Brain-based Education – An Overview. The Second Principle; 2013. Reference Source\n\nYelamarthi K, Drake E: A Flipped First-Year Digital Circuits Course for Engineering and Technology Students. IEEE Trans. Educ. 2015; 58(3): 179–186. Publisher Full Text" }	[ { "id": "130165", "date": "19 Apr 2022", "name": "Aidi Ahmi", "expertise": [ "Reviewer Expertise Bibliometric analysis." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nBrain-based learning seems a good topic to be explored using bibliometric analysis. However, I have major concerns about the method of this study that will reflect the whole paper as below:\nThe following search:\nTITLE-ABS-KEY (“Design”) OR TITLE-ABS-KEY (“Creativity”) AND (“brain-based learning”)\nwill only reveal all documents that have keywords design and creativity in TITLE-ABS-KEY and “brain-based learning” anywhere in the text. So, the results only show all documents that met these criteria and NOT the articles related to the topic of “brain-based learning”.\nThe screening process seems to have not been conducted. Although Figure 1 shows the screening process, it is actually a filtering process and NOT a screening process. The authors should look one by one at the title of the document to make sure all the documents being analysed are really about “brain-based learning”. Based on the dataset, it seems many documents are NOT about the topic of the study \"Brain-based learning in design and visual arts education\". In other words, the documents being analysed are totally NOT about \"Brain-based learning in design and visual arts education\".\nThe authors have to make sure that all the documents being analysed are really about the topic or at least related to the topic of the study. The screening and cleaning process should be conducted for each of the documents before the data is downloaded from the Scopus database. Any irrelevant documents should be removed in order to make sure that all documents are really about the topic of the study and not about something else.\nDue to this, I can say that all the analyses conducted are considered invalid.\nThe authors should re-design the search query to only gathered the documents related to \"brain-based learning\".\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? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? No", "responses": [ { "c_id": "8217", "date": "13 May 2022", "name": "Hala Abdulmoneem Mahmoud El-Wakeel", "role": "Author Response", "response": "The authors appreciate the reviewer for reviewing the study and valuable suggestions. The authors have no issues re-designing the search query to gather the data; however, they disagree that all the analyses conducted are considered invalid since the authors ensured a closer look at each document and ensured that all the documents are related to BBL." }, { "c_id": "8309", "date": "31 May 2022", "name": "Hala Abdulmoneem Mahmoud El-Wakeel", "role": "Author Response", "response": "The research observed that there is a decline in the development of BBL research which is related to the topics of design, visual arts, creativity, and design education, despite the fact that BBL methods are strongly beneficial to those fields and provide significant advantages to students learning awareness and performance especially for enhancing creative design skills (as identified in the literature review). The research aimed to identify the gaps in the current literature that relates brain-based learning to creative subjects such as design and visual arts, in order to identify the nature of such research and its topics, a refined search strategy is conducted and shown on page 4: The topics ‘design’ and ‘creativity’ were used in the initial search and then refined by the term ‘brain-based learning,’ this allowed the retrieval of records used in this study; the following search strategy was applied: (TITLE-ABS-KEY (“Design”) OR TITLE-ABS-KEY (“Creativity”) AND (“brain-based learning”) The research then conducts thematic analysis and identifies the topics of each research and finds that very few research apply BBL in design education specifically, and finally recommends educators and researchers to direct their attention to BBL pedagogical activities and funded action research to benefit from neurosciences research on how the brain learns. This will increase researcher in the field of design and visual arts education that utilizes BBL methods to enhance students' learning and to keep pace with the global challenges in education. The following parts of the research describe this: The abstract (p.1): Despite the significance to apply brain-based learning strategies in design and visual arts education to boost students’ knowledge and creative skills, the findings show a decline in quantities and growth patterns in brain-based learning research directed towards design disciplines in the past twenty years. These rather small numbers reflect the big gap in the current body of literature that associates brain-based learning with creativity-based disciplines, specifically in design and visual arts education. This infers the necessity to direct the attention of academics, researchers, and educationalists in the fields of design and arts towards brain-based learning applications, research, and pedagogy. Brain-based learning for creative disciplines (p.3) BBL can help design and visual art students understand how their brains work, think, and perceive; it can also facilitate the development of creative skills with reduced frustration (El-Wakeel, 2020). Therefore, BBL provides a biologically based framework for teaching and learning in the context of design and visual arts that explains to students the concepts behind learning; essentially learning how to learn. This meta-concept encompasses a diverse range of strategies that reduce the amount of stress in the classrooms and achieve educational goals easier and faster. Yet, educationalists, especially in the field of design and visual arts, have not fully utilized results from neuroscience studies into BBL methodologies. …… Despite the relevance of BBL to design and arts education as creativity-inspired disciplines, there is a scarcity of published research that has made the proper connection between them. A very few studies were found that incorporated BBL principles into learning in the field of ‘Arts’ in general but not particularly in design and visual arts. P.4 The necessity for more specialized studies and application of BBL in design and visual arts motived the authors to perform a bibliometric analysis to identify the gaps, trends, subject development, and growth in the published body of literature on BBL in design, visual arts, and creativity-based subjects. Identifying such gaps will help direct more focused and applicable future research. Research aim and objectives (p.4) Aiming to identify the gaps in the current literature that relates brain-based learning to creative subjects such as design and visual arts. Methods Data selection and method (p.4) The topics ‘design’ and ‘creativity’ were used in the initial search and then refined by the term ‘brain-based learning,’ this allowed the retrieval of records used in this study, the following search strategy was applied: (TITLE-ABS-KEY (“Design”) OR TITLE-ABS-KEY (“Creativity”) AND (“brain-based learning”) Productive sources (p.9) while there were only 3 sources that were directly related to design and visual arts studies and/or education, and they were not detected in the top ten results. This shows that there is a very slim opportunity for researchers to publish on platforms dedicated to this field which explains the extended literature gap in this area. Productive authors (p. 9) On the other hand, the low impact of authors specialized in design and visual arts education raises the question of why researchers, academics, and educationalists in design disciplines are not directed towards liking BBL to design education despite the significance of this topic and its high relevance to enhancing design students’ knowledge acquisition and creativity. Analysis of author keywords P.12: Searching for keywords such as Design and Visual arts may not yield many results; however, the keyword Neuroscience was found in the same cluster as Design and Visual Arts. The occurrences were very low, but there is a direct association between these fields researchers must relate to. Creativity and Creative thinking are keywords that find somewhat relevant literature related to design disciplines. Thematic evaluation by topic P.13: More interestingly, this unigram shows that several topics such as ‘thinking’, ‘designing’, ‘model’, ‘effect’ and ‘skills’ are not showing any relationship with the topic ‘design’, contrary to what may be assumed. The visualization also reveals that in 2017-2020, a few new topics have emerged such as ‘thinking’, and ‘skills’ which are strongly related to ‘mathematics’ and ‘education’. It is also worth mentioning that the topic ‘visual arts’ is missing from the unigram, meaning its frequency was not detected. The thematic evolution analysis substantiates that there is a decline in the development of BBL research relating to the topics of design, visual arts, creativity, and design education. Conclusion P.18: This research identified the relevance of brain-based learning in the field of design and arts education as it carefully considers how the brain learns, especially in creativity-based subjects. However, the initial literature review indicated the absence of publications relating BBL pedagogical methodologies to design and visual arts education despite the associated relevance regarding these vital topics. …. A comparison of authors’ keywords with all keywords indicated that the subject approach of author keywords is direct, more precise, and relatable to the topic. However, the keywords that appeared the most in the studied publications mainly focused on learning and education in general, instructional design and collaborative learning, neuroscience, and creativity. No keywords related to ‘design’ and ‘arts’ as a topic were found. This indicates that there is a large gap in the current body of literature that relates BBL to creativity-based disciplines such as design and visual arts despite the apparent relevance between them. In addition, the thematic evolution analysis carried out in this research substantiates that there is clear regression in the development of BBL research relating to the topics of design, visual arts, creativity, and design education. … Academics, researchers, and educationalists in design and visual arts institutes are advised to direct their attention to BBL pedagogical activities and funded action research to benefit from neurosciences research on how the brain learns. This will increase students’ conscious learning, expand their imagination, improve creativity and support multiple intelligences that develop their learning experience. This will also contribute to increasing the number of studies aiming at improving BBL methods to keep pace with the global challenges in education that we are currently facing." } ] }, { "id": "153359", "date": "02 Nov 2022", "name": "Nadeem Siddique", "expertise": [ "Reviewer Expertise Bibliometrics", "Scientometrics", "systematic review", "library automation" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper presents a bibliometric study conducted on 186 documents. The researchers did not explain the motivation behind this study. How would the study be helpful for the relevant audience, and what is the study’s significance? The methodology has some flaws. I could not retrieve the same number of records by using the query mentioned in the methodology section. I have retrieved only 51 documents by using the query in different ways in the Scopus database. The researcher did not provide details about the irrelevant and duplicate documents. The researchers should compare the previous research with their findings.\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? Partly", "responses": [ { "c_id": "9040", "date": "01 Dec 2022", "name": "Hala Abdulmoneem Mahmoud El-Wakeel", "role": "Author Response", "response": "The researchers did not explain the motivation behind this study. It is mentioned at the end of the introduction and conclusion. How would the study be helpful for the relevant audience, and what is the study’s significance? It is mentioned in the introduction and conclusion. The methodology has some flaws. I could not retrieve the same number of records by using the query mentioned in the methodology section. I have retrieved only 51 documents by using the query in different ways in the Scopus database. The error shows if the query copy and paste into the search as some unnecessary brackets appear, instead type the query in advance search which now showing 238 results as on 21/11/2022. The researcher did not provide details about the irrelevant and duplicate documents. It is mentioned below the search query. The researchers should compare the previous research with their findings. Unfortunately, there are no previous scientometric studies found on this topic, hence, it motivated researchers to conduct one." } ] } ]	1	https://f1000research.com/articles/11-402
https://f1000research.com/articles/12-767/v1	30 Jun 23	{ "type": "Research Article", "title": "Association between high mobility group box-1 circulation level and Graves' ophthalmopathy", "authors": [ "Mohammad Robikhul Ikhsan", "Nyoman Kertia", "Supanji Supanji", "Bambang Udji djoko Rianto", "Dhite Bayu Nugroho", "Mohammad Robikhul Ikhsan", "Nyoman Kertia", "Supanji Supanji", "Bambang Udji djoko Rianto" ], "abstract": "Background: Graves' disease is a prevalent autoimmune disorder that causes hyperthyroidism. Despite being widely recognized, the risk factors for its associated condition, ophthalmopathy, are not well understood. High Mobility Group Box 1 (HMGB1), a damage-associated molecular pattern biomarker, has been linked to autoimmune diseases and may play a role in Graves' ophthalmopathy. The aim of this study is to assess the correlation between the levels of circulating HMGB1 and the occurrence of Graves' ophthalmopathy (GO). Methods: This cross-sectional study evaluated 44 recently diagnosed Graves' disease patients at Sardjito Hospital. The presence of Graves' ophthalmopathy (GO) was determined using criteria set by Bartley and Gormans. The levels of HMGB1 were measured in the blood of both groups (22 GO patients and 22 controls without GO) using ELISA. Statistical analysis, including binomial logistic regression and Mann-Whitney test, was conducted to analyze the data and adjust for confounding factors with multinomial logistic regression. Results: The baseline characteristics of 22 GO patients and 22 non-GO patients were similar, including age (30.91±6.06 vs. 30.68±6.63 years, p>0.05), gender distribution (77.3% vs. 81.8% female, 22.7% vs. 18.2% male, p>0.05), and duration of diagnosis (5.13±2.21 vs. 4.82±1.89 months, p>0.05). However, a significant difference (p<0.001) was found in the levels of circulating HMGB1, with GO patients having a median value of 15.49 pg/mL (5.12-47.59 pg/mL) compared to 2.33 pg/mL (0.82-15.66 pg/mL) in the control group. The risk of developing ophthalmopathy increased 12 times when Graves disease patients had HMGB1 levels above 8.86 pg/mL. Conclusion: The study found a significant association between elevated levels of HMGB1 (> 8.86 pg/mL) and an increased risk (12 times) of Graves’ ophthalmopathy in newly diagnosed Graves' disease patients. The results suggest that HMGB1 may be a potential biomarker for predicting the development of ophthalmopathy in Graves' disease patients.", "keywords": [ "Graves' disease", "ophthalmopathy", "High Mobility Group Box-1" ], "content": "Introduction\n\nGraves' disease is the most common form of hyperthyroidism, occurring in 1% to 1.5% of the general population.1 The underlying causes and mechanisms of Graves' disease remain elusive.2 Autoimmune thyroid disorders like Graves' disease involve complex immune processes.3 In Graves' disease, the autoimmune response affects the orbital fibroblast tissue and triggers inflammation, leading to orbital fibroblast remodeling.4 Graves' ophthalmopathy is a hallmark of Graves' disease and an additional thyroid manifestation that is of great importance.5\n\nGraves' ophthalmopathy occurs in 23% of cases before diagnosis, 39% after diagnosis, and 37% concurrent with diagnosis.6 The exact pathophysiology of Graves' ophthalmopathy is not well understood, with numerous factors influencing its progression and contributing elements.7 The involvement of damage-associated molecular patterns (DAMPs), endogenous compounds released during cellular stress and injury, as well as non-apoptotic cell death, may contribute to the inflammation in Graves' ophthalmopathy.8\n\nThe connection between DAMPs and autoimmune diseases, such as rheumatoid arthritis, systemic lupus erythematosus, psoriatic arthritis, and others, has been established.8 However, the role of DAMPs in the pathogenesis of autoimmune thyroid disease and Graves' ophthalmopathy is not well understood. The immunological pathways involved in the progression of Graves' disease and the onset of Graves' ophthalmopathy, as well as the high incidence of Graves' ophthalmopathy in patients who experience remission, suggest that DAMPs may play a crucial role in the development of severe Graves' ophthalmopathy.9\n\nStudies in individuals with autoimmune thyroid disease showed elevated levels of HMGB1, which correlated with thyroid antibody levels in the body.10 Lacheta et al. investigated the impact of DAMPs on inflammation in Graves' ophthalmopathy by conducting an orbital tissue biopsy to assess HMGB1 expression in orbital fatty tissue. They found an increase in HMGB1 expression that corresponded to the severity of Graves' ophthalmopathy.11\n\nThis study aims to compare circulating levels of HMGB1 in two groups of Graves' disease patients: those with ophthalmopathy and those without. The goal is to examine the relationship between HMGB1 levels and the presence of Graves' ophthalmopathy.\n\n\nMethods\n\nThis cross-sectional study compared two groups to assess the difference in blood circulation levels and the effect of HMGB1 in Graves' ophthalmopathy. Graves' Disease patients with ophthalmopathy comprised the case group, while Graves' Disease patients without ophthalmopathy comprised the control group.\n\nParticipants were identified through medical records and assessed for eligibility. Eligible participants were scheduled for a screening visit where they provided informed consent and underwent a medical history, physical examination, and Thyrotropin Receptor Antibody (TRAb) level measurement. To be eligible, participants had to have been diagnosed with Graves' disease within the past six months, be between the ages of 18 and 60, and have a Thyrotropin Receptor Antibody (TRAb) level greater than 1.75 IU/L. These criteria suggest that the study was focused on individuals who were in the early stages of Graves' disease and had elevated levels of TRAb, which is a biomarker associated with the disease. Those who met eligibility criteria were enrolled and underwent baseline assessments including laboratory tests and questionnaires. Exclusion criteria included chronic comorbidities such as diabetes, heart failure, stroke, kidney failure, cancer, thyroid ablation/surgery, other eye conditions, and active autoimmune diseases to ensure participant safety and study validity.\n\nIn 1995, the Bartley and Gorman criteria were developed to diagnose ophthalmopathy. The criteria are composed of three main components: eyelid retraction, thyroid dysfunction, and specific eye-related symptoms. Eyelid retraction is characterized by the abnormal elevation of the upper eyelid. The second criterion, thyroid dysfunction, refers to the improper functioning of the thyroid gland, which can cause a variety of symptoms, such as weight gain or loss, fatigue, and temperature sensitivity. The third criterion involves the presence of eye-related symptoms, such as optic nerve dysfunction, exophthalmos, or extra-ocular muscle involvement. Optic nerve dysfunction can cause visual disturbances, while exophthalmos is a condition in which the eyes protrude from the sockets, resulting in a “bulging” appearance. Lastly, extra-ocular muscle involvement can lead to double vision or difficulty focusing due to weakened or dysfunctional eye muscles.12\n\nCirculating HMGB1 levels were measured using Enzyme-Linked Immunosorbent Assay (ELISA) method. A plasma blood sample was collected from the patients and analyzed using the HMGB1 express ELISA Kit from TECAN IBL International in Hamburg, Germany.\n\nThis study took place from September 2021 to February 2022 at RSUP Dr. Sardjito, in the Internal Medicine Clinic of Endocrinology Division, the Eye Clinic of the Oculoplasty Reconstruction Division, and the Oncology.\n\nThis study was previously approved by the subjects with written informed consent. The ethical committee of the Faculty of Medicine, Public Health, and Nursing at Universitas Gadjah Mada in Yogyakarta, Indonesia reviewed and approved this study under protocol number KE/FK/0980/EC/2021. The research adheres to the 2013 version of the Declaration of Helsinki, which outlines ethical principles for medical research involving human subjects.\n\nThe statistical methods used in this study include univariate and multivariate linear regression analyses to determine the standardized beta coefficients of independent variables and their association with Graves' disease ophthalmopathy status, as well as independent sample t-tests, Mann-Whitney tests, and Fisher's exact tests to compare characteristics between subjects with and without ophthalmopathy.\n\nThe statistical analysis for this study was conducted using R Studio, with support from the tidyverse and gtsummary packages. The tidyverse package was utilized for data manipulation and cleaning, while gtsummary was used to generate easily readable summary statistics and tables. It is possible that additional R packages were used for further data analysis.\n\n\nResults\n\nThe study included 22 patients with Graves' disease and ophthalmopathy and 22 patients with Graves' disease without ophthalmopathy who met the inclusion criteria.19 The clinical characteristics of the Graves' disease patients without ophthalmopathy are outlined in Table 1.\n\n1 n/N (%); Mean (SD); Median [Q1-Q3]\n\n2 Independent Sample t-test; Mann-Whitney-test; Fisher's exact test\n\nBasic characteristics, including demographics, comorbidities, family history, and disease duration, were not significantly different between Graves' disease patients with and without ophthalmopathy.\n\nHMGB1 levels were significantly higher in Graves' patients with ophthalmopathy compared to those without, with a median value of 15.49 pg/mL in the ophthalmopathy group and 2.33 pg/mL in the non-ophthalmopathy group (p0.001). The lowest and highest values were 5.12 pg/mL to 47.59 pg/mL in the ophthalmopathy group and 0.82 pg/mL to 15.66 pg/mL in the non-ophthalmopathy group.\n\nAccording to the findings of this study, the levels of HMGB1 in the blood circulation were found to be significantly different between Graves' disease patients with ophthalmopathy and those without ophthalmopathy (Figure 1).\n\nBefore the regression analysis was performed, it was important to identify an appropriate cut-off value for the independent variable (HMGB1 level) which would be evaluated. This value was determined through analysis of the Receiver Operating Characteristic (ROC) curve, which aimed to find a cut-off value that had a high degree of both sensitivity and specificity. The results of the ROC analysis revealed a cut-off value of 8.86 pg/mL, with a sensitivity of 81% and a specificity of 73%.\n\nBinary logistic regression analysis was then conducted to determine the impact of HMGB1 levels in circulation on the incidence of Graves' ophthalmopathy. The results of this analysis, showed that patients with Graves' disease and HMGB1 levels greater than 8.86 pg/mL had a 12 times higher risk of developing ophthalmopathy compared to those with HMGB1 levels less than 8.86 pg/mL (Table 2).\n\n1 OR = Odds Ratio, CI = Confidence Interval.\n\nA stepwise analysis was conducted to determine which variables had the greatest role as predictors of the onset of Grave's disease ophthalmopathy. The results showed that high levels of TRab and HMGB1 were the variables with the greatest impact on the status of ophthalmopathy in Grave's patients. Multivariate analysis showed that even when controlling for TRab, there was still a significant statistical relationship between Grave’s ophthalmopathy and HMGB1. Table 2 showed that a high level of Hmgbox1 can increase the risk of developing Grave's ophthalmopathy by 7.06 times with a p-value of 0.012 (95% CI 1.61-36.1)\n\n\nDiscussion\n\nIn the study, a significant difference was observed in the levels of HMGB1 between patients with Graves' disease and ophthalmopathy and those with Graves' disease without ophthalmopathy. The median levels of HMGB1 in the group with ophthalmopathy were considerably higher compared to the group without ophthalmopathy, with a median value of 15.49 pg/mL and 2.33 pg/mL, respectively. The results of the ROC curve analysis suggested that a cut-off value of 8.86 pg/mL for HMGB1 levels had a high degree of sensitivity and specificity in predicting the presence of ophthalmopathy in patients with Graves' disease. Binary logistic regression analysis revealed that patients with Graves' disease who had elevated levels of HMGB1 (above 8.86 pg/mL) had a risk of developing ophthalmopathy that was 12 times higher compared to patients with lower levels of HMGB1. These findings align with the previous study conducted by Han et al. that concluded that patients with symptomatic Graves had higher levels of HMGB1 compared to those with stable Graves or healthy individuals.13\n\nThe study results showed a significant difference in the levels of HMGB1 in the circulation of Graves' disease patients with and without ophthalmopathy. HMGB1, a known effector molecule involved in inflammation, is believed to play a role in the development of Graves' disease and its associated complications, including ophthalmopathy. Its high levels have been linked with other autoimmune diseases such as rheumatoid arthritis and systemic lupus erythematosus, where increased HMGB1 levels and increased numbers of HMGB1-producing cells are found in inflammatory areas. Through its interaction with RAGE and TLR receptors, HMGB1 contributes to the pathogenic inflammatory processes. The study findings suggest that HMGB1 may be a useful biomarker to reflect the level of inflammation in Graves' disease patients, especially those with active disease, as increased HMGB1 secretion was found in response to high levels of pro-inflammatory cytokines such as IL-1 or TNF.13\n\nThe presence of elevated levels of HMGB1 in patients with Graves' disease and ophthalmopathy suggests a potential role of HMGB1 in the development of ophthalmopathy. HMGB1 is known as a Damage-Associated Molecular Pattern (DAMP) molecule and is released by damaged or necrotic cells, or cells that die without undergoing apoptosis. This provides a theoretical explanation for the high levels of HMGB1 found in patients with Graves' disease and ophthalmopathy.14\n\nDamage-associated molecular patterns (DAMPs) play a dual role in the body as both intracellular regulators and extracellular signals of cell damage. They are typically not recognized by the immune system as long as they remain inside the cell, but are detected when they are released into the extracellular environment and trigger an immune response.14\n\nThe role of damage-associated molecular patterns (DAMPs) in the initiation of inflammation is essential for the survival of an organism. When cells are damaged or dying, DAMPs are released, acting as alarm signals to surrounding cells and activating the immune system. This process is known as the “danger signal hypothesis”.15 The immune system's response to DAMPs includes the activation of both the innate and adaptive immunity, where innate immunity acts as the first line of defense and adaptive immunity provides a more specific and prolonged response. DAMPs activate immune cells, such as macrophages and neutrophils, which phagocytose cellular debris and release cytokines and chemokines, leading to an increase in blood flow and immune cell recruitment to the site of injury. This process helps to remove damaged tissue and promote tissue repair and healing.13 Additionally, the presence of DAMPs can also aid in the formation of immunological memory, helping the immune system to respond more effectively in the future to similar threats.15 Overall, DAMPs play a crucial role in the body's defense mechanisms against cell damage and contribute to the regulation of tissue repair and healing.\n\nThe findings of Han et al. showed a strong correlation between the high expression of HMGB1 and its receptors with the inflammatory processes in Graves' disease with ophthalmopathy. Their research also indicated that the high expression of receptors in orbital fibroblast tissues can lead to excessive inflammation, which contributes to the growth and development of ophthalmopathy symptoms such as angiogenesis and changes in the connective and adipose tissue. Based on these findings, it is proposed that the HMGB1 signalling pathway can be targeted and inhibited through its receptors as a potential treatment option for reducing the symptoms of ophthalmopathy in patients with Graves' disease.13\n\nThe study by Peng et al. demonstrated that the levels of HMGB1 and RAGE were elevated in monocytes collected from patients with autoimmune thyroid disease, including Graves' disease, compared to monocytes obtained from healthy individuals. This indicates a crucial role of RAGE and HMGB1 in the development and progression of Graves' disease.16\n\nThe results of this study indicated that patients with Graves' disease who had circulating HMGB1 levels greater than 8.86 pg/mL had a 12 times higher risk of developing ophthalmopathy compared to those with levels less than 8.86 pg/mL. This highlights the significant role of HMGB1 in the development of ophthalmopathy in Graves' disease patients.\n\nHigh levels of HMGB1 in the bloodstream can indicate a heightened level of DAMPs production, which acts as a marker for cell damage caused by overactive inflammation. The exact mechanism behind HMGB1 secretion is not fully understood. One possible explanation involves an inflammatory environment that triggers an increase in HMGB1 acetylation within cells, leading to its cytoplasmic translocation and release in response to a second stimulus. Research by Lu et al. suggests that inflammasomes, particularly NLRP3, play a role in the release of HMGB1 from cells.17\n\nHMGB1 functions as a DAMP molecule and signals damage to cells in the surrounding environment. It triggers inflammation and activates both innate and adaptive immunity through its interaction with various receptors. RAGE (receptor for advanced glycation end products) is one of the first identified receptors for HMGB1 and is a multifunctional protein of the immunoglobulin superfamily. In normal conditions, RAGE expression is limited in most tissues, but it increases significantly in pathological situations like inflammation.18\n\nFibroblasts located in the connective tissue of the orbital are called orbital fibroblasts and have been identified as target cells on Graves’ ophthalmopathy. Orbital fibroblasts play an important role in lymphocyte infiltration and differentiation of B cells. IL-1β also regulates the expression of cyclooxygenase-2 by increasing its gene promoter activity and mRNA stability in fibroblast and encourages the synthesis of prostaglandin-E2 in orbital fibroblasts. CD40L cells promote the synthesis and secretion of hyaluronic acid, IL-6, IL-8, and CCL2 in fibroblast. IL-6 can facilitate immunoglobulin synthesis, plasma cell development, IL-4 production and differentiation of subsets of T cells into Th2 cells. CCL2 and IL-8 are powerful monocyte chemotactic factors that increase the infiltration of monocytes into orbital connective tissue in Graves’ disease with ophthalmopathy patients.19\n\nOrbital fibroblasts, fibroblasts found in the connective tissue of the orbit, play a crucial role in the development of Graves' ophthalmopathy. These cells are involved in B cell differentiation, lymphocyte infiltration, and cytokine production. They are known to be responsive to signals from cytokines, such as IL-1, CD40L, and IL-6 (17). IL-1, an inflammatory cytokine, affects the expression of the enzyme cyclooxygenase-2 (COX-2) in fibroblasts, which boosts its gene promoter activity and mRNA stability. It also stimulates the synthesis of prostaglandin-E2 in orbital fibroblasts. CD40L, another cytokine, stimulates fibroblasts to produce and secrete hyaluronic acid, IL-6, IL-8, and CCL2. IL-6, in particular, has the ability to promote immunoglobulin synthesis, plasma cell development, IL-4 production, and Th2 cell differentiation from certain subsets of T cells. Meanwhile, CCL2 and IL-8 are powerful monocyte chemotactic agents that increase monocyte infiltration into the orbital connective tissue of Graves' disease patients with ophthalmopathy.19\n\nThese findings highlight the significance of orbital fibroblasts in the pathogenesis of Graves' ophthalmopathy and emphasize the importance of targeting these cells to control the progression of the disease.\n\nWhile the study's strict inclusion and exclusion criteria and standardized diagnostic criteria enhance the internal and diagnostic validity, the study's limitations including a small sample size, cross-sectional design, single-point measurement of HMGB1 levels, lack of control for potential confounding variables, and single-center location may constrain the generalizability and causal interpretation of the findings.\n\n\nConclusion\n\nThe results of the study indicate a strong correlation between elevated levels of circulating HMGB1 and the occurrence of Graves' ophthalmopathy. The findings offer new perspectives on the management and treatment of ocular disease in Graves' patients by administering anti-HMGB1. By reducing HMGB1 levels, the study suggests that it may be possible to prevent the development of ocular disease and control its clinical activity in patients diagnosed early on. These results provide important implications for the clinical management of Graves' disease patients with ocular manifestations.", "appendix": "Data availability\n\nFigshare: hmgb1_robi.xlsx, https://doi.org/10.6084/m9.figshare.22126892. 19\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nWiersinga WM: Graves’ disease: Can it be cured? Endocrinol. Metab. 2019; 34: 29–38. Korean Endocrine Society. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTomer Y: Mechanisms of autoimmune thyroid diseases: From genetics to epigenetics. Annu. Rev. Pathol. Mech. Dis. 2014; 9(212): 147–156. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTomer Y: Genetic susceptibility to autoimmune thyroid disease: past, present, and future. Thyroid: official journal of the American Thyroid Association. 2010; 20: 715–725. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMaheshwari R, Weis E: Thyroid associated orbitopathy. Indian J. Ophthalmol. 2012 Mar; 60(2): 87–93. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRiordan P, Augsbuerger JJ: Vaughan and Asbury’s General Ophthalmology. Mc Graw Hill Education; 2018; vol. 369. .\n\nNabi T, Rafiq N: Factors associated with severity of orbitopathy in patients with Graves’ disease. Taiwan J. Ophthalmol. 2020; 10(3): 197–202. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHuang Y, Fang S, Zhang S, et al.: Progress in the pathogenesis of thyroid-associated ophthalmopathy and new drug development. Taiwan J. Ophthalmol. 2020; 10: 174. Publisher Full Text\n\nRoh JS, Sohn DH: Damage-associated molecular patterns in inflammatory diseases. Immune Network; 2018; vol. 18. .\n\nMusumeci D, Roviello GN, Montesarchio D: An overview on HMGB1 inhibitors as potential therapeutic agents in HMGB1-related pathologies. Pharmacol. Ther. 2014; 141: 347–357. PubMed Abstract \| Publisher Full Text\n\nPeng S, Li C, Wang X, et al.: Increased toll-like receptors activity and TLR ligands in patients with autoimmune thyroid diseases. Front. Immunol. 2016; 7(DEC). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nŁacheta D, Poślednik KB, Czerwaty K, et al.: RAGE and HMGB1 Expression in Orbital Tissue Microenvironment in Graves’ Ophthalmopathy. Mediat. Inflamm. 2021; 2021: 1–7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBartley GB, Gorman CA: Diagnostic criteria for Graves’ ophthalmopathy. Am J. Ophthalmol. 1995; 119(6): 792–795. Publisher Full Text\n\nHan SY, Choi SH, Shin JS, et al.: High-Mobility Group Box 1 Is Associated with the Inflammatory Pathogenesis of Graves’ Orbitopathy. Thyroid. 2019; 29(6): 868–878. PubMed Abstract \| Publisher Full Text\n\nLand WG: The role of damage-associated molecular patterns in human diseases: Part I - Promoting inflammation and immunity. Sultan Qaboos Univ. Med. J. 2015; 15(1): 9–21.\n\nVénéreau E, Ceriotti C, Bianchi ME: DAMPs from cell death to new life. Front. Immunol. 2015; 6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLu B, Wang H, Andersson U, et al.: Regulation of HMGB1 release by inflammasomes. Protein Cell. 2013; 4(3): 163–167. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKierdorf K, Fritz G: RAGE regulation and signaling in inflammation and beyond. J. Leukoc. Biol. 2013; 94(1): 55–68. PubMed Abstract \| Publisher Full Text\n\nHuang Y, Fang S, Li D, et al.: The involvement of T cell pathogenesis in thyroid-associated ophthalmopathy. Eye. 2019; 33(2): 176–182. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNugroho D: hmgb1_robi.xlsx. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "183544", "date": "18 Jul 2023", "name": "Gusty Rizky Teguh Ryanto", "expertise": [ "Reviewer Expertise Cardiology", "Respiratory Medicine", "Lung 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 manuscript “Association between high mobility group box-1 circulation level and Graves' ophthalmopathy” investigated the correlation between circulating HMGB-1 with ophthalmopathy associated with Graves’ disease with additional inclusion of basic parameters in their analysis. While the findings in this study are interesting, there are several points that need to be addressed.\nMajor points:\nThe authors might be better served to expand their analysis to include the clinical parameters of the patients in their analysis. For example, they have already mentioned in the discussion themselves, other factors could be involved in GO pathogenesis, such as inflammatory cytokines that could be produced by the immune cells. As such, it would be wise for the authors to also take this into consideration and include immune cells-related clinical parameters (e.g. WBC counts or leukocyte differential counts) in their model.\n\nOf course, inclusion of other basic clinical and laboratory findings would also strengthen their results.\n\nSaying in the conclusions (both abstract and in the main text) that their results may be able to “predict” GO or “reducing HMGB-1 can prevent” GO might be jumping the gun a little, as their current study design is not able to do much more than simple association. The authors might want to be a little careful in their choice of words.\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": "210666", "date": "13 Dec 2023", "name": "Rona Z Silkiss", "expertise": [ "Reviewer Expertise Oculofacial plastic surgery Thyroid eye 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\nVery interesting, well written article regarding the correlation between Graves ' ophthalmopathy and HMGB-1.\nIt would be useful to list the endocrine status of each patient in both the TED and control group. For the TED patients, what was their endocrine status at the time of testing? Were they taking antithyroid medication? Had they been treated with steroids? biologics? radiation therapy? Were the authors able to follow these patients over time and demonstrate consistent changes in the HMGB-1 levels. How did these changes correlate to CAS? thyroid levels< TSI (TRAb) levels?\nConclusions overreaching. in terms of predictive and treatment value. Authors might scale their conclusions back a bit.\nIn part of the paper a 7.06 x incidence risk v 12 x risk reported. Please clarify.\n\nPage 1 Paragraph 1 line 5 should read: Graves' disease and an additional extrathyroidal manifestation...\nPage 1 Paragraph 6 the study does not study the effect of HMGB1 - this should be deleted.\nPage 6 Paragraph 5 which contributes to the growth and development. The word growth should be removed.\nPage 7 Paragraph 6 should read: Fibroblasts located in the connective tissue of the orbit ....as target cells in .....\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? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-767
https://f1000research.com/articles/12-764/v1	30 Jun 23	{ "type": "Study Protocol", "title": "Assessing use of vancomycin powder in craniotomy: randomized controlled trial (AVIC)", "authors": [ "Sirajeddin Belkhair", "Muhammad Mohsin khan", "Younis Baregzai", "Khalida Walizada", "Ahmed Eid", "Ahmed Taha", "Saleh Safi", "Amr Mohammad", "Abdullah llleyyan", "Tarek Ben Zabih", "Ali Raza", "Adnan khan", "Firas Hammadi", "Raed Jarir", "Ali Ayyad", "Talal Alrabayah", "Sirajeddin Belkhair", "Younis Baregzai", "Khalida Walizada", "Ahmed Eid", "Ahmed Taha", "Saleh Safi", "Amr Mohammad", "Abdullah llleyyan", "Tarek Ben Zabih", "Ali Raza", "Adnan khan", "Firas Hammadi", "Raed Jarir", "Ali Ayyad", "Talal Alrabayah" ], "abstract": "Background: Surgical-site infections (SSIs) can lead to greater postoperative morbidity, mortality, and health care costs. Despite current prophylactic measures, rates of SSIs have been reported in up to 5% of patients post craniotomy. Intrawound vancomycin powder has been studied extensively in spinal fusion surgeries and been found to reduce rates of surgical site infections (SSIs) significantly. Despite its success in spinal surgeries, topical vancomycin has not been extensively studied with respect to cranial neurosurgery. Methods: Our study is Prospective Randomized clinical trial. Patients will be divided in this Trial into two groups, first group (intervention arm) they will receive the drug (vancomycin) in the wound before the closure of the skin at the end of the surgical procedure. The second group (control arm) they will not receive the drug, otherwise both groups they will receive identical measure to decrease the postoperative SSI. The primary outcome variable will be SSI rate factored by cohort. Secondary outcome will be to monitor the safety and any complication related to the use of vancomycin . SSI found to be around 0.49% when vancomycin was used, while SSI in standard care found to be 5%, to get power of study 80% and level of significance 5%. Sample size will be 250 in each group using sample size calculator. Discussion: This study is designed to evaluate the efficacy of vancomycin compared to standard method in neuro-surgical cases undergoing craniotomy . Additionally, safety of vancomycin will be assessed in these patients.", "keywords": [ "vancomycin", "craniotomy", "infection", "brain", "surgery" ], "content": "Trial registration\n\nClinicalTrials.gov Identifier: NCT04917627, registered on June 8, 2021\n\n\nIntroduction\n\nSSI after Craniotomy is a significant cause of morbidity and mortality besides its high health care cost.\n\nIn each hospital, all measures are taken to decrease SSI.1 Despite current prophylactic measures, SSI rates have been reported in up to 5% of patients post-craniotomy. Intrawound vancomycin powder has been studied extensively in spinal fusion surgeries and has been found to reduce rates of surgical site infections (SSIs) significantly. Despite its success in spinal surgeries, topical vancomycin has not been extensively studied concerning cranial neurosurgery.2\n\nUsing vancomycin powder during spinal fusion surgery can significantly lower the likelihood of postoperative infections3 and reduce medical costs associated with those infections. Godil et al., in their study, suggest that the use of vancomycin powder for high-risk patients in spinal fusion surgery is a cost-effective option that can save up to $438,165 for every 100 spinal fusions performed.4\n\nTopical vancomycin is safe, effective, and cost-effective in preventing SSIs.\n\nFollowing Craniotomy.5\n\n\nObjectives\n\n\n\nI. Primary objective: to assess the effectiveness of vancomycin in Craniotomy on the surgical site infection rate compared to controls.\n\nII. Secondary objective: to assess the complications of intrawound vancomycin like seroma, long-term benefit, and cost-effectiveness of vancomycin use on hospital stay and patient recovery.\n\n\nTrial design\n\nOur study is a Prospective Randomized Clinical Trial, parallel-group allocation with an equal number of patients. We will do block randomization by a biostatistician through SAS software and determine the superiority of intervention to the control group. Patients will be divided in this Trial into two groups, first group (intervention arm) will receive the drug (vancomycin). The second group (control arm) will not receive the drug; otherwise, both groups will receive identical measures to decrease the postoperative SSI.\n\n\nMethods\n\nThe Hamad General Hospital in Qatar, a government-run health facility and the main center for neurosurgery in Qatar was selected as the primary location for recruiting participants in this study. This hospital is very accessible and affordable for the majority of the country’s population, making it a good representation of the community as a whole. Plus, the hospital provides continuous healthcare services for the people of Qatar free of cost.\n\nPatient inclusion and exclusion criteria:\n\nInclusion criteria:\n\n1) Any Craniotomy, whatever the cause\n\n2) Age more than 18 years\n\n3) Patient with no evidence of any source of infection\n\nExclusion criteria:\n\n1) Any evidence of infection\n\n2) Age less than 18 years\n\n3) Previous and multiple craniotomies\n\nThe consent will be taken by investigators of the study that MRC approves.\n\nNo biological specimen is required in the study.\n\n\nInterventions\n\nIn our study, not to cause any potential bias in the selection process, the comparative arm of the study is chosen from the same hospital setting where all patients are admitted. Our study’s inclusion and exclusion criteria are applied to ensure that the selection process is fair and unbiased.\n\nAfter the surgery, we will be performing a thorough irrigation, a single vial of vancomycin powder containing 1000 mg of the drug will be applied post-op to the surgical bed and wound at the end of the surgery.\n\nThis intervention is only a one-time occurrence; participants can leave the study at any point and withdraw their consent. In our study, there are no specific criteria for discontinuing or modifying the interventions that have been allocated to them.\n\nData collectors will provide phone reminders regarding their follow-up appointments to ensure that our study participants in both groups adhere to the study protocol.\n\nIf a participant develops any other extra-cranial infection or disease during the study, they will be referred to urgent emergency care based on the Hamad Medical Corporation (HMC) guidelines. The participant will receive appropriate treatment free of cost.\n\nAll necessary treatments for cancer and other conditions will be provided to the participants free of charge at the Hamad Medical Corporation following their guidelines and the patient’s diagnosis.\n\nIn trail in addition to assessing the effectiveness of using intra-wound topical vancomycin to prevent surgical site infections (SSIs) after open craniotomies, this study will also examine the incidence of meningitis as well as morbidity and mortality rates.\n\nPrimary outcome: surgical site infection.\n\nSecondary outcome: complications of intrawound vancomycin, hospital cost.\n\nSSI was found to be around 0.49%5 when vancomycin was used, while SSI in standard care was 5%, to get the power of study 80% and level of significance 5%. The sample size will be 250 in each group using a sample size calculator.\n\nThe statistical formula used in the computation of the required and adequate sample size because of the primary outcome, i.e.,\n\nSSI rate between the two groups:\n\nThe sample size was computed using the following statistical formula and sample size determination equation:\n\nWhere Zα/2 is the critical value of the Normal distribution at α/2 (e.g., for a confidence level of 95%, α is 0.05 and the critical value is 1.96), Zβ is the critical value of the Normal distribution at β (e.g., for a power of 80%, β is 0.2, and the critical value is 0.84) and p1 and p2 are the expected sample proportions of the two groups (SSI rate between the two groups, i.e., vancomycin and control groups).\n\nReference: Wang, H. and Chow, S.-C. 2007. Sample Size Calculation for Comparing Proportions. Wiley Encyclopedia of Clinical Trials.\n\nAfter assessing the eligibility and exclusion criteria, it was done through the patients presenting to hamad general hospital for Craniotomy.\n\n\nAssignment of interventions: allocation\n\nBefore the study randomization list was generated with a coded file with each code randomized to either arm (intervention arm or control arm), the patient will be assigned to the subsequent arm according to the code. The code was blinded to the rest of the team doing wound assessment on follow-up.\n\nThe participants in our study will be randomly allocated into either the intervention or control group to minimize selection bias. Concealment of group allocation will also be performed to prevent potential bias. Before the intervention, an investigator who will not be involved in patient follow-up will allocate eligible participants into the two groups according to the randomization list. The investigators approved by MRC. who will be following up with the patients will be blinded to the randomized group to prevent any potential bias in the study.\n\nOne investigator is assigned to generate the allocation list, enrol participants, and assign patients to one of the groups according to the randomization list.\n\n\nAssignment of interventions: Blinding\n\nTo minimize performance and ascertainment bias in our study, blinding will be implemented for the data analyst. The data entry process will also be blinded by providing each subject with a unique code before entering the data for analysis. Plus, the team responsible for following up with the patients’ wounds will be blinded to the randomization of the patients.\n\nOne investigator will have access to both the coded and randomization lists, and unblinding will only occur after a team meeting and approval.\n\n\nData collection and management\n\nIn our study, Data will be collected using a data sheet approved by the MRC (Medical Research Council). At the initial assessment, data on demographics will be collected, and at later follow-up visits, data on wound condition will be collected by two separate investigators in our study. Both investigators and data sheets will be blinded from each other and the rest of the research team to prevent potential bias.\n\nAll patients in our study would be required to follow up regularly as per the hospital’s policy for assessment after surgery. The investigators responsible for following up with the patients will proactively contact them in case of missed appointments. Patients who are lost to follow-up will be noted in the study records.\n\nThe data collected from our study will be entered and analysed using the Statistical Package for Social Sciences SPSS® V22.0. Both electronic and paper-based data will be stored in HMC for a maximum of 10 years and destroyed afterward.\n\nTo ensure patient confidentiality in our study, all patient-related information will be coded on separate sheets. Validity-checked data will be transferred to the study statistician in the same secure manner, with identifiable patient information being password-protected. The code identification list that links the subject’s identity will be kept confidential and stored separately in a sealed envelope, locked in a cabinet, along with the study files with limited access. The team will maintain a screening/enrolment and randomization log to record screening, enrolment, and randomization details.\n\nDoes not apply.\n\n\nStatistical methods\n\nIn data analysis for our RCT, Quantitative variables will be presented as mean and standard deviations. On the other hand, categorical variables will be reported as frequencies with percentages, the intervention and control groups will be described in a table with all their characteristics, and percentages of categorical variables will be compared using the Chi-square test. Following the analysis, Regression analysis will be conducted to stratify the data and eliminate potential confounders and effect modifiers. in our RCT, a p-value of 0.05 (two-tailed) would be considered the threshold for statistical significance.\n\nWe will do the interim analysis of our study when we reach 250 research participants, with 125 in each group.\n\nSubgroup and regression analyses will be conducted to investigate the effects of age, chemotherapy, and chronic illness on the outcome of RCT; this analysis will aim to understand better how these variables may influence the efficacy of intrawound topical vancomycin for preventing surgical site infections after open craniotomies.\n\nIn our RCT, the intention-to-treat principle will be applied during the study analysis, meaning that all participants will be analysed in the randomized group, regardless of whether they completed the study or not. Early discontinuation of the study will be treated as an independent right censoring in the primary analysis. Since all patients will undergo regular follow-ups for wound care and stitch removal, we do not anticipate any lost-to-follow-up cases during the study.\n\nYes, on request.\n\n\nOversight and monitoring\n\nInstitutional Review Board (IRB) will ensure human research participants’ protection, safety, and welfare under its supervision. The HMC IRB monitors and assigns this duty to Clinical Research Monitor(s) (CRM). The HMC IRB office designates the CRM, which takes responsibility for site initiation and monitoring visits. The IRB’s risk assessment of the study determines the monitoring schedule.\n\nBefore conducting visits, the monitor(s) must be well-versed in the study protocol and all related procedures. Throughout the study, initial site training, routine monitoring, and close-out monitoring will be carried out. The initial monitoring visit will occur after enrolling the first 20 subjects, with subsequent visits occurring midway through and at the study’s conclusion. The research will adhere to the principles of the “Declaration of Helsinki,” Good Clinical Practice, and the laws and regulations set forth by Qatar’s Ministry of Public Health, emphasizing autonomy, justice, informed consent, and fast-track ethical approval under protocol number (MRC-01-18-220). Participation or non-participation will not impact the standard care received by patients.\n\nThe MRC ethical committee will conduct formal external independent monitoring. This monitoring process involves site visits to the research location in order to review informed consent forms, as well as remote inspections of Cerner’s database and related documentation.\n\nDuring our study, adverse effects and reporting will always adhere to the HMC (MRC) policy. Our research indicates minimal risk, vancomycin’s safety profile is well-established, and its low application poses even fewer risks. In compliance with HMC’s policy, any patient experiencing an adverse effect will receive an immediate referral for evaluation by the neurosurgery team in the emergency department.\n\nAfter enrolling the initial 20 subjects, the first monitoring visit will occur. Subsequent visits are scheduled for the middle and conclusion of the study. During these visits, the monitor(s) will examine 50% of the data collection sheets and consent forms. Following each visit, the CRM will provide feedback to the study team, commending them on aspects executed well and identifying areas requiring improvement. At the final visit, the monitor(s) will confirm that all questions have been addressed, the study product has been accounted for and either returned or disposed of, and all study documents have been appropriately archived.\n\nObtaining approval for any protocol modifications or amendments will be required from the HMC ethical committees. All alterations will be documented in the study registration.\n\n\nDissemination plans\n\nThe study protocol and its findings will be published in prominent journals to share the results. Individuals involved in the study will be granted authorship following the International Committee of Medical Journal Editors (ICMJE) guidelines. Professional writers and those not directly involved in the writing process will not be considered for authorship.\n\n\nDiscussion\n\nIn neurosurgical procedures, Craniotomy is the backbone of all procedures. That is used to Operate multiple cases. There are different kinds of Craniotomy. It involves the removal of the bone flap and gives you access to the brain. Postoperative wound infections in neurosurgery can be lethal and devastating. Our study includes vancomycin to decrease this postoperative risk of infection.\n\nMoreover, to see if it helps decrease wound infection rates in craniotomy patients, vancomycin is a safe drug and can be used for local applications on the wound. Moreover, its safety has been well documented in the literature.\n\nWe are recruiting patients at present.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare. Spirit checklist, DOI: http://dx.doi.org/10.6084/m9.figshare.23059115.\n\n\nReferences\n\nBakhsheshian J, Dahdaleh NS, Lam SK, et al.: The use of vancomycin powder in modern spine surgery: systematic review and meta-analysis of the clinical evidence. World Neurosurg. 2015 May; 83(5): 816–823. PubMed Abstract \| Publisher Full Text\n\nRavikumar V, Ho AL, Pendhakar AV, et al.: The Use of Vancomycin Powder for Surgical Prophylaxis Following Craniotomy. Neurosurgery. 2017 May 1; 80(5): 754–758. PubMed Abstract \| Publisher Full Text\n\nKhan NR, Thompson CJ, DeCuypere M, et al.: A meta-analysis of spinal surgical site infection and vancomycin powder. J. Neurosurg. Spine. 2014 Dec; 21(6): 974–983. PubMed Abstract \| Publisher Full Text\n\nGodil SS, Parker SL, O’Neill KR, et al.: Comparative effectiveness and cost-benefit analysis of local application of vancomycin powder in posterior spinal fusion for spine trauma: clinical article. J. Neurosurg. Spine. 2013 Sep; 19(3): 331–335. PubMed Abstract \| Publisher Full Text\n\nMallela AN, Abdullah KG, Brandon C, et al.: Topical Vancomycin Reduces Surgical-Site Infections After Craniotomy: A Prospective, Controlled Study. Neurosurgery. 2018 Oct 1; 83(4): 761–767. PubMed Abstract \| Publisher Full Text" }	[ { "id": "205225", "date": "27 Sep 2023", "name": "Nam Tran", "expertise": [ "Reviewer Expertise Neurosurgical oncology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract:\nAuthors should clarify that previous prospective non-randomized trial determined SSI to be around 0.49% when vancomycin was used, while SSI in standard care found to be 5%....\nIntroduction:\nLast paragraph in introduction should further expand on the by Mallela et al\nMethods:\n\nSpecify when the patient will be screened and randomized. Pre-op or intra-op?\n\nInclusion eligibility should specify all craniotomies will be screened for the trial\n\nRemove criteria 3 in Inclusion\n\nExclusion eligibility should specify patients with evidence of any cranial or systemic infection\n\nClarify the exclusion criteria #3 “Previous and multiple craniotomies”. Does this mean redo craniotomies are excluded? Does this exclude any patient who has had a previous craniotomy, even at a different site?\n\nExclusion criteria should exclude those with Vancomycin allergies\n\nShould exclusion criteria exclude those with previous brain radiation?\n\nWill watertight dural closure be a prerequisite for vancomycin administration?\n\nSpecify whether Vancomycin is applied above or below the bone flap.\n\nDiscuss the types of pre-operative antibiotics. What are the selection criteria for pre-operative antibiotics? Will MRSA screens be used to us Vancomycin pre-operatively? What will be the length of peri-operative antibiotics. Only once at the start of surgery or for a 24 hr period?\n\nWill hospital length of stay be collected, as this factor has been shown to increase risk of infection\n\nWill types of craniotomies be collect? Trauma and cancer has higher risk of infection.\nOutcomes:\nDefine the criteria for SSI, ie cellulitis, drainage, fever, meningitis, positive cultures, ect…\n\nSpecify the Hamad Medical Guidelines for referral of patients to urgent care\n\nDefine followup dates. Will patients be followed beyond 2 weeks to determine early and late infections. Should be followed for at least 90 days post-op\n\nDefine how Adverse Events will be categorized, ie according to the CTCAE\n\nAuthors state that they will perform a subgroup analysis of chemotherapy. They types of chemotherapy, whether patient had pre-operative or post-operative chemotherapy should be recorded. Will non-chemotherapy, ie immunotherapy or targeted systemic therapy be considered?\nOverall, a prospective randomized clinical trial on topical vancomycin is needed. Many details need to be clarified.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "205224", "date": "27 Sep 2023", "name": "Stefan Acosta", "expertise": [ "Reviewer Expertise Vascular surgery" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall evaluation\nI acknowledge the hard work behind planning such a study and I wish the investigators the best and endurance to be able to get to the end. The registration in Clinical Trials was performed on June 8, 2021, and now more than two years later – a study protocol is submitted for publication. Well, better late than never.\nStrengths. It appears that the investigators have planned for a double-blind study – correct? Will the patient know if he or she received vancomycin powder? Those involved in assessing the wound postoperative are blinded. It should be stated in the abstract.\nThe sample size should be increased to not get disappointed at the end. Lost-to- follow-up (I mean 6-12 weeks of follow up). Do you intend to perform per-protocol analysis? (deaths and reoperation within 6-12 weeks will occur).\nYou risk of having attrition bias, since all patients that dies will not be properly evaluated, and may have not had the chance to develop an SSI. Conflict of interest -or industry company bias. Please state somewhere that neither of the investigators has any shares in the producer of vancomycin or any other connection to the producer of this pharmacological agent.\nPlease define accurately how you measure SSI. CDC, ASEPSIS score or another tool. That is totally missing in this protocol.\nPatient inform consent and ethical approval issues should be much better declared.\nSpecific comments\nTitle – indicate that this paper is a study protocol\n\nAbstract-Methods. State by which method you will assess SSI\n\nIntroduction – Topical vancomycin “is” safe …..in preventing which SSIs? Spinal fusion surgery?\n\nSecondary objective – so far -can you assess seroma or should it be deleted? Long-term benefit – what is that – suggest to delete.\n\nSecondary objective- Cost-effectiveness. To assess cost-effectiveness you should measure quality of life before and after in all randomized patients to calculate QALY. A better term for what you intend to do is cost-benefit analysis: cost per hospital stay. How is patient recovery assessed?\n\nInformed consent. I can not see that there is a paragraph on patient consent. Will it be written and oral information and written informed consent or not. Please state which way, and explain. It appears the patient does not need to give informed consent? I mean you include emergency and elective cases so many patients will not be able to give informed consent prior to craniotomy.\n\nNo ethical approval needed?\n\nTable 1. “Define OPD in the footnote.\n\nSequence generation. Is this computer-assisted randomization or not? Does it take place during the operation - in the operation room or not. Please specify.\n\nStatistical methods. Should follow CONSORT guidelines. The intervention arm and control arm should be compared by chi square test, nothing more. CONSORT advices against logistic regression and adjustment for confounders.\n\nWell, lost to follow-up – It is advisable to add 5% of 500 (50 patients) lost- to follow up in your sample size. Follow-up until 3 months – remember – that is something else than just removing the stitches. How will you do with deaths prior to 3 months and reoperation prior to 3 months. Still intention to treat? Need to perform per protocol analysis? If a per protocol analysis seems appropriate to perform – please add.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-764
https://f1000research.com/articles/12-761/v1	28 Jun 23	{ "type": "Systematic Review", "title": "How to link organizational resilience to transformational entrepreneurship behavior as theoretical framework gap – A systematic literature review", "authors": [ "Michael Gunawan", "Budi Soetjipto", "Lily Sudhartio", "Budi Soetjipto", "Lily Sudhartio" ], "abstract": "Background: Numerous enterprises face great challenges during uncertain economic conditions. This is particularly true for micro, small, and medium-scale companies, which are slumped against disruption from the COVID-19 pandemic—owing to lockdowns, decreased demand, and a disrupted supply chain. This has impacted the economy worldwide but also the social community and the environment that forms its ecosystem. Organizational resilience allows for socio-economic growth and enterprises to build environmental sustainability and balanced community development. Therefore, the behavior of companies must be transformed in building entrepreneurship to encourage socio-economic growth. Methods: We conducted an advanced search on Business Source Premier, ABI/INFORM (ProQuest), Emerald Insight, and Web of Science database between March and June 2022. We screened the bibliographies of the articles from the database search using a set of inclusion criteria such as studies with quantitative design with unit analysis population sample based microfinance institutions and cooperative-based microfinance institutions, MSEs, and MSMEs as well as other industries such as travel agents, property, restaurants, food and beverages, manufacturing and plantations; exploration of transformational entrepreneurship behavior and organizational resilience determinant factors and conceptual manuscripts written in English; and published between 2005 till 2019 for transformational entrepreneurship and 1997 till 2000 for organizational resilience.\n\nResults: This study reviewed 22 articles focusing on the role and influence of organizational resilience on transformational entrepreneurship behavior from a lens that posits the importance of organizational resilience in the face of uncertain economic turbulence. The orientation of entrepreneurship behavior has been neglected in research so far. This systematic literature review study reveals important research gaps, such as the influence of organizational resilience in promoting the development of transformational entrepreneurship behavior and the determinants that build organizational resilience. Conclusions: Research related to a company’s transformational entrepreneurship behavior offers a broad area of scientific research; hence, encouraging further investigation is necessary.", "keywords": [ "Organizational resilience", "transformational entrepreneurship behavior", "socio-economic growth", "environmental sustainability", "community development" ], "content": "Introduction\n\nEconomic growth has suffered dramatically owing to the ongoing COVID-19 pandemic, which has shown no end as of yet. The situation continues impacting socio-economic development, environmental sustainability, and people’s welfare. Meanwhile, the epidemic situation, which resulted in a decline in demand and purchasing power, prompted companies to be proactive, innovate, and take risks to recover and improve their economic performance (Covin & Slevin, 1991; Miller, 1983; Scherer et al., 1989). The efforts exerted, thus far, to achieve economic growth have fallen short of achieving sustainable growth. Therefore, transformational behavior from organizational leaders, which includes innovative, proactive, and risk-taking behavior, is needed to achieve socio-economic growth, where social development can include environmental sustainability and community development in an optimal and balanced manner (Maas et al., 2019; Maas & Jones, 2017). Similarly, Roth and DiBella (2015) argued for the importance of encouragement from top management to foster transformational behavior within a company and certain skills, such as how to read the current environmental conditions, be able to absorb new knowledge from existing situations and conditions, and influence the transformation at various levels in the company to implement a new approach.\n\nThis is a conceptual paper produced through an in-depth literature review. It attempts to answer the following questions:\n\n1. Transformational entrepreneurship behavior is so important to achieve socio-economic growth that it includes environmental sustainability and community development in a balanced way; then, why is this entrepreneurship behavior lacking?\n\n2. What determinants shape transformational entrepreneurship behavior toward socio-economic growth?\n\n3. What are the determinants that shape and build organizational resilience?\n\nThis conceptual study contributes to the literature on transformational entrepreneurship behavior (Table 1) and the impact of organizational resilience (Table 2). The following contributions have resulted in a research framework (Figure 1) and provided a pathway for further research. This study provides a novel opportunity to take a closer look at the influence of organizational resilience and other determinants on transformational entrepreneurship behavior. To the best of the authors’ knowledge, this study is the first in-depth and systematic review of the literature to consider the transformational entrepreneurship behavior essential for a company to achieve sustainable goals. Second, this study builds a logical theoretical framework model to connect several determinant factors in building organizational resilience. The conceptual framework was formed through a literature review and theoretical gaps.\n\nThe remainder of this paper is structured as follows: (1) We describe the classification and provide a thorough explanation of organizational and transformational entrepreneurial behaviors. (2) We review and briefly describe an approach to descriptively review and analyze a collection of literature. (3) We systematically design the conceptual framework referring to the previous step as the basis. (4) The main findings obtained are then discussed, fostering a potential pathway for a detailed description for further research. This paper also describes its limitations; the final section presents the conclusions.\n\nCompanies need leaders who foster transformation to survive in a turbulent environment and face uncertainty. Leaders who do this successfully have high integrity and motivate and encourage the efforts of their employees to achieve organizational goals and targets to improve company performance (Lafley, 2009). Therefore, entrepreneurship behavior, which includes innovative, proactive, and risk-taking behaviors, is essential (Covin & Slevin, 1991; Miller & Friesen, 1982). Meanwhile, Bass (1985) and Howell and Avolio (1993) held that transformational leaders encourage the development of innovation in their organizations. This is also supported by Crant (2000) and Deluga (1998), who found that transformational leadership encompasses proactive, innovative, and risk-taking behavior. In other words, transformational leadership has been recognized to be connected to entrepreneurship.\n\nTherefore, there is a need for renewed thinking to stimulate entrepreneurship to support socio-economic growth. In this context, ‘transformational entrepreneurship’ refers to a holistic and heuristic orientation in terms of promoting entrepreneurship and bringing together individuals and other subsystems, such as communities and institutions that interact and collaborate to create a positive framework within which opportunities can be leveraged that extend beyond the local area (Maas et al., 2019).\n\nThen, how important is the role of entrepreneurship in encouraging sustainable socio-economic growth to ensure that organizations may realize the right capabilities, capacities, and policies, including the ecosystem that supports them, to change or maintain a progressive socio-economic landscape—including community development in Indonesia through balanced optimal growth? Entrepreneurship can potentially precipitate a measure of success in dealing with volatile situations and conditions with high uncertainty. In times of strife, a company must not merely seek survival but also the ability to grow sustainably. Therefore, companies do not solely need economic returns (short-term) but also social impacts (long-term), such that the company’s success contributes to societal welfare (Maas et al., 2019; Ratten & Jones, 2018; Xu & Maas, 2019).\n\nWealthy people are economically capable of sustaining a company’s progress, thus allowing the company to grow sustainably. Entrepreneurship also seeks to make a social impact by developing socially-oriented entrepreneurship. However, social entrepreneurship focuses on “community work, voluntary and public organizations, and private enterprises working for purely social purposes rather than for profit” (Shaw & Carter, 2007). Solutions tend to rarely be formulated with consideration for economic scalability for sustainable socio-economic growth (Marmer, 2012). On the contrary, we need entrepreneurship that can transform profit-oriented companies to include a social growth perspective in their goals.\n\nThus, a new approach is needed in socio-economic development through a systemic and holistic process to accommodate the needs of individuals economically and socially (Maas et al., 2019). Without a new paradigm in the form of new approaches, such as transformational entrepreneurship, the potential for socio-economic development will remain limited and only benefit a small number of individuals, businesses, and organizations. As it is necessary to establish principles related to transformational entrepreneurship and the ecosystems that support it, practical cases are provided to illustrate the global concept of transformational entrepreneurship (Maas et al., 2019). Therefore, transformational entrepreneurship behavior focuses on dynamically stimulating socio-economic development to achieve balanced optimal growth (Maas et al., 2019; Ratten & Jones, 2018).\n\nTo address this need, the concept of transformational entrepreneurship is introduced. Transformational entrepreneurship encourages the advancement of entrepreneurship by bringing together individuals, communities, and institutions that interact and collaborate to take advantage of existing opportunities and reach a wider scale to promote optimal and balanced socio-economic growth (Maas et al., 2019; Ratten & Jones, 2018; Xu & Maas, 2019). Additionally, transformational entrepreneurship encourages entrepreneurial activities that bring about meaningful changes in markets and industries, sociocultural life, and environmental and community development (Marmer, 2012).\n\nAccording to Maas et al. (2019), balanced socio-economic growth must be achieved through activities that encourage the development of entrepreneurship and change in society at large, which positively impacts socio-economic growth, including community development. Therefore, to overcome current phenomena such as poverty, low welfare, inadequate health, unemployment, and negative business growth, a transformation is needed by supporting entrepreneurship as part of a comprehensive system, namely a system consisting of community, public, private, environmental, and natural resource management that provides benefits.\n\nResearch has demonstrated that company performance can be improved if top leadership exhibits entrepreneurship behavior (Andole & Matsui, 2021; Dess & Lumpkin, 2005; Llanos-Contreras et al., 2020; Majid & Koe, 2012; Scherer et al., 1989). However, entrepreneurship behavior is more focused on obtaining economic benefits, even though what is needed is to build a sustainable company (Aldrich & Zimmer, 1986; Chell & Baines, 2000; Dubini & Aldrich, 1991). A sustainable company can bring the company to achieve long-term business goals through its processes and actions from time to time by incorporating economic, social, and environmental aspects into its business strategy (Baumgartner & Rauter, 2017; Haugh & Talwar, 2010).\n\nConsequently, entrepreneurship behavior is no longer adequate; therefore, Maas et al. (2019) introduced transformational entrepreneurship behavior (TEB), which includes transformational proactive behavior, transformational innovative behavior, and transformational risk-taking behavior. The aim is enhancing people’s welfare and prosperity, thus increasing their purchasing power and consumption.\n\nSeveral previous studies have explained the factors driving TEB, including Xu and Maas (2019), Roth and DiBella (2015), and Maas et al. (2019), wherein the TEB is formed in a dynamic context. Meanwhile, entrepreneurship behavior, especially for transformation, must be action-oriented and, indubitably, require the capability to realize these actions. Therefore, it takes the company’s capabilities to realize the TEB. Moreover, Roth and DiBella (2015) posited that five capabilities are needed to enable transformational change: company awareness about the situation and market conditions and the environment in which the company is located related to competitiveness, ability to innovate, the balance of encouragement from top management, and absorption of new knowledge about the current situation.\n\nThese capabilities not only adapt to change but also recover when hit by change (Duchek, 2020; Garud et al., 2007; Kantur & İşeri-Say, 2012; Wenzel et al., 2021). These three capabilities form the core of organizational resilience (Duchek, 2020). Korber and Naughton (2018) held that OR is a determinant of entrepreneurship behavior and intentions; thus, OR is often manifested in self-efficacy or optimism.\n\nAccording to Duchek (2020), organizations that prepare themselves to anticipate a crisis (self-preparation capability) can act proactively, creatively, and innovatively by preparing human resources, organizational resources, and infrastructure to build systems to deal with potential crises. Further, Duchek (2020) posited that when a crisis occurs, companies that are already prepared can respond to the crisis and then absorb and adapt to the changes caused by it. Proactiveness, creativity, and innovation are crucial components of entrepreneurship behavior, including TEB, whereas self-prepared organizations are more resilient when experiencing change. Therefore, arguably, OR may affect TEB.\n\nOther determinant factors include how the organization can take advantage of existing opportunities and customers and seek new opportunities—new customers. On the one hand, the organization can exploit existing opportunities; on the other hand, it can seek new opportunities with a balanced creative and innovative approach (Benner & Tushman, 2003; Cao et al., 2009; Gibson & Birkinshaw, 2004; Lubatkin et al., 2006; O’Reilly & Tushman, 2008, 2013; Tamayo-Torres et al., 2017).\n\nCompanies—in maintaining and retaining existing customers, as well as opportunities to find new customers—must have a strategy of having a competitive advantage because the company also has competitors in the region where it is located. Therefore, companies need to have competitive and unique products and services superior to those of similar competitors to create a competitive advantage (Barney, 1991, 1995; Flamholtz & Randle, 2012; Porter, 1989, 1996; Stonehouse & Snowdon, 2007).\n\nConsidering that the occurrence of turbulence, situations, and conditions categorized as social and environmental conditions are currently experiencing an uncertain and unpredictable situations, efforts are needed to increase resilience to include organizations, individuals, regions, and social communities (Kantur & İşeri-Say, 2012). Therefore, resilience encompasses a broad range of industries and scientific disciplines (Gunderson & Holling, 2002; Werner & Smith, 1977).\n\nHence, in organizational studies, an understanding of organizational resilience is the ability of an organization or a region to apply crisis management to face disasters, so organizations need high and even the highest reliability to overcome problems that occur suddenly and cause serious disruption. (Sutcliffe & Vogus, 2003; Weick et al., 1999; Weick & Sutcliffe, 2001). Horne and Orr (1997) defined resilience as “a fundamental quality in terms of the capacity and capability of individuals, groups, organizations, and the system as a whole to respond effectively and productively” to large and sudden changes that are massive so that they disrupt or damage the existing system and can cope within a short period. Meanwhile, Mallak (1998) stated that resilience is necessary under sudden shocks such as natural disasters or terrorist attacks and is also relevant for an organization, a region, and an individual faced with sustainable socio-business and environmental transformation.\n\nSimilarly, Robb (2000) posited that organizations with strong resilience can provide outstanding performance following current organizational goals and continue to innovate and adapt to changing market conditions and technology. Overall, practitioners believe that organizations with strong resilience automatically can successfully avoid disturbances while also coping with turbulence disturbances that occur effectively.\n\nAccordingly, transformational entrepreneurship behavior that brings innovation faces the challenge of implementing it in companies at various scales, as well as the difficult challenge of becoming a mission and transformational behavior in MSMEs, as well as how micro- and small-scale financial institutions foster the growth of MSME companies to achieve socio-economic sustainability and community development (Maas et al., 2019; Xu & Maas, 2019). The literature has largely ignored the determinants of transformational entrepreneurship behavior. Entrepreneurship behavior still dominates contemporary companies—namely, the current flow of research that is merely oriented toward economic growth (Guiso et al., 2021; Zahra, 2021) and, thus, largely ignores sustainable growth—both environmental and socio-economic (Maas et al., 2019; Xu & Maas, 2019). These facts are extremely important, considering that the nature of transformational entrepreneurship behavior differs from entrepreneurship behavior, where transformational entrepreneurship behavior is frequently associated with socio-economic growth (Maas et al., 2019).\n\nFacing conditions and a volatile and uncertain environment, companies need to have capable leaders with high integrity to ensure that they can transform the company to achieve its goals and objectives in creating socio-economic growth, including community development (Maas et al., 2019).\n\nIn conducting transformational entrepreneurship, companies are not only innovative, proactive, and risk-taking behavior (Bass, 1985; Covin & Slevin, 1991; Crant, 2000; Deluga, 1998; Howell & Avolio, 1993; D. Miller & Friesen, 1982) for economic purposes only, but sustainable as well—by possessing transformational proactive behavior, transformational innovative behavior, and transformational risk-taking behavior to achieve socio-economic growth comprising environmental sustainability and community development interests simultaneously and in optimal balance (Maas et al., 2019).\n\nHowever, in reality, extant research still discusses entrepreneurship that focuses on the economic aspect (Guiso et al., 2021; Zahra, 2021), elucidating how entrepreneurship brings organizations or companies to grow and develop to achieve competitive advantage and economic advantage. These studies do not explore the fact that the competitive advantages and economic benefits as explicated may only be relatively short-term and unsustainable, whereas producing competitive advantages and economic benefits that are relatively long-term and sustainable requires the support of the surrounding environment sustainability in the form of community development that is concurrently related with socio-economic performance (Maas et al., 2019).\n\nThus, widely discussed in various journals, entrepreneurship is likely to exhibit a limited impact because the solutions are rarely designed with scalability and long-term sustainable economic and social development (Maas et al., 2019; Xu & Maas, 2019). Therefore, understanding entrepreneurship from a social perspective and the development of the environment and society from a balanced and simultaneously economic perspective is necessary.\n\nThe second challenge is the realization of transformational entrepreneurship. Considering the wide scope of transformational entrepreneurship behavior, it is likely that only strong and resilient organizations can support leaders to do so. A strong and resilient organization is one with high organizational resilience. Meanwhile, according to Doe (1994), Horne (1997), Horne and Orr (1997), Mallak (1998, 1999), and Warner and Pyle (1997), organizations with effective resilience capabilities can face and survive in turbulent, chaotic, and uncertain situations. Organizations that have high resilience are also prepared to face even the worst situations and respond “appropriately and quickly” (Sullivan-Taylor & Wilson, 2009; Wilson et al., 2010).\n\n\nMethods\n\nThe author conducted a literature review to study and develop a body of knowledge based on the results of journal-journal research as a guide for future research agendas. According to Tranfield et al. (2003), an in-depth study of existing journals should be conducted through systematic reviews, which help find research gaps and determine the future scope of investigation in the field.\n\nFrom March to June 2022, a search was conducted using the Business Source Premier, ABI/INFORM (ProQuest), Emerald Insight, and Web of Science. From the database search, we screened the bibliographies of articles according to a set of inclusion criteria outlined below, including studies with quantitative designs involving unit analyses with population samples and cooperatives. It explores transformational entrepreneurship behavior and organizational resilience determinant factors as well as conceptual manuscripts written in English, including MSEs and MSMEs, as well as other industries such as travel agents, property, restaurants, food and beverage, manufacturing, and plantations. Articles on transformational entrepreneurship published between 2005 and 2019 and organizational resilience published between 1997 and 2000 were selected for this review. ProQuest, Emerald Insight, and Web of Science databases (via e-Library of the University of Indonesia) were used to search Google Scholar, Business Source Premier, and Business Source Premier.\n\nThe authors researched related journals through the string “AND” and “OR” (Tremml, 2019; Whitten et al., 2007), which are “Transformational Entrepreneurship” AND “Socio-Economic Growth,” “Organizational Resilience” AND “Competitive Advantage.” Then “Transformational Entrepreneurship Behavior” AND “Innovation, Risk-Taking and Proactive,” thus “Organizational Resilience” AND “Leader-Member Exchange, Psychological Capital” AND “Competitive Advantage,” “Transformational Entrepreneurship (Behavior)” AND “Competitive Advantage.” Moreover, “Transformational Entrepreneurship Behavior AND Transformational Entrepreneurship” were searched for the latest journals in the 2010-2020 period and Organizational Resilience for the period 1997-2020, which became a theoretical foundation like “transformational entrepreneurship (behavior) theory” (Maas et al., 2019; Maas & Jones, 2017; Marmer, 2012; Xu & Maas, 2019) and “organizational resilience” (Duchek, 2020; Horne, 1997; Horne & Orr, 1997; Kantur & İşeri-Say, 2012; Välikangas & Romme, 2012). These collected and reviewed journals can be classified as validated such that they significantly impact the knowledge derived and research conducted (Keupp et al., 2012; Podsakoff et al., 2005).\n\nTransformational entrepreneurship\n\nInclusion criteria:\n\n- Quantitative research and literature review papers\n\n- Published in between 2005-2019\n\n- Accessible without paying\n\nExclusion criteria:\n\n- Articles published before 2005 and after 2019\n\nOrganizational resilience:\n\nInclusion criteria:\n\n- Quantitative research and literature review papers\n\n- Published in between 1997-2020\n\n- Accessible without paying\n\nExclusion criteria:\n\n- Articles published before 1997 and after 2020.\n\n- Both quantitative research and literature review paper.\n\nFollowing Tremml (2019) and as recommended by Booth et al. (2022), a careful selection process produced 148 manuscripts, which were analyzed in full depth. Based on the inclusion and exclusion criteria, 45 articles were shortlisted for the review, 28 articles for organizational resilience, and 17 articles for transformational entrepreneurship. This is in accordance with Tremml, who argued that it is necessary to examine a reference in more detail as a technical search to ensure that it lends a meaningful addition to reference checking as an additional search technique (Booth et al., 2022). Ultimately, 22 studies were included in this review. Figure 1 presents the systematic search and selection process. The articles obtained were then carefully examined and studied related to transformational entrepreneurial behavior strategies, organizational resilience, psychological capital, leader-member exchange, ambidexterity, and competitive advantage, and can be applied in all industries, including MSMEs, microfinance institutions, and multi-finance cooperatives.\n\nDuring the process of a systematic literature review, the authors were aware of potential sources of bias and took steps to minimize their impact. This involved using strict inclusion and exclusion criteria to identify relevant studies as well as assessing the quality and validity of the research methods employed in each study. We considered the potential impact of bias on the conclusions drawn from the research and reported any limitations or biases that may have influenced the findings. To link organizational resilience to transformational entrepreneurship behavior, it is essential to identify and address any potential sources of bias that may impact the theoretical framework of the research. This involved a thorough and critical review of the existing literature as well as a clear understanding of the underlying concepts and theories involved. By carefully considering the potential for bias at each stage of the research process, we developed a robust and reliable theoretical framework that can guide future research in this area. This literature review assesses the risk of bias by considering the tendency of primary studies and research published in proceedings and journals to be examined with only a significant effect; those that are not significant are not included.\n\nTransformational Entrepreneurship (behavior measured for research) is a relatively new topic; therefore, the timeframe for publishing a journal is shorter and more limited than organizational resilience (much longer and has become a significant issue in the 1990s). Transformational entrepreneurship (behavior) departs from entrepreneurship (behavior/orientation) and social entrepreneurship; The review started in 2005 through Mel et al. regarding entrepreneurs possessing qualities of high willingness to take risks and high managerial and financial literacy to innovate. Miller and Collier (2010) attempted to develop transformational entrepreneurship following Schoar (2010). Furthermore, Marmer (2012), through the Harvard Business Review, emphasized transformational entrepreneurship (TE) in four quadrants, which is the future of organizations. Companies must develop TE to achieve socio-economic growth and environmental and community development in an optimal and balanced manner. Jones, Lockyer, and Maas and the Jones and Maas couple developed TE continuously through thoughts and concepts, as well as case and empirical studies from 2019 until now.\n\nWhile the topic of organizational resilience has been around since the 1990s, resilience also includes regional/city resilience to natural disasters, earthquakes, agency hurricanes, and organizational/company resilience to sudden economic turbulence. Therefore, the period for organizational resilience in this manuscript review began earlier, from 1997 to 2020, and is still ongoing today (mainly when the Covid-19 pandemic occurred).\n\nWe conceptualize resilience as a meta-capability, including the determinants and ecosystems that shape it, and break down the construct into its parts or the dimensions that make it up.\n\nOur analysis is based on the data and information in organizational resilience journals and transformational entrepreneurship journals. We understand organizational resilience well, especially as it relates to organizations/companies, so organizational resilience has an ecosystem that shapes it. Be it human resources, environmental resources, financial resources, and the social-economic-community environment. Therefore, leaders and employees within an organization or company must possess transformational entrepreneurship behavior to achieve sustainable growth.\n\nFrom the journal period reviewed for Transformational Entrepreneurship (TE) from 2005 to 2019 and Organizational Resilience (OR) from 1997 to 2020, we see a common thread through meta-analysis, where we find theoretical gaps that contribute to generating novelty in the form of conceptual propositions.\n\n\nResults\n\nFigures 2 and 3 explain the number of publications obtained per year and reveal the trend of increasing research using these variables or constructs, as well as building novelty and providing socio-economic and industrial impacts and contributions. The trend of increasing this research follows the increasing number of publications in the field of transformational entrepreneurship—transformational entrepreneurship behavior, starting in the 1990s and 2010 and continuing to grow and develop, respectively, in the last 10 years, and organizational resilience has fluctuated and tended to be stable in the last 25 years.\n\nThe framework model ascertains the proposition of organizational transformational entrepreneurship behavior, which is determined by the organization’s resilience and the ecosystem in which the organization is located. How strongly organizational resilience is influenced by individual aspects within the organization, namely, the psychological capital of the top leadership of the organization and quality of the relationship between the top leadership of the organization and its subordinates (Dansereau et al., 1975; Graen et al., 1982; Graen & Cashman, 1975; Hind et al., 1996; Horne, 1997; Kantur & İşeri-Say, 2012; Luthans et al., 2015; Mallak, 1998, 1999; Wilson & Ferch, 2005; Youssef, 2004), as well as by aspects of organizational aspects, namely the organization’s ability to explore and exploit simultaneously, and the organization’s competitive strategy (Adler et al., 1999; Caspin-Wagner et al., 2012; Doe, 1994; Gibson & Birkinshaw, 2004; Horne, 1997; Iyer et al., 2006; Kantur & İşeri-Say, 2012; Katila & Ahuja, 2002; Mallak, 1998).\n\nMeanwhile, the determinants of transformational entrepreneurship behavior from the internal side of the organization include the capability to explore and exploit opportunities simultaneously and in a balanced manner (ambidexterity) (Benner & Tushman, 2003; Gibson & Birkinshaw, 2004; O’Reilly & Tushman, 2008, 2013; Tamayo-Torres et al., 2017) according to transformational innovative and risk-taking behavior. Likewise, the internal determinants of TEB include a competitive advantage strategy because it must be owned by every organizational company (Barney, 1991, 1995; Porter, 1989, 1996; Stonehouse & Snowdon, 2007), which follows transformational innovative and proactive behavior.\n\nCull et al. (2013) argued that a need exists for joint efforts to measure environmental quality that impacts business growth and investment to provide benefits to socio-economic and environmental growth in a region. Therefore, the World Bank (2013) provides guidelines on the ease-of-doing-business index based on the complexity of business regulations and respect for protecting property rights. This index is measured to determine the ease of doing business, starting a business, including managing and obtaining permits, process and traveling time, including permits to build company areas or business buildings, ease of obtaining loans, and protection of investors, including permits to establish banks and manage money markets.\n\nCiccone and Papaioannou (2007) argued that the process of registering a new business entity for an existing business is significantly negatively related to new business investment. Meanwhile, Klapper, Laeven, and Rajan (2006) found that easier and more concise regulations will help capital inflows invest, including the growth of business activities in the building of industry. Therefore, the complexity of regulations determines the quality of the environment and space in conducting business, which significantly impacts economic growth (Cull et al., 2013).\n\nReferring to the research framework (Figure 4), external factors, such as the environment, are the determining factors that influence companies, especially MSMEs, as well as microfinance institutions and multi-finance cooperatives. Therefore, the company’s orientation toward organizational resilience and transformational entrepreneurial behavior and the results obtained can certainly be influenced by external factors, namely the environment that is a sustainable supporter; in this case, government regulations play an extremely noteworthy role in succeeding the socio-growth of industry, business, and MSMEs, as well as microfinance institutions.\n\nA suitable increase in the resilience advantage is required to deal with unpredictable and uncertain catastrophe and loss conditions. Resilience includes organizational, individual, community, and regional resilience (Kantur & İşeri-Say, 2012). Resilience in the real sense also includes all aspects of conducting assessments, including various disciplines (Gunderson & Holling, 2002; Werner & Smith, 1977).\n\nOrganizational resilience capabilities are prepared and built by implementing crisis management and preparing human resource capabilities and organizational resources with high reliability so that they can anticipate and cope with sudden and disruptive disasters and environmental changes (Sutcliffe & Vogus, 2003; Weick et al., 1999; Weick & Sutcliffe, 2001).\n\nMoreover, Horne and Orr (1997) argued that resilience is the capacity and capability possessed by organizations, individuals, communities, and regions to prepare themselves for disasters and volatile conditions so that they can respond carefully and overcome these problems quickly. Similarly, Mallak (1998) held that an organization’s resilience can transform it to achieve sustainable socio-business and environmental growth.\n\nRobb (2000) also stated that organizations with strong resilience can provide great performance following current organizational goals and continue to innovate and adapt to changing market conditions and technology so that organizations can grow and develop sustainably. Therefore, organizations with strong resilience automatically have good capabilities to avoid disturbances while also dealing with turbulence disturbances that occur effectively.\n\nKantur and İşeri-Say (2012) developed an organizational resilience framework and identified its determinants:\n\n1. The perceptual stance describes the organization’s positive perception, especially that of top leaders. Individuals with positive perceptions have high psychological capital.\n\n2. Contextual integrity describes employees’ involvement and empowerment. Employees with high involvement and empowerment have a quality relationship with the organization’s top leadership. With these quality relationships, employees gain the trust of the organization’s top leadership so that they get the support of resources that allow them to be more involved and empowered than others.\n\n3. Strategic capacity describes an organization’s ability to deal with uncertain situations. This ability is reflected in the ability to conduct exploration and exploitation simultaneously, considering that this uncertain situation may present new opportunities that need to be explored further, but at the same time, existing opportunities need to be continuously exploited.\n\n4. Strategic acting describes an organization’s creative, flexible, and proactive actions. These three actions are included in the organization’s competitive strategy to outperform its competitors. By acting creatively, flexibly, and proactively, organizations can offer products that are different from those in the market or offer similar products at more competitive prices. Therefore, it is necessary to build a competitive advantage, which is a decisive factor in the long-term success of a business. When a business can create a competitive advantage over its competitors, growth and revenue will increase (Barney, 1991).\n\nIt is also important to have a competitive advantage based on the organizational culture built, strategic assets owned, and the business model applied to retain existing, loyal, and potential customers and serve the target market through a high-efficiency process (Barney, 1991, 1995; Flamholtz & Randle, 2012; Porter, 1989, 1996; Stonehouse & Snowdon, 2007).\n\nPsychological capital\n\nThe attitude of having a desirable perception represents a perception of the existing reality rooted in the wisdom to create a positive mindset and have high commitment. Building a positive perception and widespread dissemination within the organization will become a guideline and commitment of employees and the organization to strengthen the resilience of the organization. Meanwhile, understanding the existing reality will build a perception of self-image, which is an important element in building organizational resilience (Hind et al., 1996).\n\nAccording to Coutu (2002), the characteristics of strong organizational resilience are based on the meaning of real reality. This meaning builds a positive image so that the perception of the meaning of organizational resilience is to face bad and disturbing problems and situations (Mallak, 1998). According to Flach (2004), optimism (optimism) and hope (hope) are important elements in building perceptions. This positive perception increases the resilience of an organization.\n\nAccording to Flach (2004), optimism and hope are noteworthy elements of constructive perception. This positive perception increases organizational resilience, as needed in the perceptual stance element. The perceptual stance construct is compatible with psychological capital. Therefore, psychological capital (PsyCap) is a decisive factor that determines organizational resilience to support the success of transformational entrepreneurship behavior in increasing employee performance.\n\nThis aligns with Youssef (2004) and Luthans, Youssef, and Avolio (2015), who held that psychological capital (PsyCap: Psychological Capital), as it is now widely recognized human and social capital, is a take-off from economic capital, where existing resources are invested and utilized for future returns. Operationally, PsyCap can be explained as follows: (1) having high self-efficacy in making the decisions needed to succeed in ever-changing challenges; (2) creating a positive korsa spirit (optimism) regarding how to “build success now and in the future”; (3) tenacious, persistent and diligent in achieving the goal, and directing all power and ability to reach the path to the expected goal; and (4) when facing problems and challenges, being able to recover and then rise again through effective resilience to achieve success (Luthans et al., 2004, 2015). Thus, in sum, PsyCap, individually and as an organization, is an important determinant of building organizational resilience.\n\nLeader-member exchange\n\nEmployee engagement and empowerment are essential for employees to demonstrate appropriate behavior when faced with adversity or an unpredictable turbulent environment. Therefore, the unity of thought and action between leaders and employees is needed.\n\nFacing great pressure from disasters, organizations must prepare themselves carefully, overcome these problems, and then adapt to changing environments and conditions. Mallak (1998) emphasized the importance of empowerment in the decision-making process from leaders to employees as an important element of organizational resilience. Empowering employees in decision-making enables them to produce creative solutions with increased authority and capability.\n\nThe leader–follower relationship is a mutually supportive interpersonal relationship. Mutual trust and respect are essential in an organization (Dulebohn et al., 2012), and thus, understanding the distance at the point of a two-way relationship between “leaders and followers/subordinates” is highly important to increase positive outcomes for employees and organizations (Dansereau et al., 1975; Graen et al., 1982; Graen & Cashman, 1975)”. According to Anand et al. (2018), the power distance factor between leaders and followers is important for improving communication and good relationships. Similarly, Antonakis and Atwater (2002) and Napier and Ferris (1993) posited that communication within the organization runs smoothly because of the good relationship between leaders and subordinates so that the goals and missions of achieving organizational performance are met.\n\nAccording to Gouldner (1960), leadership-subordinate relationships must be rooted in reciprocal personal relationships that support each other, communicate with each other, and are open to each other. In building high-quality relationships, leaders provide empowerment, trust, and support in the form of resource allocation, improvement in the quality of key tasks and functions, and through coaching and mentoring (Ilies et al., 2007; Maslyn & Uhl-Bien, 2001; Settoon et al., 1996). Therefore, to form high-quality relationships, a leadership role is needed to motivate, build relationships, and provide trust and empowerment to subordinates to ensure that they are expected to contribute to producing an effective performance for the organization (Settoon et al., 1996; Wayne et al., 1997).\n\nFurthermore, Weick (1993) posited that continuous open communication is an important factor in coordinating superiors and subordinates in an organization. Likewise, Horne and Orr (1997) recommended that to foster effective organizational resilience, leaders must communicate effectively about the company’s goals, mission, and vision to their employees to build trust—an important principle in building such resilience.\n\nVan Breukelen, Schyns, and Le Blanc (2006) proposed an approach to building a good leader-member relationship process through open and honest two-way interactions. This confirms that LMX theory is a characteristic of a dynamic causal relationship between leaders and their subordinates while simultaneously fostering commitment to advancing the organization (Northouse, 2012).\n\nAmbidexterity\n\nMarch (1991) identified two categories of implementation in an organization: (1) explorinh novel opportunities and findings because they are related to innovation, and (2) exploiting to develop and deepen existing resources, as well as to update and improve the quality and capabilities of organizational resources. Companies and organizations must “conduct exploration and exploitation simultaneously and in a balanced manner by utilizing available resources and good managerial capabilities to obtain better organizational performance (Chandrasekaran et al., 2012; Kristal et al., 2010; Salvador et al., 2014).\n\nOrganizations or companies sometimes face an unstable and hostile environment requiring organizations to engage in “exploration and exploitation, thus becoming an ambidextrous organization (Benner & Tushman, 2003; Lubatkin et al., 2006; Raisch & Birkinshaw, 2008; Tamayo-Torres et al., 2014, 2017).” Therefore, ‘ambidexterity’ is a company’s capability to carry out exploration and exploitation activities simultaneously and in a balanced manner (O’Reilly & Tushman, 2004).\n\nOrganizations need to maintain an appropriate combination of exploration and exploitation—a balance between the organization’s ability to exploit and explore existing and new opportunities—to produce optimal company performance (Cao et al., 2009; Lubatkin et al., 2006). This is according to O’Reilly and Tushman (2004), who highlighted the need for simultaneous execution of exploration and exploitation to achieve a balance that results in the survival and success of the organization or company. Therefore, combining exploration and exploitation is important to achieve improved long-term organizational performance (Benner & Tushman, 2003; Gibson & Birkinshaw, 2004; Lubatkin et al., 2006; Tamayo-Torres et al., 2017). In essence, organizations that conduct exploration and exploitation activities simultaneously and in a balanced manner, can deal with situations and environmental conditions that change dramatically. This aids organizations to receive new opportunities as an organization with effective resilience capabilities (Mallak, 1998).\n\nTherefore, companies must take advantage of existing opportunities and customers and seek new opportunities and customers with a proactive, creative, and innovative approach in a balanced and concurrent way (ambidexterity; (Benner & Tushman, 2003; Cao et al., 2009; Gibson & Birkinshaw, 2004; Lubatkin et al., 2006; O’Reilly & Tushman, 2008, 2013; Tamayo-Torres et al., 2017).\n\nFurthermore, the company uses the ability to act proactively, creatively, and innovatively by exploiting existing markets/opportunities while simultaneously developing creative and innovative behavior by exploring new opportunities by daring to take risks. This is in line with transformational innovative behavior and proactive behavior that such behaviors aim to change and transform.\n\nCompetitive advantage strategy\n\nThe capability of the organization to prepare itself by anticipating potential disasters and crises must be followed by strategic organizational capacity and strategic actions, where the behavior of employees in the organization must be creative, agile, sensitive, resilient, and proactively oriented toward innovation-resulting solutions (Duchek, 2020; Kantur & İşeri-Say, 2012; Wenzel et al., 2021).\n\nCompetitive advantage strategy has proven to be an extremely important element of how organizations grow and develop to achieve their goals and objectives (Ehie & Muogboh, 2016; Kharub & Sharma, 2016, 2017; Korutaro Nkundabanyanga et al., 2014; Olhager & Feldmann, 2018; Stonehouse & Snowdon, 2007). Based on a literature review, the competitive advantage strategy comprises the following four categories: (1) These manuscripts describe the concept of competitive strategy (Kathuria et al., 2007; Porter, 1985, 2000; Skinner, 1969, 1985). (2) These studies define competitive advantage strategies (Dangayach & Deshmukh, 2006; Ward & Duray, 2000). (3) The literature correlates the direct effect of competitive advantage strategy and firm performance (Amoako-Gyampah & Acquaah, 2008; Olhager & Feldmann, 2018). (4) These studies emphasize the development of resource capabilities to support a company’s competitive advantage strategy (Jarzabkowski et al., 2016; Sharma & Kharub, 2014).\n\nOrganizations must build a competitive advantage to develop a business focusing on its target market. Meanwhile, in business, a competitive advantage category is needed, according to Barney (1991), VRIN: Valuable, Rare, Inimitable, and Non-Substitution. If this competitive advantage is built properly, the continuity of the organization or company will continue in the long term (Jacobsen, 1988; Porter, 1985). According to Porter (1989, 1995), Barney (1991, 1995), Christensen (2006), Sigalas, Economous, and Georgopoulos (2013), Stonehouse and Snowdon (2007), and Nkundabanyanga, et al. (2014).\n\nMeanwhile, organizations that face environmental pressures with dynamics at an uncertain level of turbulence must be able to act creatively, flexibly, and proactively for the emergence of solution-oriented and elastic organizational behavior to ensure that they can compete (Kantur & İşeri-Say, 2012). These three actions are included in the organization’s competitive strategy to outperform its competitors. By acting creatively, flexibly, and proactively, organizations can offer products that are different from those in the market or offer similar products at more competitive prices.\n\nTo compete and win against competitors, the company must have a competitive advantage strategy by encouraging different advantages, such as price advantages focusing on the target market, advantages of the network owned, advantages of having resources, and advantages of good name/reputation. This will encourage the company to act creatively and innovate continuously, ahead of similar competitors and dare to take risks (Korutaro Nkundabanyanga et al., 2014; Sigalas et al., 2013; Stonehouse & Snowdon, 2007). This is in line with transformational entrepreneurship behavior that always transforms by daring to take risks, act proactively and innovate continuously.\n\nUltimately, Doe (1994) emphasized that organizations with high resilience capabilities must be supported by resource capabilities, including good human resources. This will help them absorb crises and disasters resulting in drastic changes and view change as an opportunity that must be seized because it benefits the organization as a whole.\n\nThe characteristics of organizations with high resilience include timely and appropriate responses and the capacity for creative renewal (Kantur & İşeri-Say, 2012). That is, the response consists of proactive, innovative, and risk-taking behaviors (Kantur & İşeri-Say, 2012). Meanwhile, Hunter (2006) argued that resilient individuals who have high resilience can change crises by carrying out organizational transformation through transformational entrepreneurship behavior (Maas et al., 2019; Maas & Jones, 2017) to generate individual and organizational growth on an ongoing basis.\n\nChange-oriented organizational leaders invariably anticipate sudden changes that disrupt environmental situations and conditions to continue bringing the organization to improve its performance (Lafley, 2009). This leader must bring the organization to an entrepreneurial spirit by innovating, acting proactively, and taking risks (Covin & Slevin, 1991; Miller & Friesen, 1982). Bass (1985) and Howell and Avolio (1993) argued that transformational leadership is related to innovation in organizations. Likewise, Crant (2000) and Deluga (1998) found that transformational leaders are associated with transformational behavior, including transformational behavior that is proactive, innovative, and willing to take risks.” In other words, transformational leadership has been known to be associated with entrepreneurship.\n\nTherefore, a need exists to renew thinking to stimulate entrepreneurship to support socio-economic growth, including community development. In this context, “transformational entrepreneurship” is comprehensive and holistic in promoting entrepreneurship, including socio-economic development and community development, so that they can interact and collaborate synergistically to create positive opportunities and benefits and reach a wider scale (Maas et al., 2019).\n\nEntrepreneurship plays an extremely important role in encouraging sustainable socio-economic development. It needs to be studied further to determine whether the organization has a capable capability, adequate capacity, and a supportive ecosystem so that the right policies are needed to build socio-economic growth, including community development, in an optimal balance. As mentioned above, the key to success in dealing with volatile situations and conditions with high uncertainty is not just survival but sustainability. Therefore, companies do not need only economic benefits (short-term) but also social impacts (long-term) to ensure that the company’s success increases societal welfare (Maas et al., 2019; Maas & Jones, 2017; Xu & Maas, 2019). According to Marmer (2012), entrepreneurship can transform institutions so that they are profit-oriented (e.g., companies) to incorporate a social perspective into their goals.\n\nThe author argues that it is necessary to develop propositions to empirically prove the model review framework, as presented in Figure 4; this can be applied to companies in all industries, including microfinance institutions, multi-finance cooperatives, and MSMEs to create socio-economic growth and build the sustainability of the company itself, in addition to environmental and community development (Maas et al., 2019; Xu & Maas, 2019). This transformation of entrepreneurship behavior is needed in all organizations or companies for a sustainable existence. Therefore, this idea is needed, which is obtained through case studies of the entrepreneurship industry via the three main categories of organizational resilience, ambidexterity, and competitive advantage strategy (Kantur & İşeri-Say, 2012; Korutaro Nkundabanyanga et al., 2014; Lubatkin et al., 2006; Sigalas et al., 2013).\n\nThrough an in-depth study of the bibliography, the author realizes that the conceptual paper that builds a framework review model is still limited. The author supports that TEB can be applied to all companies and industries, including microfinance institutions, multi-finance cooperatives, and MSMEs. However, adopting a different approach is necessary, and examining the determinant factors and ecosystems supporting TEB formation may be required.\n\n\nDiscussion\n\nThe purpose of this in-depth study, review of the literature, and collection of research questions is collating all conceptual approaches to TEB and organizational resilience in companies and various industries to promote socio-economic growth and achieve environmental sustainability and balanced community development. Furthermore, an in-depth systematic review yielded a model framework (Figure 4). Based on the model, this framework is subsequently analyzed to identify research gaps and offer avenues for further research.\n\nThis literature review clearly describes the ecosystem that drives the development of transformational entrepreneurial behavior (Xu & Maas, 2019) and the determinants of organizational resilience (Kantur & İşeri-Say, 2012). However, research on transformational entrepreneurship behavior for a company can predominantly be conducted in the context of the private sector, state-owned companies, MSMEs, microfinance institutions, and multi-finance cooperatives. Therefore, the articles in the literature review regarding organizational resilience and its influence on transformational entrepreneurial behavior are still conceptual and represent a theoretical gap with respect to producing a basic framework or model.\n\nThe author attempts to link the research flow of organizational resilience and transformational entrepreneurial behavior more closely; Mass and Jones (2017) recommended conducting empirical research to be applied by companies in various industries to prove conceptual thinking. Likewise, they argued for considering the different determinants and ecosystems that shape them concerning transformational entrepreneurship behavior.\n\nReferring to the construct that forms transformational entrepreneurial behavior (Maas et al., 2019), the existence of an ecosystem, namely, factors outside the company that shape it (Xu & Maas, 2019). The importance of TEB in encouraging socio-economic growth does not stand alone (Maas et al., 2019; Xu & Maas, 2019). It is necessary to provide an ecosystem that supports infrastructures, policies/regulations, culture (from the parent company/coach, government, environment, and society), markets, and finance/funding (Isenberg, 2011; Mason & Brown, 2014; Oh et al., 2016; Smith, 2006; Xu & Maas, 2019) to ensure that the climate of innovation and entrepreneurship is formed. Ecosystems that include infrastructure, policies/regulations, culture, parent company support, the environment, and society significantly contribute in the literature review, particularly in building transformational entrepreneurship behavior (Xu & Maas, 2019).\n\nFurthermore, the author argues that the developed model framework can be implemented using quantitative studies through theory development, which is a theoretical gap in line with the definition of organizational resilience and transformational entrepreneurship behavior. Thus, the adaptation of constructs that shape organizational resilience and the determinants of transformational entrepreneurship behavior can be applied to companies in various industries.\n\nThis conceptual study, created through a literature review, explains the determinants of organizational resilience and transformational entrepreneurship behavior, but it has several limitations in this case. The first limitation is that the literature review focuses on academic journals located in Scopus, hosted by EBSCO and Web of Science (WoS) databases, both conceptual and empirical. Likewise, Podsakoff et al. (2005) argued that it is necessary to conduct an intensive literature review and improve the quality of the literature review and the findings obtained to ensure that a holistic picture is obtained. The next limitation is that the information obtained from the literature review is sometimes inadequate; therefore, the model of the review framework needs to be further developed to obtain a different view of other potential ecosystems.\n\nThe author refers to Pawson (2006) in selecting a paper that must follow the intended focus of its suitability and purpose. Indubitably, how the influence of organizational resilience on transformational entrepreneurship behavior can be applied in companies of all industries, especially for MSMEs and microfinance institutions, and multi-finance cooperatives. Furthermore, the limited quality of the information obtained from the literature review prompted us to develop only a probable theoretical framework.\n\n\nConclusion\n\nThe stream of research that focuses on TEB is still rare. Currently, this research is increasing, but more so on a conceptual level. Thus far, both conceptual and empirical research has focused more on entrepreneurship behavior that aims to achieve economic gain. Therefore, the literature review in this conceptual paper aims to produce research paths for the present and the future, including the determinants and ecosystems that shape TEB, and to generate broad insights that can be implemented in contemporary companies of all industries. Furthermore, this study also focuses on the effect of organizational resilience on transformational entrepreneurship behavior and the determinant factors shaping organizational resilience, rooted in an in-depth literature review.\n\nThe author conducts a careful review of the literature to identify the theoretical gaps that have been vague and then combines two streams of research—namely, organizational resilience and transformational entrepreneurship behavior—in building a model framework. Therefore, we developed an integrative review framework (Figure 4) as an empirical research model. Finally, numerous future research opportunities exist to develop other review framework models previously developed by scholars.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare: PRISMA and PRISMA abstract checklists and flow chart for ‘How to link organizational resilience to transformational entrepreneurship behavior as theoretical framework gap’. https://doi.org/10.6084/m9.figshare.22591693.v1. (Gunawan, 2023).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAdler PS, Goldoftas B, Levine DI: Flexibility versus efficiency? A Case study of model changeovers in the Toyota production system. Organ. Sci. 1999; 10(1): 43–68. Publisher Full Text\n\nAldrich HE, Zimmer C: Entrepreneurship through social networks.Sexton DL, Smilor RW, editors. The Art and Science of Entrepreneurship. 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Publisher Full Text\n\nZahra SA: The Resource-based view, resourcefulness, and resource management in startup firms: A Proposed research agenda. J. Manag. 2021; 47(7): 1841–1860. Publisher Full Text" }	[ { "id": "183922", "date": "10 Jul 2023", "name": "Andreas Walmsley", "expertise": [ "Reviewer Expertise Entrepreneurship" ], "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 uses a systematic literature review to explore the relationship between organisational resilience and transformational entrepreneurship. The focus on transformational entrepreneurship in particular is welcome; it is an important concept with an increased amount of research being afforded its investigation (as also demonstrated in the paper, Figure 2). The study, based on 22 included articles that were reviewed, develops a theoretical framework whereby a number of factors of the ecosystem are presented that influence transformational entrepreneurship behaviour outcomes. The four categories of factors that together offer organisational resilience are: psychological capital, ambidexterity, competitive strategy and leader/member exchange. All of this takes place within a broader government regulatory framework. The study thereby also taps into a stream of literature that seeks to better understand the role of context in shaping entrepreneurship. Results should be of interest to those interested in transformational entrepreneurship specifically, but also the wider community of enterprise/entrepreneurship scholars.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [] }, { "id": "183921", "date": "10 Jul 2023", "name": "Gideon Maas", "expertise": [ "Reviewer Expertise Entrepreneurship." ], "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 systematic literature review that attempts to explore transformational entrepreneurship behavior, socio-economic growth and sustainability, community development, and organizational resilience. The authors explained the systematic literature review process they followed in detail. They provided limitations of this research which include the limited number of research articles. As the research grows over time, more detailed and deeper discussions would be possible.\n\nThe article can do with another round of light touch editing.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [] }, { "id": "183920", "date": "10 Jul 2023", "name": "Odafe Egere", "expertise": [ "Reviewer Expertise Transformational entrepreneurship and entrepreneurial development." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe systematic review provided a well structured insight into understanding TEB considering OR. The background and rationale is well presented. The method and analysis is well detailed and would help future research. The review would help further research exploring TEB and the propositions discussed would inform additional layers of research, which is focus in deepening this knowledge area. An effective conclusion is discussed and provided the review contribution and future research opportunities.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-761
https://f1000research.com/articles/12-758/v1	28 Jun 23	{ "type": "Systematic Review", "title": "Secondary polycythemia and venous thromboembolism: a systematic review", "authors": [ "Amelia Panjwani", "Venkata Sathya Burle", "Rhea Raj", "Sneha Thomas", "Vasavi Gorantla", "Amelia Panjwani", "Venkata Sathya Burle", "Rhea Raj", "Vasavi Gorantla" ], "abstract": "Background Secondary polycythemia is an acquired condition characterized by an elevation in red blood cell (RBC) mass either in response to tissue hypoxia or inappropriate erythropoietin (EPO) secretion. It is proposed that the elevation of RBC mass in secondary polycythemia can lead to hyperviscosity and VTE. This systematic review aims to assess the relationship between secondary polycythemia and venous thromboembolism and discuss diagnostic strategies and management of secondary polycythemia and VTE. Methods This systematic review was conducted on September 2, 2022, and followed PRISMA guidelines to select and analyze relevant articles using the following databases: PubMed, ScienceDirect, and CINAHL. The queries used were “secondary polycythemia AND venous thromboembolism,” “secondary polycythemia AND deep vein thrombosis,” “secondary polycythemia AND pulmonary embolism,” “chronic obstructive pulmonary disease AND venous thromboembolism,” “chronic obstructive pulmonary disease AND deep vein thrombosis,” “chronic obstructive pulmonary disease AND pulmonary embolism,” “high altitude AND venous thromboembolism,” “high altitude AND deep vein thrombosis,” “high altitude AND pulmonary embolism,” “smoking AND venous thromboembolism,” “smoking AND deep vein thrombosis”, “smoking AND pulmonary embolism”, “hypoventilation AND venous thromboembolism”, “hypoventilation AND deep vein thrombosis”, “hypoventilation AND pulmonary embolism”, “testosterone AND venous thromboembolism”, “testosterone AND deep vein thrombosis”, and “testosterone AND pulmonary embolism.” The search duration was set from 2012–2022. Relevant publications were selected based on the inclusion and exclusion criteria. Results The initial search generated 5,946 articles. After narrowing the search based on inclusion and exclusion criteria, 30 articles were selected for this systematic review. Conclusion We found evidence to support the relationship between secondary polycythemia and VTE. Therapies targeting the factors that lead to secondary polycythemia can correct it and prevent VTE progression. If VTE occurs as a result of secondary polycythemia, anticoagulation therapy is recommended or inferior vena cava filters if contraindicated.", "keywords": [ "Secondary Polycythemia", "Venous Thromboembolism", "Chronic Obstructive Pulmonary Disease", "Smoking", "High Altitude", "Obstructive Sleep Apnea", "Testosterone Therapy", "erythropoietin" ], "content": "Introduction\n\nPolycythemia is an increase in red blood cell mass and can be categorized as primary or secondary polycythemia.1,2 Primary polycythemia encompasses germline mutations that cause an overproduction of red blood cells (RBCs).1 Germline mutations could affect hematopoietic growth factor erythropoietin (EPO) function or circulation, partial pressure of oxygen (P50), or intracellular oxygen sensing.3 Conversely, secondary polycythemia is acquired over a patient’s lifespan. This could result from a malignant neoplasm of hematopoietic stem cells or other organ disease states. Tissue hypoxia is one of the most frequent disease states responsible for the development of secondary polycythemia.3 Other causes are pulmonary disease, cyanotic heart disease, obstructive sleep apnea, renal cell carcinoma, and renal lesions.1,2 Further, acquired polycythemia can directly affect the expression of EPO, triggering a dramatic increase in EPO production.2 EPO is critical for starting the cascade of pathways necessary for red blood cell production.2 Thus, other parts of the red blood cell production pathway downstream of EPO can be impacted to lead to acquired polycythemia.\n\nIn hypoxia-induced disease states, reduced tissue oxygenation results in an upregulation of EPO as a compensatory mechanism.2 Red blood cell mass increases in an effort to improve tissue perfusion but does not mediate the longstanding hypoxemia.4 As a result, EPO, and subsequently red blood cells, are continuously produced. Blood viscosity dangerously increases to a point where unintentional blood coagulation can occur.2 Studies have also suggested that plasma fibrinogen plays a prominent role in the hemostatic imbalance, as it has impaired functionality in patients with secondary polycythemia.5 This highlights just one aspect of the complex blood profile of patients with secondary polycythemia in which there is an increased risk of thrombosis.\n\nDue to the complex hemostatic profile of patients with secondary polycythemia, thrombosis is an outcome that must be analyzed for necessary interventions to be made; in particular, venous thromboembolism will be explored as it pertains to secondary polycythemia and its hypercoagulable state.2 Venous thromboembolism (VTE) encompasses both deep vein thrombosis (DVT) and pulmonary embolism (PE).6 DVT is classified as a thrombosis originating in a deep vein, typically characterized as either an upper extremity DVT or a lower extremity DVT.7 PE differs from DVT in that it describes a thrombus that travels from its origin and gets lodged within the pulmonary arteries.8 PE may result in immediate death.8 Our systematic review will expand on the correlation between patients with diagnosed secondary polycythemia – excluding patients with Polycythemia Vera and other malignant neoplasms leading to secondary polycythemia – and subsequent VTE. Tissue hypoxia, chronic obstructive pulmonary disease, smoking, high altitude, obstructive sleep apnea, and testosterone therapy will be closely examined due to their association with secondary polycythemia. We will also discuss possible management methods and diagnostic interventions for patients with secondary polycythemia and VTE.\n\n\nMethods\n\nThis systematic review paper strictly adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.9 PRISMA was followed as it is a reliable method for selecting relevant publications to be included in systematic reviews and meta-analyses.9 A literature search for all articles about Secondary Polycythemia and VTE was conducted on September 2, 2022, using the following databases: PubMed, ScienceDirect, and CINAHL. The keywords used to identify publications were “secondary polycythemia AND venous thromboembolism,” “secondary polycythemia AND deep vein thrombosis,” “secondary polycythemia AND pulmonary embolism,” “chronic obstructive pulmonary disease AND venous thromboembolism,” “chronic obstructive pulmonary disease AND deep vein thrombosis,” “chronic obstructive pulmonary disease AND pulmonary embolism,” “high altitude AND venous thromboembolism,” “high altitude AND deep vein thrombosis,” “high altitude AND pulmonary embolism,” “smoking AND venous thromboembolism,” “smoking AND deep vein thrombosis,” “smoking AND pulmonary embolism,” “hypoventilation AND venous thromboembolism,” “hypoventilation AND deep vein thrombosis,” “hypoventilation AND pulmonary embolism,” “testosterone AND venous thromboembolism,” “testosterone AND deep vein thrombosis,” and “testosterone AND pulmonary embolism.” A focused keyword search was utilized to eliminate articles that did not contain both terms, as there were not a significant amount of studies containing both terms. The search duration was set from 2012-2022. We included case-control, cohort studies, comparative studies, clinical studies, prospective studies, retrospective studies, longitudinal studies, and observational studies. Once the search was complete, four co-authors manually screened the results and drew out relevant data from each article. We acknowledge that despite our genuine and maximal efforts, some relevant publications may have accidentally been left out. Our initial search generated 5,946 articles. After the manual screening, we narrowed the selection using our inclusion and exclusion criteria, and a total of 27 articles were ultimately included in this systematic review (Figure 1).\n\nThe following inclusion criteria were applied: studies in English, human studies or in vivo, published over the past 10 years, primary or original research publications, full-text articles, and relevance to the research topic.\n\nCriteria for exclusion were as follows: animal studies or in vitro, review or systematic review articles, editorials and letters to the editor, practice guidelines, abstracts, book chapters, not full-text articles, publications with publication dates outside of the range (2012–2022), duplicates, and articles that are not relevant to our review. This information is visually presented in the PRISMA flow diagram (Figure 1).\n\n\nResults\n\nOur literature search yielded 5,946 articles: 454 from PubMed, 5,471 from ScienceDirect, and 21 from CINAHL. A total of 5,819 articles were removed based on the exclusion criteria (animal studies, reports, reviews or systematic reviews, abstracts, letters to the editor, book chapters, abstracts, articles that were not full-text, duplicates) and then 127 research articles were left to continue to be sorted through. Then, articles based on the content of diagnostic techniques, management, and treatment of VTE/PE/DVT and relevance to our topic were also screened and checked for eligibility. Based on this screening, an additional 97 articles were excluded, leaving 27 relevant publications to be incorporated into the systematic review (Figure 1). There were four case–control studies, 16 cohort studies, one comparative study, one clinical study, two prospective, one retrospective study, one longitudinal, and one observational study. The study characteristics are included in Table 1.\n\nVTE: venous thromboembolism, DVT: deep vein thrombosis, DVT: deep vein thrombosis, COPD: chronic obstructive pulmonary disease, OSA: obstructive sleep apnea.\n\n\nDiscussion\n\nRBC mass ranges from 23 to 29 mL/kg in healthy adult women and 26 to 32 mL/kg in adult men.2,10 Polycythemia is classified as an abnormal increase in red blood cell mass.10 Hematocrit values greater than 48% in women and greater than 51% in men, and hemoglobin values greater than 16.5 g/dL in women and 18.5 g/dL in men can be indicative of polycythemia.10 An elevation in RBC mass characterizes secondary polycythemia due to a physiologically appropriate response to chronic hypoxemia or due to a physiologically inappropriate secretion of factors that promote erythropoiesis.2,10 Polycythemia increases blood viscosity, which causes a diverse set of complications, including ischemia.2,10 Causes of secondary polycythemia due to chronic tissue hypoxia include COPD, smoking, high altitudes, hypoventilation syndromes such as obstructive sleep apnea and obesity, and androgens like testosterone.2,11,12\n\nChronic hypoxemia drives erythropoiesis, which is the term used to describe the process of producing and maintaining RBC mass.2 Erythropoiesis is heavily regulated by various hormones, factors, and receptors, including erythropoietin (EPO).2,13 EPO’s expression is stimulated in response to hypoxia-inducible factors.2,13 The resultant physiological increase in erythrocytes enhances the oxygen-carrying capacity of the blood to facilitate adequate oxygen perfusion to hypoxic tissues.2 Despite this physiological process, complications may arise. Complications of secondary polycythemia can include strokes, pulmonary hypertension, blood hyperviscosity, and venous thromboembolism.2 In a 2016 study conducted in the USA, a diagnosis of VTE was found in 4.8% of patients with secondary polycythemia, whereas only 2.3% of patients without secondary polycythemia developed VTE.11 After adjusting for confounding variables like age, malignancy, strokes, previous VTEs, and pregnancies, the 2016 study concluded that patients with secondary polycythemia continued to pose a significantly greater risk in the development of VTE in comparison to patients without a secondary polycythemia diagnosis (p<0.01, OR: 1.87%; 95 CI: 1.58–2.22).11 Furthermore, a 2010 Serbian-based study on patients with chronic hypoxemia indicated that patients with secondary erythrocytosis had a significantly higher risk of developing pulmonary embolisms in comparison to chronic hypoxemic patients without secondary erythrocytosis (p<0.001).14 Articles and statistical findings discussed in this review strongly associate Secondary Polycythemia and its causes, such as COPD, smoking, high altitudes, obstructive sleep apnea, and testosterone, with the development of venous thromboembolism.\n\nThe pathophysiology detailing the mechanisms of how COPD leads to hypoxemia, resulting in secondary polycythemia and increasing the risk of VTE, DVT, and PE, still needs to be clearly defined. This section aims to compile the currently proposed pathophysiological mechanisms to gain further comprehension of the role of secondary polycythemia in the development of VTE. In a cross-sectional study, it was concluded that secondary polycythemia had a significant prevalence amongst COPD patients, as 10.8% or 26 out of 241 patients with COPD were also found to have secondary polycythemia.15\n\nCOPD is a chronic respiratory disease with obstructive breathing patterns and is classified into emphysema and chronic bronchitis.16 The underlying cause of hypoxemia in mild, advanced, and acute exacerbations of COPD is a direct result of a mismatch in the ventilation/perfusion (V′/Q′) ratio.17 Emphysema is characterized by ventilation in areas of the lungs that are not properly perfused.17 This occurs due to the destruction of elastic fibers in the alveolar walls leading to a collapse of alveoli and obstruction of airflow; moreover, there is a loss of pulmonary capillaries and total surface area of alveoli.17 As a result, patients with emphysema have a high V′/Q′ ratio leading to hypoxemia.17,18 However, chronic bronchitis results in hypoxemia in a different pathophysiological mechanism. Chronic bronchitis is characterized by decreased ventilation in perfused areas of the lungs.17 Obstruction of bronchi due to inflammation of the bronchial mucosa, hypersecretion of mucus, and fibrosis or edema is seen.17 As a result, patients with chronic bronchitis have an obstruction of airflow, leading to a low V′/Q′ ratio and hypoxemia.17 As COPD progresses, worsening of the V′/Q′ ratio mismatch and hypoxemia occurs.19 Rodríguez-Roisin et al. concluded that as COPD progressed, there was a worsening of the V′/Q′ ratio mismatch as well as irregularities in the pulmonary blood gasses; however, in Global Initiative for Obstructive Lung Disease (GOLD) stage IV, there was only a modest worsening of the V′/Q′ ratio mismatch when compared to GOLD stage I.19,20 A low V′/Q′ ratio and a decreased mixed venous oxygen tension (PvO2) are also seen in acute exacerbations of COPD (AE–COPD) due to the accumulation of mucus, inflammation of bronchi, and bronchospasm.17 Therefore, hypoxemia occurs during acute exacerbations in COPD patients.17 Overall, COPD places patients in a state of chronic hypoxemia due to the persistence of airflow obstruction, leading to an upregulation of the hypoxia-inducible transcription factor-1 (HIF-1) and the release of EPO.18 This release of EPO results in secondary polycythemia, therefore, increasing the levels of hematocrit and red blood cell mass.21 As stated previously, an increase in hematocrit results in an increase in blood viscosity and promotes a state of hypercoagulability, increasing the risk of developing a VTE.2,10,22 Ristić et al., in a prospective study, found that 39% of patients with severe exacerbations of COPD or pulmonary failure developed PE as opposed to only 11.06% of patients with severe exacerbations of COPD or pulmonary failure developed PE.23 Therefore, this study concluded that polycythemia is an important risk factor for developing PE in patients with chronic hypoxemia, including those with severe exacerbations of COPD or pulmonary failure.23\n\nNumerous studies have concluded that an association between COPD and the development of VTE, DVT, and PE exists. Chen et al. found that patients with COPD had an increased incidence of deep vein thrombosis, 18.78 per 10,000 person-years, compared to the non-COPD patients, 13.36 per 10,000 person-years.24 A retrospective cohort study with over a million participants revealed that patients with COPD had a greater prevalence of DVT and PE than the general population.25 In the general population, there were 138 participants with DVT and 113 participants with PE; however, in COPD patients, there were 637 patients with DVT and 1,185 patients with PE.25\n\nDespite the prevalence of DVT, many studies concluded that pulmonary embolisms are more prevalent in COPD patients. A clinical study revealed that the common initial VTE in COPD patients is PE with or without DVT (59%).26 Bertoletti et al., in a prospective cohort study, stated that pulmonary embolisms are the most common type of VTE amongst COPD patients, and the incidence of PE is higher in comparison to patients who do not have COPD (OR 1.64, 95% confidence interval, 1.49–1.80).26 In a retrospective cohort study, de-Miguel-Diez et al. also concluded that COPD patients are more likely to experience PE than patients with COPD because the study found that patients with COPD had a higher incidence of PE than patients without COPD.27 Another clinical study found that COPD patients had a higher incidence of PE (1.37/10,000 persons/year) when compared to the control group who did not have COPD and had a four-times decrease in the incidence of PE (0.35/10,000 person/year).28 Kubota et al. also concluded that pulmonary embolisms are associated stronger with COPD than with DVTs and discovered that the risk of VTE was increased in patients with respiratory symptoms and normal spirometry (hazard ratio: 1.40) or COPD (hazard ratio: 1.33).29 Pulmonary embolisms are also the common type of VTE seen in patients with asthma–COPD overlap syndrome (ACOS) as opposed to patients without ACOS (adjusted HR of pulmonary embolism is 2.08, 95% CI, 1.56–2.76).30\n\nThe risk of VTE is typically increased as COPD severity increases.31–33 In a retrospective clinical study with 551 COPD patients, the severity of COPD described by the GOLD staging system revealed an increased risk of VTE as the severity of COPD increased (OR = 1.77, p=0.035).33 Likewise, Børvik et al. found the HR for VTE in patients with stage I and stage II COPD was 1.09, while the HR for VTE in patients with stage III and IV COPD was 1.92.32 Børvik et al. findings also show an increased risk of VTE as the COPD severity increased.32 However, Morgan et al. discovered that although there is a 17% increase in the risk of VTE from GOLD Stage 1 to Stage 2 (OR =1.17; 95% CI: 1.03–1.33), there was no increase in odds of developing a VTE in GOLD Stages 3 and 4 when compared to GOLD Stage 1 (OR: 1.16; 95% CI: 1.02–1.33).31 As mentioned above, the lack of increased odds of developing a VTE can be attributed to only a modest worsening of the V′/Q′ ratio mismatch in GOLD Stage IV compared to GOLD stage I.19\n\nAn increased risk of developing VTE can be identified by noticing the signs and symptoms of COPD. Dong et al., in a retrospective clinical study, noted that visible emphysema is an independent risk factor for the development of VTE events in patients with COPD (OR: 3.54, p=0.03).33 Similarly, COPD patients with severe respiratory symptoms such as dyspnea, phlegm, and cough had more than a 1.4–2-fold risk of developing VTE.32\n\nThe current pathophysiological mechanisms of how COPD results in secondary polycythemia can be associated with the prevalence of VTE patients with COPD. As a result, it is probable that an increased risk of developing VTE is correlated to developing secondary polycythemia in COPD patients.\n\nThe pathophysiology describing how cigarette smoking leads to hypoxemia, resulting in secondary polycythemia and increasing the risk of venous thromboembolism (VTE), has not been clearly defined or investigated. This section aims to assemble proposed pathophysiological mechanisms to understand further the role of secondary polycythemia in developing VTE.\n\nSmoking results in chronic hypoxemia leading to a type of secondary polycythemia known as smoker’s polycythemia.2,10 Smoker’s polycythemia is identified as a combination of secondary polycythemia and relative polycythemia due to a decrease in the plasma volume as a result of exposure to chronic tobacco smoke.22 Cigarettes contain over seven thousand different chemicals from which nicotine and carbon monoxide have been identified to result in smoking-related hypoxia.10 Nicotine acts as a peripheral vasoconstrictor, resulting in decreased delivery of oxygen to the peripheral tissues, leading to hypoxia.10 Additionally, the carbon monoxide in cigarettes impairs the body’s normal gas exchange, further contributing to the hypoxia seen in cigarette smokers.10 Carbon monoxide has a higher affinity for hemoglobin than oxygen; as a result, carbon monoxide binds with hemoglobin more preferentially, resulting in the formation of carboxyhemoglobin.34 This formation of carboxyhemoglobin increases hemoglobin’s affinity for oxygen, causing a left shift of the carboxyhemoglobin dissociation curve, and decreases oxygen release from hemoglobin, causing a reduced delivery of oxygen to the kidneys and the release of erythropoietin.2,34 In a clinical study, cigarette smoking was found to reduce subcutaneous tissue oxygen tension for approximately fifty minutes following a cigarette; therefore, a person smoking one cigarette pack a day would experience tissue hypoxia for approximately 15–20 hours each day.35 Thus, chronic smokers experience sustained hypoxemia, leading to erythropoietin (EPO) release and erythropoiesis resulting in an increase in red blood cell plasma concentration.2,34 Despite this, some studies concluded that smoking and EPO levels have an inverse relationship, indicating that the secondary polycythemia which develops is not a result of increased EPO.36,37 In a clinical study with 40 smokers and 40 non-smokers, the smokers lacked elevated EPO; however, an increase in EPO receptor mRNA expression was found, which supported the increase in RBC count, hemoglobin, and hematocrit levels seen.37 In addition to the changes in EPO levels and erythropoiesis, smoker’s polycythemia also causes hemoconcentration, which is a shrinkage of the plasma volume leading to a relative increase in hematocrit2,34,38 Overall, cigarette smoking increases the hemoglobin, mean corpuscular volume, and mean corpuscular hemoglobin concentration, which in turn increases the hematocrit levels in the plasma.10 The resulting elevation in hematocrit levels directly increases blood viscosity.2,22 Hematocrit levels and blood viscosity share a non-linear relationship in which minute increases in hematocrit generate disproportionate increases in blood viscosity.22 The resulting blood hyperviscosity precipitates a hypercoagulable state increasing the risk of developing a VTE.2,10,34\n\nSeveral studies have concluded that an association between smoking and the development of VTE exists. In a prospective cohort study, the cohort with chronic hypoxemia and secondary erythrocytosis had a statistically significantly (p<0.001) higher incidence of pulmonary embolism (39%) when compared to the cohort with chronic hypoxemia without secondary erythrocytosis (10%).14 Additionally, a comparative study investigating cardiovascular risk factors for VTE concluded that smoking status is associated with a higher risk of venous thromboembolism (HR: 1.38 in the Emerging Risk Factors Collaboration) with similar hazard ratios for deep vein thrombosis and pulmonary embolism in the UK Biobank (HR: 1.23, 95% CI).39 A meta-analysis of 13 studies found a relative risk of 1.30 for venous thromboembolisms in current smokers after adjusting for body mass index (BMI), concluding an increased risk of VTE in current cigarette smokers.40 Another prospective cohort study found that current smoking and the incidence of VTE were positively associated with hazard ratios of 1.52 and 1.32 in women and men, respectively.41 Moreover, cigarette smoking and the risk for VTE were found to be positively correlated as a dose-response relationship.41,42 A systematic review and meta-analysis of 21 studies found a dose-response relationship between the number of cigarettes smoked per day (1–14, 15–24, and >25 cigarettes) and the relative risk of VTE (RR: 1.20, 1.33, and 1.63), respectively.42 In women, smoking an additional five cigarettes per day has a 7% increase in the risk of venous thromboembolism in women revealing a positive association between smoking and VTE.43\n\nThe current proposed pathophysiological mechanisms of how smoking leads to secondary polycythemia can be linked to the incidence and prevalence of VTE/DVT/PE in current smokers. Therefore, it is plausible that the development of secondary polycythemia increases the risk of developing VTE.\n\nVenous thromboembolism development has been studied extensively among orthopedic surgeons to minimize the risk factors contributing to pulmonary emboli and deep vein thrombosis development.44 Several orthopedic procedure studies have identified higher altitudes as a modifiable risk factor predisposing individuals to develop VTEs.44 For example, a 2016 case–control study indicated high altitude as a significant risk factor in the development of VTE among patients undergoing knee arthroscopies.45 In a study conducted in 2006, the risk of developing DVT increased 24.5-times among lowland residing soldiers in higher altitudes for an extended period compared to lowland soldiers residing in low altitudes for an extended period.46 In an American-based retrospective study evaluating DVT and PE development 90 days after lumbar fusion surgery, it was noted that fusions performed at altitudes below 100 feet resulted in fewer reported cases of PE and DVT in comparison to fusions conducted at altitudes above 4,000 feet (p=0.01, p=0.078).47 Another retrospective cohort study conducted in 2018 on patients with total shoulder arthroplasties supports the notion that high altitude is a risk factor for VTEs.44 The evidence provided in the 2018 study highlighted that higher altitude patients had a higher rate of PE both 1 month (p<0.001) and 3 months (p<0.03) after total shoulder arthroplasty operations in comparison to lower altitude patients receiving the same operation.44 Moreover, a case–control study performed in 2018 on patients undergoing total hip arthroplasty denoted that patient residing in higher altitudes had an increased rate of PE development when compared to patients at low altitudes at both 30 and 90 days postoperatively (p=0.003 and p<0.001).48 Another orthopedic study that evaluated VTE risks at varying altitudes indicated that high altitude patients had significantly increased odds of developing PE 30 days and 90 days postoperatively in comparison to lower altitude patients (OR: 1.47, p=0.029 and p<0.001).49 Similarly, a retrospective cohort study on patients who underwent knee arthroplasty highlighted patients at high elevation centers were at a significantly increased risk of VTE in comparison to low elevations (p<0.0001).50\n\nIn addition to the extensively documented research that suggests higher altitudes as a modifiable risk factor in the development of VTE following orthopedic procedures, a prospective study on individuals residing at varying altitudes showcased a 56.8% and an 81.9% incidence of DVT and PE among higher altitudes residents.51 The same study indicated a 13% and a 21.9% incidence of DV and PE among lower altitude residents.51\n\nThe body's compensatory mechanisms, when at higher altitudes, are believed to be a critical factor in the predisposition of patients to VTE.52 Hypoxia exposure at high altitudes leads to compensatory changes in blood oxygen affinity to aid in survival.53 Erythrocytosis, or the increased production of erythrocytes, is a thoroughly documented physiologically compensatory response to hypoxia found in populations living in higher altitude regions.54,55 The hypoxic environment stimulates hypoxia-inducible factors that act on the kidney and erythroid progenitor cells to secrete EPO.2 The EPO-stimulated red blood cell production improves tissue oxygenation and carrying capacity.2,54 Despite this improvement, the hematocrit can exceed 45% leading to hyperviscosity and complications such as thromboembolism.2,53\n\nA prospective study that evaluated thrombosis as a complication of extended stays at high altitudes associated a 30 times higher risk of vascular thrombosis with extended stays at higher and extreme altitudes.56 Some studies suggest that factors contributing to Virchow's Triad predispose individuals living at high altitudes to develop VTE.52 Virchow's triad includes blood stasis, hypercoagulability of blood, and vessel or endothelial damage.52,57 Individuals at high altitudes are exposed to environmental conditions such as hypoxia, hemoconcentration, low temperature, dehydration, severe weather, and thermally constrictive clothing.52 These exposures promote blood stasis and endothelial damage. In addition, the secondary polycythemia experienced by individuals residing in higher altitudes contributes to the hypercoagulable state of blood.52 Thus, VTE may occur due to the presence of all three factors leading to Virchow's triad at high altitudes.52\n\nSome literature suggests that VTE development in high altitude environments is attributed to the activation of the coagulation cascade leading to an increased risk of thrombosis.44 Other studies suggest that subjects living in areas of higher altitude have higher rates of thrombosis due to decreased levels of anticoagulants such as tissue factor pathway inhibitor (p<0.001), thrombomodulin (p=0.016), enhanced coagulation (FXa: p<0.001) (PVIIa: p<0.001), and dampened fibrinolysis.58 The enhancement of coagulation and dampening of anticoagulant factors could promote thrombus formation and subsequent VTE development in high altitude patients. In addition, other studies postulate that high altitude induced VTEs are caused by increased expression of platelet activation genes and elevated mean platelet count (p=0.005).51,59 Moreover, another study suggests that elevated VTE rates in high altitude patients are caused by a thrombotic milieu achieved by an agglomeration of erythrocytosis, elevated platelet count, increased plasma activation, raised fibrinogen levels, dehydration and hypoxia.44\n\nObstructive sleep apnea (OSA), a sleep-breathing disorder, is caused by recurrent episodes of complete or partial collapse of the airway during rest.60 OSA leads to sleep fragmentation and hypoxia, which results in polycythemia.61 The notion that OSA can lead to the development of secondary polycythemia was made evident in a 2015 study.60–63 Within this study, 77,518,944 discharges were analyzed, and a statistically significant association was made between OSA and secondary polycythemia (OR: 5.90, 95% CI or CI 5.64–6.17).63 Moreover, growing evidence suggests obstructive sleep apnea may be a risk factor for VTE.60,64 This is highlighted in a German-based prospective cohort study that stated high risk pulmonary embolism frequency was significantly greater among patients with moderate to severe sleep apnea (p=0.005).65 Further, research suggests that the severity of OSA may be indicative of acute pulmonary embolism manifestation.66 This phenomenon can be explained by increased hypoxia-inducible factor-1 (HIF-1) expression to compensate for the hypoxic environment created by the recurrent episodes of airway collapse in obstructive sleep apnea.60 Hypoxia-inducible factors act on the kidney and erythroid progenitor cells to upregulate the secretion of erythropoietin (EPO).2 EPO then stimulates erythrocyte production, resulting in polycythemia, to improve tissue oxygenation and O2 carrying capacity.2 The elevated hematocrit, blood viscosity, and hypercoagulability created by secondary polycythemia increase the risk of VTE.60,67\n\nThe pathophysiological mechanisms describing the role of testosterone in secondary polycythemia and VTE development is not entirely understood. This section aims to gather proposed pathophysiological mechanisms to comprehend the role of secondary polycythemia in developing VTEs. Testosterone replacement therapy (TRT) is a treatment commonly used to increase testosterone levels in aging men experiencing symptomatic hypogonadism.68,69 TRT has many benefits, including increasing libido, sexual function, muscle strength, bone density, and bone strength.69 Despite these benefits, a common adverse effect seen in TRT is a remarkable increase in hematocrit and hemoglobin levels, indicating either polycythemia or erythrocytosis.68 Testosterone and hematocrit have a linear dose–response association showing that testosterone directly increases hematocrit levels.70 Testosterone achieves this increase in hematocrit and polycythemia by increasing the set point of EPO for higher physiological hemoglobin levels and by increasing the bioavailability of iron by decreasing ferritin and hepcidin levels.71 Osterberg et al. concluded that using testosterone can increase hemoglobin levels by 5–7% and that more than 20% of men treated with TRT develop polycythemia.69 The prevalence of secondary polycythemia developing while using testosterone varies from 2.5% to greater than 40%, depending on the testosterone formulation and dose.70 Moreover, studies have noted that testosterone increases the risk of polycythemia by four-fold in men who are androgen deficient.70 Another issue of concern with using testosterone is the development of VTE. In 2014, the US Food and Drug Administration (FDA) mandated warning labels to be added to testosterone, stating that testosterone may increase the risk of developing VTE.68 This risk of VTE may be linked to the increases in hemoglobin and hematocrit in secondary polycythemia. Ory et al., in a retrospective cohort study found that men who were being treated with testosterone and had secondary polycythemia experienced an increased risk of developing VTE (OR: 1.35, p<0.001).12 As a result, this study concluded that during the first year of testosterone therapy, testosterone is a risk factor for developing VTE.12 As previously discussed, an increase in hematocrit results in hyperviscosity of the blood, which places the person in a hypercoagulable state, increasing the risk of VTE.2,22,10\n\nSecondary polycythemia can develop from various conditions and situations, including smoking, chronic obstructive pulmonary disease, high altitudes, hypoventilation syndromes, and testosterone therapy.2 As a result, a detailed history and physical examination are the first tools to diagnose secondary polycythemia.2 A physician should also aim to ask many questions to elicit the etiology of the secondary polycythemia, such as a history of smoking, COPD, recently moved or stayed in an area of higher altitude, shortness of breath or snoring, and testosterone therapy or use of anabolic steroids.2 Additionally, patients with secondary polycythemia may have symptoms such as headache, dizziness, fatigue, and pruritus, which are also essential to elicit from patients.2 During a physical examination, fingernail clubbing, cyanosis, staining of nails and teeth due to nicotine, high body mass index, or scratch marks may be seen.2\n\nMoreover, the use of diagnostic and laboratory tests are vital and supplementary to diagnosing secondary polycythemia. Secondary polycythemia is defined as an abnormal increase in red blood cell (RBC) mass which can be evaluated by a complete blood count (CBC) or using chromium-51.2 Patients with increased hemoglobin and hematocrit levels typically have an increase in RBC mass; therefore, a CBC can be used as it can evaluate both hemoglobin and hematocrit levels.72 In a healthy adult, the RBC mass is 26–32 mL/kg in males and 23–29 mL/kg in females; as a result, values higher than 32 mL/kg and 29 mL/kg are seen as elevations in RBC mass.2 Hemoglobin and hematocrit values greater than 185 g/L and 51% and 165 g/L and 48% for males and females, respectively, are typically associated with elevated RBC masses.2 Another method to assess RBC mass is using chromium-51; however, due to its limited supply, it is rarely utilized.2 Secondary polycythemia usually has increased serum levels of EPO, while primary polycythemia has decreased serum levels of EPO.72 Therefore, it is vital to check the levels of serum EPO to differentiate between primary and secondary polycythemia. However, it is imperative to note that normal levels of EPO can be seen in patients with secondary polycythemia.2 One of the primary causes of secondary polycythemia is hypoxia.2 Oxygen saturation can be checked using pulse oximetry, and oxygen saturation lower than 92% indicates hypoxia.2 Renal, hepatic, neurological, and genetic etiologies may also result in secondary polycythemia.2 As a result, a renal ultrasound and computed tomography (CT), hepatic ultrasound and CT, brain CT, and genetic mutation testing for hypoxia inducible factor-2 alpha (HIF2A) and erythropoietin receptor may be necessary depending upon each patients presentation.2\n\nCorrection of precipitating factors that lead to secondary polycythemia is the first line of management.2 If smoking precipitates hematologic abnormalities, it is recommended that the patient quit smoking and offer supportive, pharmacological, and psychological interventions.2 Low-flow O2 therapy to correct hypoxia is recommended in COPD-induced secondary polycythemia.2 However, oxygen toxicity and respiratory depression may develop from O2 therapy.2 Acute oxygen toxicity can manifest as central nervous system effects such as disorientation, dizziness, fatigue, paresthesias, tinnitus, and hyperventilation.73 Thus, it is imperative to monitor low O2 flow therapy administration.2 Phlebotomy, the removal of blood from a patient, can provide temporary relief in patients with secondary polycythemia.2 However, phlebotomy is contraindicated in patients who develop secondary polycythemia due to high altitude living.2 In patients who reside in high altitudes, secondary polycythemia is a physiologically appropriate compensation mechanism instilled to maintain proper tissue oxygenation.2 When managing patients with secondary polycythemia induced by high-altitude living, a continuous evaluation is necessary to maintain a balance between circumstantial tissue oxygenation and hyperviscosity.2 The management of secondary polycythemia varies based on the development of complications, such as thromboembolic episodes.2 Although not extensively studied in patients with secondary polycythemia, aspirin may be useful in preventing thromboembolic episodes as per data extrapolated from studies involving polycythemia vera.2,74 Additionally, venesection, a technique performed to decrease cardiovascular death and thrombosis in polycythemia vera, may be useful in managing severe secondary polycythemia complications.2,75\n\nVenous thromboembolisms are classified into two types: deep vein thrombosis and pulmonary embolism.76 Although DVTs and PEs share some diagnostic tests, some available tests are used only for either DVTs or PEs. Before imaging and laboratory tests are run, physicians first must suspect a DVT or PE based on the patient’s symptoms.76 Some symptoms of DVT are unilateral leg pain, tenderness, warmth, swelling, and redness, whereas some symptoms of PE are chest pain, dyspnea, hemoptysis, tachycardia, hypotension, and syncope.77 Once VTE is suspected, a physician must delegate the pretest probability (low, intermediate/moderate, or high) of a VTE in the patient so that a proper diagnostic plan can be chosen.76 The Wells model can determine the pretest probability for DVT, while the Wells model or the revised and modified Geneva rule can be used for PE.3 D-Dimer testing is a diagnostic test for DVT and PE.7 If the D-Dimer levels are higher than 500 ng/mL, it suggests that a patient has a PE; however, the age-adjusted D-Dimer threshold levels to rule out DVT are currently in progress.77 However, the American Society of Hematology (ASH) guidelines recommend against using positive results for D-dimer testing as the sole diagnostic test for VTE and suggests using additional diagnostic tests to diagnose VTE.7 Grégoire Le Gal et al., in the ASH 2018 guidelines, found that the sensitivities and specificities of D-Dimer testing for PE and DVT varied: PE (0.97, 0.39), upper extremity DVT (0.96, 0.47), and lower extremity DVT (0.96, 0.35), respectively.7\n\nCompression ultrasonography is a commonly used diagnostic test for DVT and is beneficial for first-time DVTs.76 Compression ultrasonography has a sensitivity of 0.90 and a specificity of 0.99 for diagnosing lower extremity DVT.7 Moreover, Doppler can be added to compression ultrasonography when needed to identify blood vessels precisely and when doubt arises regarding the compressibility of a specific segment of a blood vessel.76 Duplex ultrasound is used to diagnose upper extremity DVT and has a sensitivity of 0.87 and a specificity of 0.85.7 Another test that can be used to diagnose DVT is magnetic resonance venography which is typically used as an alternative when ultrasonography provides inconclusive results and when DVT is unable to be ruled out.77\n\nComputerized tomographic pulmonary angiography (CTPA) and V′/Q′ lung scans are the two most commonly used diagnostic tests for PE.76 CTPA is preferred over V′/Q′ scans because it diagnoses roughly 33% more PE and is readily available.76 However, CTPA exposes patients to ionizing radiation and utilizes a contrast medium.77 The contrast medium in CTPA can result in allergic reactions, can be toxic to the kidneys, and is contraindicated in patients who have severe renal impairment.77 The sensitivity and specificity of CTPA in diagnosing PE are 0.93 and 0.98, respectively.7 Magnetic resonance imaging (MRI) can be used in patients who cannot undergo CTPA as no intravenous contrast, and ionizing radiation is used.77 V′/Q′ scans are also commonly used to diagnose PE because it does not use intravenous contrast, expose the patients to significantly lower amounts of radiation, and have similar sensitivity and specificity to CTPA.77 Lastly, compression ultrasonography can also be used, and its sensitivity and specificity are 0.49 and 0.96, respectively.7\n\nVTE is categorized as deep vein thrombosis and pulmonary embolism6 and is a potentially critical consequence of secondary polycythemia.2 The general goal of VTE therapy is to prevent the extension of a thrombus and PE formation and to relieve symptoms while simultaneously preventing thromboembolic events in the future.76 The general management of VTEs includes three months of anticoagulant therapy such as low molecular weight heparins (LMWH), vitamin K antagonists, or direct factor Xa or direct factor IIa inhibitors.78 Regarding outpatient management of VTEs, LMWH and Vitamin K antagonists are generally employed.78\n\nIn patients with an acute phase of VTE, prompt initiation of full-dose anticoagulation with LMWH, UFH, fondaparinux, apixaban, or rivaroxaban is recommended to prevent morbidity and mortality.78,79 LMWH or UFH can be continued as monotherapy or transitioned to vitamin K antagonists, edoxaban, or dabigatran therapy.79 Thrombolytic therapies such as alteplase and reteplase are reserved for patients with severe VTE, massive PE, or DVT coupled with threatened limb loss.77,78,80 They are reserved for critical cases as thrombolytic drugs have the potential to worsen life-threatening conditions such as disseminated intravascular coagulation (DIC) and heparin-induced thrombocytopenia (HIT).80 In circumstances where anticoagulation therapy is contraindicated or has failed in patients with acute VTE, insertion of vena cava filters may be employed.77–79,81 Studies have shown that low intensity treatments are less effective at preventing recurrent thrombosis when compared to standard anticoagulation.76 Moreover, standard anticoagulation is as effective as high intensity treatments.76 However, if a patient refuses higher intensity and standard intensity treatment, lower intensity treatment is better at preventing recurrent thrombosis than an absence of therapy.\n\nVTE recurrence risk can be classified into an abundance of categories. If a patient has never reported a VTE but receives one due to trauma or surgery, the recurrence rate is low.76 However, patients with malignancy have an elevated risk of recurrent thrombosis.76 Thus, it is recommended that these patients receive anticoagulation therapy for six months with LMWH if renal function is not impaired.76,82 In pregnant women who develop DVTs, LMWH is recommended.76 Additionally, inferior vena cava filters may be considered in pregnant women who develop PE near term due to the risk of hemorrhage.76,81\n\n\nConclusion\n\nIn conclusion, compelling evidence exists to support the relationship between secondary polycythemia and the development of VTEs. Secondary polycythemia is a hematologic condition classified by an increase in RBCs driven by chronic hypoxia. We found evidence that supports the notion that secondary polycythemia can be precipitated by underlying hypoxic and pro-inflammatory conditions such as COPD, smoking, high altitude living, obstructive sleep apnea, and testosterone therapy, ultimately leading to VTE. The aforementioned conditions generate environments that elevate the expression of erythropoietin, causing a state of erythrocyte proliferation which leads to polycythemia. If erythrocyte proliferation exceeds a certain viscosity, unintentional blood coagulation can occur, leading to thrombotic and thromboembolic conditions. History taking and physical examination are pivotal in determining the underlying cause of secondary polycythemia. However, to accurately diagnose secondary polycythemia, elevated hematocrit, hemoglobin, serum EPO, and hypoxia must be observed. Further, if VTE is suspected, a pretest probability is recommended via the Wells model or Geneva criteria. D-dimer and compression ultrasonography can also be performed to diagnose VTE. PE specific diagnostic strategies include CTPA and V/Q scans. Furthermore, the treatment of secondary polycythemia begins with the correction of precipitating factors that lead to the development of the condition. Low oxygen flow therapy may be employed but must be monitored closely to avoid complications of oxygen toxicity. Repeated monitoring of high-altitude patients with secondary polycythemia is strongly advised, as erythrocytic compensation is necessary for survival at higher altitudes. If VTE develops as a consequence of secondary polycythemia, anticoagulation therapy must be employed. In patients wherein anticoagulation therapy is contraindicated, inferior vena cava filters may be considered. Finally, polycythemia vera management strategies such as aspirin therapy in the prophylaxis of thromboembolic episodes and venesection should continue to be explored in terms of efficaciousness in secondary polycythemia management.\n\n\nEthical statement\n\nNot applicable. No patient data or animal studies were used in this review.\n\n\nConsent from patients\n\nIn this review, no patient information was used. Consent is not applicable.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nPanjwani, Amelia; Burle, Venkata Sathya; Raj, Rhea; Thomas, Sneha; Gorantla, Vasavi (2023): Secondary Polycythemia and Venous Thromboembolism: A Systematic Review. figshare. Figure. https://doi.org/10.6084/m9.figshare.22535791.v1\n\n\nReferences\n\nKremyanskaya M, Mascarenhas J, Hoffman R: Why does my patient have erythrocytosis? Hematol. Oncol. Clin. North Am. 2012; 26(2): 267–283. PubMed Abstract \| Publisher Full Text\n\nHaider MZ, Anwer F: Secondary Polycythemia. 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PubMed Abstract" }	[ { "id": "194240", "date": "09 Aug 2023", "name": "Anders Erik Astrup Dahm", "expertise": [ "Reviewer Expertise General hematology", "venous thrombosis", "AML in elderly." ], "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 have done a systematic search for articles investigating non-malignant secondary polycythemia and association with VTE. In addition to searching for polycythemia and VTE they have searched for a number of conditions known to cause polycythemia and their association with VTE. The main result is a table of the included articles with their main findings. The Discussion addresses the various diseases and conditions related to polycythemia and the relation to VTE. The authors also addresses diagnosis and treatment of VTE in general and diagnosis and treatment of secondary polycythemia in general.\nGeneral comments:\nInvestigating whether or not non-malignant secondary polycythemia increases the risk for VTE is an interesting question, but I do not think the authors have selected a good method to do so. There are a number of weaknesses in the selection of articles, the referral to the selected articles, and the discussion of the articles. This may be because the rational for the systematic review also is unclear to me, and appear to be based on lack of knowledge on how polycythemia may cause thrombosis.\nSpecific comments:\nThe Introduction:\nWhat we know of polycythemia and thrombosis mainly stems from Polycythemia Vera (PV). Since this review is investigating all other causes of secondary polycythemia (understood as erythrocytosis) except PV, it would be useful to briefly describe PV and its relation to thrombosis for the reader, and also for the authors I think. Isn’t the underlying question here, although not directly stated by the authors, if non-malignant secondary polycythemia increases the risk of thrombosis like PV does? In short what we know of PV and thrombosis is that PV increases the risk of both arterial and venous thrombosis. About 2/3 of the thrombotic events are arterial, and about 1/3 are venous. Thus, VTE is not the main problem. The mechanism is unclear, but it is related to thrombocytosis and leukocytosis, not so much erythrocytosis. It also may be related to the acquired JAK2 mutation.\n\nMoreover, the main clinical problem with hyperviscosity of any cause, including erythrocytosis, is bleeding. Thus, the sentence “Blood viscosity dangerously increases to a point where unintentional blood coagulation can occur” is partly wrong. This is repeated in the Discussion several times.\n\nIt would perhaps have been more relevant to focus on both arterial and venous thrombosis, and avoid references to hyperviscosity as the main mechanism for polycythemia related thrombosis.\n\nThe sentence “Further, acquired polycythemia can directly affect the expression of EPO, triggering a dramatic increase in EPO production.” is also wrong. And this is not what reference 2 says. In PV, EPO is suppressed. In hypoxia/hypoxemia, the increase of EPO is the cause of the polycythemia.\n\nI think the selection of references in the Introduction is somewhat odd. Reference 2 is imprecisely referring to an abstract, but it should be referred to the full book chapter. Reference 5 is linked to a sentence about secondary polycythemia and fibrinogen, but the article is about cyanotic patients with congenital heart disease, which is not covered by this review. And wouldn’t it be relevant to refer to other similar articles? I quickly stumbled over a systematic review of by VR Bhatt on the same issue. Are there more?\n\nThe Methods:\nI think the article would have benefited from a PICO approach, even if interventions were not investigated. A stricter definition of the population, the comparator and the outcomes would have been better.\n\nI do not think it is wise to search for (almost) all diseases/conditions that are known to cause erythrocytosis and see if these diseases are associated with VTE. The risk of confounding is simply too high. For example, all diseases/conditions that cause hypoxemia may cause erythrocytosis, but hypoxemia is also at the same time a powerful stimulator of several parts of the coagulation system such as platelets, endothelial cells and tissue factor through other mechanisms. Hence, the causal link between hypoxemia and VTE may very well not be erythrocytosis. This is important. You should therefore exclude all articles which do not compare polycythemia with normocythemia.\n\nI rather think that the authors should have focused only on articles comparing erythrocytosis with non-erythrocytosis where the outcome was VTE or VTE + ATE. There are a few such articles included, e.g. Ory et al.\n\nAll systematic reviews are better if it includes a meta-analysis.\n\nThe Results:\nThe results are table 1 where the articles investigated are listed and the main interpretation written.\n\nI have not looked up all the articles, but some of them.\n\nAs a minimum I think the articles included should have measured whether the patients had polycythemia or not. I suspect that most of them have not, e.g., most of the articles on COPD and high altitude.\n\nAt least two of the articles are only abstracts (Giri 2016, and Ristic 2013), which makes it difficult to evaluate. I think they should have been excluded.\n\nThe authors tend to over-interpret the findings in the articles, which sometimes are different from the interpretation that the original article authors did. For example, in Børvik 2019 the original authors mention a number of possible causes for how hypoxemia in COPD patients may cause VTE, but polycythemia is not mentioned at all. In Giri’s 2016 abstract from ASH the authors specifically states that one cannot infer causality between polycythemia and VTE. The study by Ory et al from 2022 is one of the few relevant studies included in my opinion, but the odds ratio reported is not for VTE as the author state (in the Discussion), it is for the combination of MACE and VTE, i.e., both arterial and venous thrombosis. Also the odds ratio is very small.\n\nThe Discussion:\nThe discussion is too unfocused and covers too much.\n\nAll discussion regarding diseases and conditions that give hypoxemia, but where there are no measurements of polycythemia vs. normocythemia could be excluded. It is not relevant enough.\n\nThe paragraphs of diagnosis and treatment of polycythemia and diagnosis and treatment of VTE is not relevant and should not be part of this article. There are also a number of statements in these paragraphs that I disagree with professionally.\n\nThe Conclusion:\nBased on the selection of articles included in this review I disagree with the authors that “compelling evidence exists to support the relationship between secondary polycythemia and the development of VTEs”. On the contrary, I am not sure there are any evidence at all, but it is hard to say because it is not clear from table 1 which of the articles that are really relevant for this problem.\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? No", "responses": [] }, { "id": "234738", "date": "27 Feb 2024", "name": "François Girodon", "expertise": [ "Reviewer Expertise hematology" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAmelia Panjwani report a systematic review of the literature on the subject of venous thrombotic risks in secondary polycythemia. This is a question that deserves to be analyzed. The question should be: do patients with a given disease and polycythemia have a greater risk of thrombosis than patients with the same disease but without polycythemia? However, many of the articles cited explore only the incidence of venous thrombosis in a pathological context likely to give rise to polycythemia, compared with a healthy population, which includes a selection bias. In addition, the term polycythemia is somewhat overused, as it is not defined by the authors: is it only an increase in haemogram parameters (haemoglobin, haematocrit?) Compared with what threshold to define it? Polycythemia vera is defined as an increase in blood volume >125% of the theoretical value. An increase in hemoglobin or hematocrit is not always synonymous with true polycythemia; the absence of a clear definition can lead to misinterpretation of results (around 30% of men with hemoglobin > 180g/L do not have absolute polycythemia (cf Johannson P et a, BJH 2005). What thresholds did the authors use to define polycythemia? In practice, these thresholds differ from study to study.\nWhat is the information in the table results? For example, Article 1, Park et al, 2016 : Patients with COPD have a greater prevalence of PE and DVT in comparison to the general population. And so what ? To prove that it is through secondary polycythemia that this risk is higher, it would be necessary to compare 2 populations with COPD, one with polycythemia, the other without (with the same cardiovascular risk factors in the 2 groups, and that only polycythemia differs in the 2 groups). Polycythemia would be a marker of severity of COPD, but to prove a cause and effect link, other arguments are needed.\nIn conclusion, all the articles do not answer the same question, i.e. whether it is polycythemia that is responsible for the increased risk of thrombosis, or whether it is other factors associated with the respiratory situation. One of the articles cited relies on an elevated risk of thrombosis linked to hyperviscosity, which is then used as an argument for a risk linked to polycythemia: but on closer examination, we realize that it's hyperviscosity linked to monoclonal gammapathy, not polycythemia.\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", "responses": [] } ]	1	https://f1000research.com/articles/12-758
https://f1000research.com/articles/12-336/v1	27 Mar 23	{ "type": "Genome Note", "title": "The genome sequence of the Loggerhead sea turtle, Caretta caretta Linnaeus 1758", "authors": [ "Glenn Chang", "Samantha Jones", "Sreeja Leelakumari", "Jahanshah Ashkani", "Luka Culibrk", "Kieran O'Neill", "Kane Tse", "Dean Cheng", "Eric Chuah", "Helen McDonald", "Heather Kirk", "Pawan Pandoh", "Sauro Pari", "Valeria Angelini", "Christopher Kyle", "Giorgio Bertorelle", "Yongjun Zhao", "Andrew Mungall", "Richard Moore", "Sibelle Vilaça", "Steven Jones", "Glenn Chang", "Samantha Jones", "Sreeja Leelakumari", "Jahanshah Ashkani", "Luka Culibrk", "Kieran O'Neill", "Kane Tse", "Dean Cheng", "Eric Chuah", "Helen McDonald", "Heather Kirk", "Pawan Pandoh", "Sauro Pari", "Valeria Angelini", "Christopher Kyle", "Giorgio Bertorelle", "Yongjun Zhao", "Andrew Mungall", "Richard Moore", "Sibelle Vilaça" ], "abstract": "We present a genome assembly of Caretta caretta (the Loggerhead sea turtle; Chordata, Testudines, Cheloniidae), generated from genomic data from two unrelated females. The genome sequence is 2.13 gigabases in size. The majority of the assembly is scaffolded into 28 chromosomal representations with a remaining 2% of the assembly being excluded from these.", "keywords": [ "Caretta caretta", "Loggerhead sea turtle", "genome sequence", "chromosomal", "reptile" ], "content": "Species taxonomy\n\nEukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Testudinata; Testudines; Cryptodira; Durocryptodira; Americhelydia; Chelonioidea; Cheloniidae; Caretta; Caretta caretta Linnaeus 1758 (NCBI txid 8467).\n\n\nIntroduction\n\nThe loggerhead sea turtle, Caretta caretta, is one of only seven extant marine turtle species and is globally distributed throughout the subtropical and temperate regions of the Mediterranean Sea and Pacific, Indian and Atlantic Oceans (Wallace et al., 2010, Casale and Tucker, 2015). The species is divided in various Regional Management Units (RMUs) and management units (MUs) that vary greatly by population size, geographic range, and population trends (Wallace et al., 2010, Casale and Tucker, 2015, Shamblin et al., 2014). Events such as fisheries bycatch (Caracappa et al., 2018, Pulcinella et al., 2019), human intrusion and disturbance (Mazaris et al., 2009), oceanic pollution (Savoca et al., 2018), and climate change and severe weather (Alduina et al., 2020) have caused the global population to continuously decline (Casale and Tucker, 2015). Consequently, the highly migratory C. caretta requires the collaborative efforts of numerous international conservation and protection organizations (Species at Risk Act, 2002), and is currently listed as Vulnerable by the International Union for the Conservation of Nature (IUCN) (Casale and Tucker, 2015). The genome of C. caretta was sequenced as part of the Canadian BioGenome Project (CBP) and CanSeq150 initiatives. The C. caretta genome will provide insights into genomic diversity and architecture, and inform conservation genomics applications.\n\n\nMethods\n\nBlood samples from an adult female and a juvenile of unknown sex were collected from the Fondazione Cetacea (43.9940 N, 12.6745 E) by Nicola Ridolfi (veterinarian; Fondazione Cetacea). Animal husbandry and welfare were overseen by Fondazione Cetacea. The specimens were transferred to Canada with two CITES permits between institutions (IT002 and CA027).\n\nHigh-molecular weight (HMW) DNA was extracted from nucleated blood using the MagAttract HMW DNA kit (QIAGEN, Germantown, MD, USA). Nanopore genome libraries were constructed according to manufacturer instructions and sequenced using the PromethION instrument (Oxford Nanopore Technologies). A PCR-free genome library was sequenced in a multiplexed pool of an Illumina NovaSeq 6000 instrument S4 flowcell with paired-end 150 bp (PE150) reads. A Hi-C library was constructed using the Arima-HiC kit 2.0 (Arima Genomics, San Diego, CA) and the Swift Biosciences Accel-NGS 2S Plus DNA Library Kit (Integrated DNA Technologies, Mississauga, ON, Canada) and subjected to PE150 sequencing on an Illumina NovaSeq 6000 instrument. All lab work were performed at Canada’s Michael Smith Genome Sciences Centre at BC Cancer.\n\nAssembly was carried out using Redbean (Ruan and Li, 2019), followed by four rounds of racon (Vaser et al., 2017) polishing and medaka (medaka, n.d.) polishing. Scaffolding with Hi-C data was carried out using nf-core/hic workflow (Servant and Peltzer, 2019), Salsa (Ghurye et al., 2019) and LongStitch (Coombe et al., 2021). The Hi-C scaffolded assembly was polished using Illumina short-reads using Pilon (Walker et al., 2014). Four rounds of manual assembly curation and re-scaffolding with nf-core/hic workflow (Servant and Peltzer, 2019) and Salsa (Ghurye et al., 2019) corrected 54 missing/misjoins. These changes were visualized using JupiterPlots (Chu, 2018) and Juicer (Durand et al., 2016b). The final sequence was analyzed using BlobToolKit (Challis et al., 2020). Software tools and versions are listed in Table 3.\n\n* BUSCO scores based on the sauropsida_odb10 BUSCO set using v5.0.0. C= complete [S= single copy, D=duplicated], F=fragmented, M=missing, n=number of orthologues in comparison.\n\n\nResults\n\nThe genomes of two unrelated loggerhead sea turtles were sequenced from the same population collected from the Fondazione Cetacea hospital, Riccione, Italy. A total of 39-fold coverage in Nanopore PromethION long reads were generated from a single adult female. Approximately 50-fold coverage in Illumina NovaSeq6000 150 bp paired-end (PE150) reads and 18-fold coverage in Illumina NovaSeq6000 Hi-C sequencing were generated from a second individual. Primary assembly contigs from Nanopore data were further polished with Illumina PE150 shotgun sequencing data and scaffolded with Hi-C data. The final assembly has a total length of 2.13 Gb in 2007 sequence scaffolds with a scaffold N50 of 130.95 Mb (Table 1). The majority (98.0%) of the assembly sequence was assigned to 28 chromosomal-level scaffolds representing the species’ known 28 autosomes (Kamezaki, 1989, Machado et al., 2020) (numbered by sequence length; Figure 1–Figure 4; Table 2). Aligned reads from the second turtle to the final assembly had an estimated heterozygosity of 0.11% (2,449,606 heterozygous hits). Determining gene coverage using BUSCO, we estimated 96.1% gene completeness using the sauropsida_odb10 reference set (Manni et al., 2021). The assembly was compared to a previous chromosome-scale assembly of the closely-related green sea turtle, Chelonia mydas (Wang et al., 2013), which has been reported to hybridize with the loggerhead sea turtle (James et al., 2004, Vilaça et al., 2012). The loggerhead sea turtle assembly showed strong synteny to the green sea turtle assembly, as shown in Figure 5. The primary haplotype (rCheMyd1.pri.v2) of the green sea turtle was downloaded from NCBI on July 16, 2022.\n\nSnail plot showing N50 metrics, base pair composition and BUSCO gene completeness for C. caretta (rCarCar2) generated from Blobtoolkit v.2.6.4 (Challis et al., 2020). The plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 2,134,012,717 bp assembly. The distribution of chromosome lengths is shown in dark grey with the plot radius scaled to the longest chromosome present in the assembly (345,741,823 bp) shown in red. Orange and pale-orange arcs show the N50 and N90 chromosome lengths (130,956,235 and 23,648,662 bp, respectively). The pale grey spiral shows the cumulative chromosome count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot displays the distribution of GC (blue), AT (pale blue) and N (white) percentages using the same bins as the inner plot. A summary of complete (96.1%), fragmented (0.4%), duplicated (0.9%), and missing (3.5%) BUSCO genes in the sauropsida_odb10 set is show in the top right.\n\nGC-coverage plot of C. caretta (rCarCar2) generated from Blobtoolkit v.2.6.4 (Challis et al., 2020). Scaffolds are coloured by phylum with Chordata represented by blue and no-hit represented by pale blue. Circles are sized in proportion to scaffold length. Histograms show the distribution of scaffold length sum along each axis.\n\nCumulative sequence length of C. caretta (rCarCar2) generated from Blobtoolkit v.2.6.4 (Challis et al., 2020). The grey line shows the cumulative length for all scaffolds. Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the BUSCO genes tax rule, with Chordata represented by blue and no-hit represented by pale blue.\n\nHiC contact map of rCarCar2 assembly visualized using JuiceBox v2.13.07 (Durand et al., 2016a). Chromosomes are shown in order of size from left to right and top to bottom. As an additional confirmation for the quality of the assembly, the microchromosomes are visible as a cluster of spatially-associated contigs in the lower right, as reported in by Waters et al., 2021.\n\nFull genome alignment of Caretta caretta genome, rCarCar2 (right), and Chelonia mydas (green sea turtle) genome (primary haplotype v2), rCheMyd1 (left), generated using Jupiter Plot (Chu, 2018). The left of the circle shows 28 green sea turtle chromosomes and the right of the circle shows 28 loggerhead sea turtle chromosomes. Coloured bands represent synteny between the genomes, and lines crossing the circle indicate genomic rearrangements, or break points in the scaffolds.\n\nAnnotation for the loggerhead sea turtle genome assembly (GSC_CCare_1.0 (GCA_023653815.1)) was generated by the Ensembl Rapid Release gene annotation pipeline (Aken et al., 2016). The resulting Ensembl annotation includes 42,302 transcripts assigned to 19,633 coding and 4,161 non-coding genes (Caretta caretta - Ensembl Rapid Release). The loggerhead sea turtle assembly was also annotated for 54,583 protein sequences using RefSeq (GCF_023653815.1, PRJNA853764).", "appendix": "Data availability\n\nNational Centre for Biotechnology Information BioProject: Loggerhead Sea turtle (Caretta caretta) genome sequencing and assembly, rCarCar2. Accession number: PRJNA826225.\n\nThe genome sequence is released openly for reuse. The C. caretta genome sequencing initiative is part of the Canadian BioGenome Project and CanSeq150 Projects initiatives. All raw sequence data and the assembly have been deposited in INSDC databases. The genome is annotated through the Reference Sequence (RefSeq) database in BioProject accession number PRJNA853764. Raw data and assembly accession identifiers are reported in Table 1.\n\n\nReferences\n\nAken BL, et al.: The Ensembl gene annotation system. Database. 2016; 2016. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlduina R, Gambino D, Presentato A, et al.: Is Caretta caretta a carrier of antibiotic resistance in the Mediterranean Sea? Antibiotics. 2020; 9(3): 116. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCaracappa S, Persichetti M, Piazza A, et al.: Incidental catch of loggerhead sea turtles (Caretta caretta) along the Sicilian coasts by longline fishery. PeerJ. 2018; 6: e5392. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCasale P, Tucker A: Caretta caretta (amended version of 2015 assessment). IUCN red list of threatened species.2015. Publisher Full Text\n\nChallis R, Richards E, Rajan J, et al.: BlobToolKit – Interactive quality assessment of genome assemblies. G3: Genes, Genomes, Genetics. 2020; 10(4): 1361–1374. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChu J: Jupiter Plot: A Circos-based tool to visualize genome assembly consistency (1.0). Zenodo. 2018. Publisher Full Text\n\nCoombe L, Li J, Lo T, et al.: LongStitch: High-quality genome assembly correction and scaffolding using long reads. BMC Bioinformatics. 2021; 22(1): 534. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDurand N, Robinson J, Shamim M, et al.: Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Systems. 2016a; 3(1): 99–101. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDurand N, Shamim M, Machol I, et al.: Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Systems. 2016b; 3(1): 95–98. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGhurye J, Rhie A, Walenz B, et al.: Integrating Hi-C links with assembly graphs for chromosome-scale assembly. PLoS Comput. Biol. 2019; 15(8): e1007273. PubMed Abstract \| Publisher Full Text \| Free 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\nJames M, Martin K, Dutton P: Hybridization between a green turtle, Chelonia mydas, and Loggerhead Turtle, Caretta caretta, and the first record of a Green Turtle in Atlantic Canada. The Canadian Field-Naturalist. 2004; 118(4): 579. Publisher Full Text\n\nKamezaki N: Karyotype of the loggerhead turtle, Caretta caretta, from Japan. Zool. Sci. 1989; 6: 421–422. Retrieved 4 August 2022. Reference Source\n\nMachado CR, Glugoski L, Domit C, et al.: Comparative cytogenetics of four sea turtle species (Cheloniidae): G-banding pattern and in situ localization of repetitive DNA units. Cytogenet. Genome Res. 2020; 160(9): 531–538. PubMed Abstract \| Publisher Full Text\n\nmedaka: Sequence correction provided by ONT Research. Accessed 4 August 2022. Reference Source\n\nManni M, Berkeley M, Seppey M, et al.: BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 2021; 38(10): 4647–4654. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMazaris A, Matsinos G, Pantis J: Evaluating the impacts of coastal squeeze on sea turtle nesting. Ocean Coast. Manag. 2009; 52(2): 139–145. Publisher Full Text\n\nPulcinella J, Bonanomi S, Colombelli A, et al.: Bycatch of loggerhead turtle (Caretta caretta) in the Italian Adriatic midwater pair trawl fishery. Front. Mar. Sci. 2019; 6: 365. Publisher Full Text\n\nRuan J, Li H: Fast and accurate long-read assembly with wtdbg2. Nat. Methods. 2019; 17(2): 155–158. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSavoca D, Arculeo M, Barreca S, et al.: Chasing phthalates in tissues of marine turtles from the Mediterranean Sea. Mar. Pollut. Bull. 2018; 127: 165–169. PubMed Abstract \| Publisher Full Text\n\nServant N, Peltzer A: nf-core/hic: Initial release of nf-core/hic (v1.0). Zenodo. 2019. Publisher Full Text\n\nShamblin BM, Bolten AB, Abreu-Grobois FA, et al.: Geographic patterns of genetic variation in a broadly distributed marine vertebrate: New insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences. PLoS One. 2014; 9(1): e85956. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSpecies at Risk Act: SC 2002, c 29.\n\nVaser R, Sović I, Nagarajan N, et al.: Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017; 27(5): 737–746. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVilaça ST, Vargas SM, Lara-ruiz P, et al.: Nuclear markers reveal a complex introgression pattern among marine turtle species on the Brazilian coast. Mol. Ecol. 2012; 21(17): 4300–4312. PubMed Abstract \| Publisher Full Text\n\nWalker B, Abeel T, Shea T, et al.: Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014; 9(11): e112963. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWallace B, DiMatteo A, Hurley B, et al.: Regional management units for marine turtles: A novel framework for prioritizing conservation and research across multiple scales. PLoS One. 2010; 5(12): e15465. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang Z, Pascual-Anaya J, Zadissa A, et al.: The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat. Genet. 2013; 45(6): 701–706. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWaters P, Patel H, Ruiz-Herrera A, et al.: Microchromosomes are building blocks of bird, reptile, and mammal chromosomes. Proc. Natl. Acad. Sci. 2021; 118(45): e2112494118. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "168076", "date": "06 Apr 2023", "name": "Richard Challis", "expertise": [ "Reviewer Expertise Genomics", "Bioinformatics" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nChang et al. present a chromosomal genome assembly of the Loggerhead sea turtle, Caretta caretta, using a combination of Nanopore long reads, HiC and Illumina. The conservation importance of having a genome assembly for this globally distributed but vulnerable species is made very clear.\nAs the second chromosomal assembly of a marine turtle it is informative to see a synteny plot comparing this to the green sea turtle, Chelonia midas. This highlights the strongly conserved synteny, similarity in overall assembly span and relative chromosome sizes between these species while maintaining the concise focussed approach typical of a Genome Note.\nOverall the article was very clearly presented, however the presentation of summary information about the 2 sets of gene annotation was slightly inconsistent and I found myself referring to the RefSeq annotation page to compare the numbers of coding vs no-coding genes with the values presented for the Ensembl annotation.\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes", "responses": [ { "c_id": "9783", "date": "27 Jun 2023", "name": "Glenn Chang", "role": "Author Response", "response": "Dear Dr. Richard Challis, Thank you for reviewing our genome note and providing valuable comments. We have carefully considered your comments and made the necessary revisions to address your concerns. In particular, we have taken steps to clarify the genome annotation sections. We have made the results of the RefSeq and Ensembl annotation pipelines more distinct in the paper. Additionally, we have provided hyperlinks to both sets of results, allowing readers to access them directly. Once again, we sincerely appreciate your time and effort in reviewing our genome note. We believe that the changes we have made effectively address your concerns and improve the clarity of our paper." } ] }, { "id": "168077", "date": "27 Apr 2023", "name": "Cinta Pegueroles", "expertise": [ "Reviewer Expertise Genomics", "bioinformatics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript describes the sequencing and annotation of the Caretta caretta genome, which is already available in public data bases. It is a high quality genome that for sure is positively impacting the sea turtles community.\nThe analyses are appropriate and results are sound (despite I miss more details, see below). A high percentage of contigs were assembled into chromosomes, and assembled chromosomes overall showed conserved synteny with the green turtle.\nI found surprising that there is no information about repetitive elements. Where they annotated? I strongly recommend to report the levels and type of repetitive elements found within the genome. They can be easily annotated using the repeatMasker software.\nIn the abstract I recommend to briefly report the quality of the genome assembly, for instance by adding the percentage of complete BUSCO.\nDespite genome notes are short by definition, in general I miss more details of how analyses were performed. For instance, there is no information of the parameters used when running the programs and it is not explained how the syntenic analyses were performed, neither the annotation of the genome.\nRegarding the annotation of the genome, I do not understand this sentence, “The loggerhead sea turtle assembly was also annotated for 54,583 protein sequences using RefSeq (GCF_023653815.1, PRJNA853764)” since there are 19,633 protein coding genes annotated in Ensembl.\nThe mitochondrial genome is not reported in this genome note but it is provided in NCBI. I think it should be mentioned here including the tools that were used for its assembly and annotation.\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? No\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes", "responses": [ { "c_id": "9782", "date": "27 Jun 2023", "name": "Glenn Chang", "role": "Author Response", "response": "Dear Dr. Cinta Pegueroles, Thank you for your thorough review of our paper. We have carefully considered your comments and have made the following changes to the revised version of the genome note: Repetitive elements: We have now used RepeatMaster to annotate the repetitive elements within the genome. The revised paper reports that we found 1.55% SINEs, 8.75% LINEs, 0.13% LTR elements, and 1.10% DNA transposons within the genomic sequences, as mentioned in the Results section. Abstract QC metrics: We have included the busco score and N50 in the abstract to provide quality control metrics right from the beginning. Software Parameters: Table 3 now includes the parameters used for each software involved in the genome assembly. In addition to the software name, version, and source, we have added a new column specifically stating the parameters used. Syntenic analyses: We have made it more explicit in the paper that JupyterPlot was specifically used to perform scaffold-level alignment and synteny plots for the syntenic analysis. Gene Annotation pipeline: The revised paper now clearly states that this genome underwent two annotation pipelines, namely the RefSeq annotation pipeline and the Ensembl gene annotation system. We have provided clearer results for both annotations in the genome annotation section. Mitochondria: We did not examine the mitochondrial genome in this study. However, it was automatically grouped with our genome by NCBI. The other mitochondrial genome study can be found here: https://pubmed.ncbi.nlm.nih.gov/22295859/ Thank you once again for your time and valuable feedback during the review process. We believe that these changes have strengthened our paper and addressed your suggestions appropriately." } ] } ]	1	https://f1000research.com/articles/12-336
https://f1000research.com/articles/11-53/v1	17 Jan 22	{ "type": "Policy Brief", "title": "Changing the method of consent to increase the numbers of cadaveric donors in Saudi Arabia: the autonomy paradox", "authors": [ "Deema AL Shawan", "Faisal Albagmi", "Heba AlNujaidi", "Faisal Albagmi", "Heba AlNujaidi" ], "abstract": "Background: In Saudi Arabia, the gap between the demand for and availability of organs persists, with a total of 13,731 patients on the waiting list in 2019. Family refusal is a major obstacle limiting donation since their consent must be obtained prior to the retrieval of organs. The cause of family refusal is mainly due to their lack of knowledge of their loved ones' wish to become a donor. This paper aimed to compare three systems of obtaining consent in terms of effectiveness, respect for autonomy, and the cultural role of families in Saudi Arabia to ensure feasibility and effectiveness in increasing the number of donors. Policy alternatives and implications: The consent systems include informed consent, presumed consent, and mandated choice. The mandated choice policy might be the optimal solution since it is the most likely to balance the respect for individual autonomy and the cultural role of families in Saudi Arabia. Conclusions and recommendations: Mandated choice ensures the respect of autonomy while influencing the next of kin's decision to donate the organs. Additionally, a recommendation to decision makers is to utilize the Tawakkalna app to send alerts to the next of kin when a user registers as a donor with the users' consent. Moreover, more research should be dedicated to investigating the Saudi public's current culture and perceptions towards organ donation to ensure feasibility.", "keywords": [ "Organ", "donation", "transplantation", "Tawakkalna", "consent", "cadaveric", "donors", "family consent" ], "content": "Introduction\n\nOrgan transplantation is one of the major advances of modern medicine: it saves and enhances the quality of the lives of patients with organ failure. Nonetheless, this achievement is hindered by organ shortages worldwide. The gap between the supply and demand of organs is also evident in Saudi Arabia, one of the first Arab countries with an organized organ procurement system (Shaheen & Souqiyyeh, 2004). Despite Saudi Arabia's efforts to increase the number of donors within the past three decades, the shortage persists, with a total of 13,731 patients who remain on the waiting list in 2019 (Saudi Center for Organ Transplantation, 2019). The consequences of organ shortage are not limited to the decreased quality and the loss of patients' lives on waiting lists. This public health crisis also has a significant economic impact due to the government funding 48% of dialysis facilities in the Kingdom (Al-Dossary et al., 2013).\n\nThe organ procurement system in Saudi Arabia is regulated by The Saudi Center for Organ Transplantation (SCOT), which is a governmental agency. The center was created after the Islamic resolution in 1982, which marked a turning point in the country's history by permitting organ and tissue donation. The main responsibilities of SCOT include allocating organs for transplantation, conducting annual statistics, raising public awareness, and developing policies to ensure the ethical retrieval and transplantation of organs. Additionally, SCOT acts as a referral center for Gulf Cooperation Council (GCC) countries and Spain (Al-Dossary et al., 2013).\n\nThere are two main types of donors: 1) living-related and nonrelated; and 2) cadaveric donors. Cadaveric donors are the main source of organs in Saudi Arabia; therefore, the shortage might not be resolved by utilizing living donors (Alsebayel et al., 2004). The current process for organ procurement in Saudi Arabia requires the intensive care unit (ICU) staff, or in some cases, the emergency room (ER) or the surgical unit staff, to identify possible cadaveric donors. A nurse assigned by SCOT notifies the center about the potential deceased donor and documents it. Then, clinical examinations are performed to ensure that the donor meets the brain death criteria developed by SCOT and the Saudi Ministry of Health (MOH). After the process is complete and the declaration of brain death is officially obtained, the ICU physician is required to approach the donor's family to obtain written consent using an official consent form (Al-Dossary et al., 2013).\n\nPossible obstacles that hinder this process include health providers not reporting cases of possible cadaveric donors, family refusal to consent, medical causes, and lack of awareness on the part of hospital staff in donor hospitals. Family refusal is a major obstacle limiting donation, with only 33% of approached families consenting to donate their loved one's organs in 2019 (Saudi Center for Organ Transplantation, 2019). Lack of knowledge of the potential donors' next of kin of their loved ones' wishes to donate their organs is one of the main reasons for the families' refusal to consent (Palmer, 2012). To overcome this issue, improvements should be made in documenting potential donors' consent in organ donation registries.\n\nThere are three known methods of consent when registering to become a donor upon death: informed consent (opt-in system), mandated choice and presumed consent (opt-out system) (Al-Dossary et al., 2013). This paper aims to analyze the different types of consent systems to address the issue of the high rate of family refusal. The study offers some important insights that will aid decision-makers in selecting an alternative that is more likely to reduce the shortage of organs.\n\n\nPolicy alternatives and implications\n\nThe current method of registering donors in Saudi Arabia is an opt-in system where individuals voluntarily state that they wish to become donors upon death. Originally, there was no organ donation registry in the Kingdom, and donors were encouraged to fill out donor cards issued by SCOT to document their wishes to be donors upon death. The lack of a registry made it difficult to identify the deceased decision to notify the family unless the donor card was found at the time of death. It is important to note that, under the current policy, families still have the right to veto that decision despite their loved one's consent to become a donor (Al-Dossary et al., 2013).\n\nDonor cards were recently replaced with online registration on SCOT's website as well as the Tawakkalna app. The app was developed by the Saudi Data and Artificial Intelligence Authority (SDAIA) to display the users' coronavirus disease 2019 (COVID-19) status upon entry to public places following government regulations. Due to most of the Saudi public downloading the app, SCOT collaborated with SDAIA to allow users to register to become donors through it (Yosri, 2021).\n\nIn terms of effectiveness, there was a drastic increase of registered donors after the utilization of Tawakkalna. According to a news article, the number of registered donors increased from 20,000 to 200,000, which is a 115% increase after the launch of the donor registration feature. This spike in the number of registered donors was attributed to the app's ease of use and accessibility (Alsharq Alawsat, 2021).\n\nNevertheless, when it comes to an opt-in system, there is still a likelihood that willing donors may not register. This issue is prevalent in several countries around the world with a similar opt-in system. For instance, in the United States, 95% of adults support organ donation, while merely 54% are registered as donors (Anderson, 2017). There are limited studies on this obstacle in Saudi Arabia; nonetheless, one study investigated the willingness of Saudi University students to become donors upon death. According to the results, about 70% of participants are willing to become donors; however, none of them carried donor cards that were the enrollment method for the study (Al-Ghanim, 2009).\n\nAs for ethical considerations, the current opt-in system respects an individual's autonomy. According to Immanuel Kant, undermining a person's autonomy is to treat that person as a mere means to an end without regard for the individual's own goals. Based on Kant's theory, organs from a deceased individual should not be harvested if the person's wish was not to be a donor, even if it intends to save others (Johnson & Cureton, 2021).\n\nUnder informed consent in Saudi Arabia, individuals might still “exercise their autonomy in choosing to accept an institution, tradition, or community that they view as a legitimate source of direction” (Holm, 2002). Therefore, an organ consent policy needs to ensure that those views are respected.\n\nIn a presumed consent system, an individual is assumed to be a donor unless they specifically opt-out. There are two variations of this policy: a hard opt-out and a soft opt-out. In a hard opt-out approach, the families of cadaveric donors are not consulted before retrieving the donated organs. In contrast, in a soft opt-out policy, the families' wishes are considered (Al-Dossary et al., 2013).\n\nSeveral countries around the world have adopted variations of the presumed consent system with different degrees of success. For instance, after adopting a hard opt-out policy in Austria, the rate of donations quadrupled within eight years (Zink et al., 2005). On the other hand, a soft approach to the policy did not impact donation rates in Spain, which indicates that a hard opt-out policy could be more effective. Despite the success and cost-effectiveness of hard opt-out policies, there are still some concerns, such as increasing the public's mistrust and the risk of undermining autonomy (Bramhall, 2011).\n\nApplying a hard presumed consent policy in the context of Saudi Arabia might be unfeasible due to ethical considerations pertaining to the role of families. In many cases, the family trumps an individuals' autonomy” (Al-Shahri, 2002). Therefore, it may be culturally insensitive to implement a hard presumed consent system that disregards the wishes of the next of kin completely, which could risk public acceptance. Additionally, a presumed consent system was found to be the least favored by the Saudi public. One of the causes of this disfavoring was the Islamic belief that a good deed must be done with intent by the individual, which may not be the case in a system that makes you a donor by default. This belief may lead to the public rejecting even a softer presumed consent system as well (Hammami et al., 2012).\n\nAnother possible solution is to replace the current policy with a mandated choice system, where citizens are required to either opt-in or opt-out of becoming organ donors. This system can be implemented in Saudi Arabia by utilizing the pre-existing organ donation registration feature on the Tawakkalna app. Currently, the app offers the option to sign up to register as a donor voluntarily; nevertheless, users can unknowingly leave it blank. By implementing a mandated choice system, the app can require individuals to fill out their choice along with the rest of their medical information.\n\nThis alternative could increase the number of registered donors by ensuring that willing donors register their wishes and inform their families before death. According to a study conducted in Saudi Arabia in 2018, most participants support organ donation, but merely 2.3% volunteered to carry organ donation cards to indicate their wishes to become donors (Alnasyan et al., 2019). Therefore, this intervention could address the issue of willing donors neglecting to document their decision.\n\nThere is sparse evidence on the effectiveness of a mandated choice system in increasing the number of registered donors. However, the limited available research from other countries indicates the likelihood of the success of this system compared to informed and presumed consent. For instance, a study in the Netherlands, a country that adopted a mandated choice, concluded that this system generated more registered donors than both informed and presumed consent systems (Van Dalen & Henkens, 2014).\n\nAs for ethical considerations, a mandated choice system makes the two choices readily available; it increases a person's likelihood of making an autonomous choice and encourages self-determination. In other words, this system eliminates the presumption involved, and each individual could explicitly state their wishes prior to death. Furthermore, this consent mechanism can further cultivate public acceptance due to its respect for families' roles. Additionally, due to the accessibility of the app, individuals can opt-out at any time, which could further ensure the next of kin that this was their loved one's wish with more confidence (Steffel et al., 2019).\n\nMandated choice is more likely to ensure that families do not go against their loved one's wishes unknowingly by donating their organs. Individuals are less likely to opt-out while they are alive if they have not been given the option of doing so, which may cause their families to possibly give consent after their deaths. Experimental studies suggest that “individuals have more confidence that they know someone else's donation preferences under mandated choice systems than with presumed consent systems” (Steffel et al., 2019, p.77).\n\n\nActionable recommendations\n\nA policy of mandated choice eliminates the presumption involved since an individual can explicitly state their wish to be a donor before death. Therefore, this policy is more likely to be feasible in the Kingdom due to its respect for the cultural role of the family as well.\n\nIn addition to changing the method of obtaining consent, there are several other recommendations to maximize the benefits of implementing a mandated choice system.\n\nThe Tawakkalna App could be modified to send alerts to notify the next of kin once a user selects their donation decision with the users' permission. Additionally, the users can be asked why they chose to opt-out of donation to investigate the underlying factors influencing donation registration rates.\n\nDecision-makers should invest in more research dedicated to assessing the feasibility of implementing a new consent system. In the case of mandated choice, analyzing the effectiveness of this policy in other countries may not be sufficient evidence. A deep understanding of the current Saudi context, including the public's beliefs, social attitudes, and perceptions, is crucial to predicting the success and cultivating public acceptance for this policy (Al-Khader et al., 2003).\n\n\nConclusion\n\nOne of the main obstacles in obtaining family consent in Saudi Arabia is family refusal. The method of obtaining consent could influence the next of kin's decision, especially if it accurately reflects the donor's decision. Due to the cultural role of families in Saudi Arabia, obtaining consent must carefully balance respect for individual autonomy and the role of families. For that reason, mandated choice may be the best alternative to address this moral dilemma.\n\n\nData availability\n\nNo data are associated with this article.", "appendix": "References\n\nAl-Dossary S, Al-Dulaijan N, Al-Mansour S, et al.: Organ Donation and Transplantation: Processes, Registries, Consent, and Restrictions in Saudi Arabia [Chapter]. Handbook of Research on ICTs for Human-Centered Healthcare and Social Care Services. IGI Global; 2013. Publisher Full Text\n\nAl-Ghanim SA: The willingness toward deceased organ donation among university students. Implications for health education in Saudi Arabia. Saudi Med. J. 2009; 30(10): 1340–1345. PubMed Abstract\n\nAl-Khader AA, Shaheen FaM, Al-Jondeby MS: Important social factors that affect organ transplantation in Islamic countries. Experimental and Clinical Transplantation: Official Journal of the Middle East Society for Organ Transplantation. 2003; 1(2): 96–101. PubMed Abstract\n\nAlnasyan AY, Aldihan KA, Albassam AA, et al.: How informed are the Saudi public about the value of organ donation: A community-based cross-sectional study. Saudi J. Kidney Dis. Transpl. 2019; 30(6): 1236. PubMed Abstract \| Publisher Full Text\n\nAlsebayel M, Al-Enazi A, Al-Sofayan M, et al.: Improving organ donation in Central Saudi Arabia. Saudi Med. J. 2004; 25: 1366–1368.\n\nAl-Shahri M: Culturally Sensitive Caring for Saudi Patients. Journal of Transcultural Nursing: Official Journal of the Transcultural Nursing Society/Transcultural Nursing Society. 2002; 13: 133–138. PubMed Abstract \| Publisher Full Text\n\nAlsharq Alawsat: The number of organ donors in Saudi Arabia increased to 115% within a month. Alsharq Alawsat. 2021. Reference Source\n\nAnderson A: Organ donation: 10 minutes. 22 people. 54 percent. ScienceDaily; 2017. Reference Source\n\nBramhall S: Presumed consent for organ donation: A case against. Ann. R. Coll. Surg. Engl. 2011; 93(4): 270–272. Publisher Full Text\n\nHammami MM, Abdulhameed HM, Concepcion KA, et al.: Consenting options for posthumous organ donation: Presumed consent and incentives are not favored. BMC Med. Ethics. 2012; 13(1): 32. PubMed Abstract \| Publisher Full Text\n\nHolm S: Principles of Biomedical Ethics, 5th edn.: Beauchamp T L, Childress J F. Oxford University Press, 2001, £19.95, pp 454. ISBN 0-19-514332-9. J. Med. Ethics. 2002; 28(5): 332–332. Publisher Full Text\n\nJohnson R, Cureton A: Kant's Moral Philosophy. Zalta EN, editor. The Stanford Encyclopedia of Philosophy (Spring 2021). Metaphysics Research Lab, Stanford University; 2021. Reference Source\n\nPalmer M: The role of families in organ donation: International evidence review. GOV.WALES; 2012. Reference Source\n\nSaudi Center for Organ Transplantaion: Annual Report for Organ Transplantation in Kingdom of Saudi Arabia. 2019. Reference Source\n\nShaheen FAM, Souqiyyeh MZ: Increasing organ donation rates from Muslim donors: Lessons from a successful model. Transplant. Proc. 2004; 36(7): 1878–1880. PubMed Abstract \| Publisher Full Text\n\nSteffel M, Williams EF, Tannenbaum D: Does changing defaults save lives? Effects of presumed consent organ donation policies. Behav. Sci. Policy. 2019; 5(1): 68–88. Publisher Full Text\n\nvan Dalen HP , Henkens K: Comparing the effects of defaults in organ donation systems. Soc. Sci. Med. 2014; 106: 137–142. PubMed Abstract \| Publisher Full Text\n\nYosri: Saudi’s Tawakkalna launches registration service for organ donation.2021.Reference Source\n\nZink S, Zeehandelaar R, Wertlieb S: Presumed vs Expressed Consent in the US and Internationally. AMA J. Ethics. 2005; 7(9): 610–614. Publisher Full Text" }	[ { "id": "120048", "date": "20 Jan 2022", "name": "Alberto Molina-Pérez", "expertise": [ "Reviewer Expertise Ethics of organ donation", "Health policy" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article first describes the organ donation system in Saudi Arabia and identifies the high rate of family opposition as one major obstacle to increasing cadaveric organ donation rates in the country. Then, the article presents the three main consent policies: opt-in (explicit consent), opt-out (presumed consent), and mandated choice, advocating for the latter one as the best alternative in the context of Saudi Arabia.\nOverall, the article is well written and provides a clear and accessible overview of the consent policy alternatives. One interesting point mentioned in the article is the use of the Tawakkalna app as a means of registration of individual preferences about organ donation. However, the article lacks depth in its analysis and suffers from some mistakes and inaccuracies that need to be addressed.\n\"Does 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?\"\n\nOnly partly. The overview is accessible to a general reader but it is not comprehensive and it lacks depth in its analysis. Also, its main hypothesis is based on insufficient evidence.\nFor instance, after mentioning that only 33% of approached families authorised in 2019 the retrieval of organs from their loved ones, the article claims that the relatives’ lack of knowledge of the deceased’s wishes as one of the main reasons for the families’ refusal. [By the way, the wording of the sentence beginning \"Lack of knowledge of the potential donor…\" should be revised.] This second claim is based on Palmer 2012. Although this reference appears to be a good review of the literature, it has not been peer-reviewed. In addition, it is also relatively outdated (meaning that other reviews have been conducted more recently) and the studies reviewed were conducted mostly in English speaking Western countries: the United States, the United Kingdom, Australia, which means that their conclusions may not necessarily be extensible to other cultural contexts such as Saudi Arabia. In other words, although it may be true that lack of knowledge by the family is, in these countries, one of the main reasons for their refusal, there is no guarantee that the same conclusion holds in other countries, especially when these countries (e.g. Saudi Arabia) have a different social organization, religion, and cultural background.\nSince the argument of the article is based on the claim that family refusals are mainly caused by the family’s lack of knowledge of the potential donor wishes (which could be addressed, according to the authors, by a mandated choice policy), stronger evidence is needed to support this claim, especially in the context of Saudi Arabia. In other words, authors should provide more updated and compelling evidence that this claim is true—or, at the very least, that it may be true in their country—before proposing a policy to address it.\n\nThere is a rich and vast literature of empirical studies on the factors of family decision-making and willingness/refusal to donate that are contemporary or posterior to Palmer 2012. Here are some peer-reviewed literature reviews I am aware of, including some systematic reviews:\nKentish-Barnes N, Siminoff LA, Walker W, Urbanski M, Charpentier J, Thuong M, et al. A narrative review of family members’ experience of organ donation request after brain death in the critical care setting. Intensive Care Med 2019;45:331–42.1 Miller C, Breakwell R. What factors influence a family’s decision to agree to organ donation? A critical literature review. London Journal of Primary Care 2018;10:103–7.2 Makmor T, Abdillah N, NurulHuda Ms, Raja Noriza RA, Roza Hazli Z. Family Decision-Making About Organ Donation: A Systematic Review. JUMMEC 2015;18:1–4.3 Ralph A, Chapman JR, Gillis J, Craig JC, Butow P, Howard K, et al. Family Perspectives on Deceased Organ Donation: Thematic Synthesis of Qualitative Studies. American Journal of Transplantation 2014;14:923–35.4 Walker W, Broderick A, Sque M. Factors Influencing Bereaved Families’ Decisions About Organ Donation: An Integrative Literature Review. West J Nurs Res 2013;35:1339–59.5. de Groot J, Vernooij-Dassen M, Hoedemaekers C, Hoitsma A, Smeets W, van Leeuwen E. Decision making by relatives about brain death organ donation: an integrative review. Transplantation 2012;93:1196–211.6 Irving MJ, Tong A, Jan S, Cass A, Rose J, Chadban S, et al. Factors that influence the decision to be an organ donor: a systematic review of the qualitative literature. Nephrology Dialysis Transplantation 2012;27:2526–33.7\nOther relevant reviews and recent articles include:\nCurtis RMK, Manara AR, Madden S, Brown C, Duncalf S, Harvey D, et al. Validation of the factors influencing family consent for organ donation in the UK. Anaesthesia 2021:anae.15485.8 López JS, Soria-Oliver M, Aramayona B, García-Sánchez R, Martínez JM, Martín MJ. An Integrated Psychosocial Model of Relatives’ Decision About Deceased Organ Donation (IMROD): Joining Pieces of the Puzzle. Front Psychol 2018;9.9 López JS, Martínez JM, Soria-Oliver M, Aramayona B, García-Sánchez R, Martín MJ, et al. Bereaved relatives’ decision about deceased organ donation: An integrated psycho-social study conducted in Spain. Social Science & Medicine 2018;205:37–47.10 Chandler JA, Connors M, Holland G, Shemie SD. “Effective” Requesting: A Scoping Review of the Literature on Asking Families to Consent to Organ and Tissue Donation. Transplantation 2017;101:S1–16.11 Shah SK, Kasper K, Miller FG. A narrative review of the empirical evidence on public attitudes on brain death and vital organ transplantation: the need for better data to inform policy. Journal of Medical Ethics; London 2015;41.12 Sharp C, Randhawa G. Altruism, gift giving and reciprocity in organ donation: A review of cultural perspectives and challenges of the concepts. Transplantation Reviews 2014;28:163–8.13 Siminoff LA, Agyemang AA, Traino HM. Consent to organ donation: a review. Progress in Transplantation 2013;23:99–104.14\nAfter mentioning the lack of evidence as \"one of the main reasons for the families’ refusal to consent\", the authors write: \"To overcome this issue, improvements should be made in documenting potential donors’ consent in organ donation registries.\" This conclusion does not necessarily follow or only partially. There are several other means to address family refusal rates, on the one hand, and the lack of knowledge issue, on the other. These means include mass media campaigns, targeted educational campaigns, the presence of a Specialist Nurse for Organ Donation (SNOD) as it is done in the UK, extensive training of transplant coordinators for the family interview as it is done in Spain, financial incentives to donation, prioritization programmes as it is done in Israel, etc. Some countries (e.g. Germany) with much lower family refusal rates than Saudi Arabia, do not have an organ donation registry but only an organ donor card. Other countries (e.g. Spain) with very low family refusal rates, do not have any registry at all (except for living wills that are barely used in practice for registering organ donation preferences) nor any official organ donor card. Fostering communication about organ donation among relatives and training the medical staff to conduct the family interview are alternative ways to increase family knowledge without requiring the registration or documentation of individual preferences.\nIn the next paragraph, the article says: \"There are three known methods of consent when registering to become a donor upon death: informed consent (opt-in system), mandated choice and presumed consent (opt-out system).\" This wording is confusing. First, the opt-in system is not based on informed consent but only on explicit or expressed consent. Second, although the opt-out system is compatible with a registry of refusals, presumed consent only applies when no registering has taken place. Third, it is important to differentiate the models of individual consent (informed, presumed) and consent policies (opt-in, opt-out, mandated choice) from the means available to individuals to express their consent or refusal to donate. Some countries have registries, others don’t, regardless of their consent policy.\nThe article then states its main objective: \"This paper aims to analyze the different types of consent systems to address the issue of the high rate of family refusal. The study offers some important insights that will aid decision-makers in selecting an alternative that is more likely to reduce the shortage of organs.\"\nThis objective presupposes that there is a causal relationship between the consent systems and the rates of family refusal. I would recommend the authors provide references or data to support such an assumption. I ignore whether this is the case or not and whether there is at least a correlation between the two. I am really curious about it. By looking at the Global Observatory on Donation and Transplantation’s Newsletter Transplant 2017, which provides data on family refusal in many countries throughout the world, I fail prima facie to see any trend that may be related to the consent systems in place.\nWith regard to the article’s proposal of a mandated choice policy, it is true that if registering a preference in favour or against organ donation was mandatory in the country, this would likely increase the registration rates and decrease the families’ lack of knowledge about their loved one’s wishes. As a consequence, the number of family refusals caused by this lack of knowledge would also likely decrease. Question is: first, is this the best way to increase organ donation rates and, second, how many family refusals are actually caused by lack of knowledge in Saudi Arabia?\nTo answer these questions, it would be good to give some perspective. According to the Global Observatory on Donation and Transplantation, Saudi Arabia had a deceased organ donation rate of 3.3 pmp in 2019 and 1.9 pmp in 2020, which is relatively low although not in the lower end of the ranking. In 2017, according to the same source, Saudi Arabia had a population of 32.2 M and a total of 92 deceased donors, that is, a rate of 2.9 donors pmp; 333 family interviews were conducted asking for authorisation, out of which 230 (69%) refused. The article mentions that, according to a 2009 study of Saudi University students, \"about 70% of participants are willing to become donors\". If this figure was representative of the general population, if all individuals had registered their wishes, if all families of those willing to donate authorised organ procurement, and if all potential donors were eventually converted into actual donors, the total number of donors in 2017 would have been 92 + (333 x 70%) = 325, increasing the donors rate to 10% which is much better (comparable to that of Germany that same year). [Another study (Alnasyan et al. 2019) also cited in the article but whose figures on willingness to donate are not mentioned by the article says that 77.7% of the general public expressed a willingness to donate, although 29.1% were willing to donate only to their relatives]\nThe problem is that we don’t know how likely is such a scenario. There are no data provided in the article regarding how many of the family refusals were caused by lack of knowledge or by other reasons such as those cited in Palmer 2012: Not wishing for surgery to the body/having concerns regarding disfigurement; Feelings that the patient had suffered enough; Disagreements among the family group; Religious/cultural reasons; Dissatisfaction with healthcare staff and process; Concerns over delay to funeral/burial process; Unable to accept death, or lack of understanding of brain death; Concerns regarding the integrity of process e.g. unfair organ allocation of organs and organ selling; Relatives deciding themselves that organs would not be suitable; Longstanding negative views on organ donation; Relatives were emotionally exhausted.\nActually, the article itself mentions that some unknown proportion of the family refusals may not be caused by lack of knowledge: \"It is important to note that, under the current policy, families still have the right to veto that decision despite their loved one’s consent to become a donor.\" Also: \"In many cases, the family trumps an individual’s autonomy (Al-Shahri, 2002)\" The reference here cited (Al-Shahri, 2002) says \"In Saudi culture, the authority of the family overrules the individuals’ autonomy. Decisions taken by patients can often be altered according to the views of the family\". I am thus curious to know the proportion of families who veto the deceased’s consent as well as their reasons to do so, because this is not caused by lack of knowledge of the deceased’s wishes, and some of the families who do lack knowledge may share the same reasons to refuse as those who don’t.\nIs the discussion on the implications clearly and accurately presented and does it cite the current literature?\nThe discussion on the implications is quite clear but it lacks accuracy and it does not cite enough updated and relevant literature.\nFor example, the authors mention that \"According to a news article, the number of registered donors increased from 20,000 to 200,000, which is a 115% increase after the launch of the donor registration feature\". This is a ten-fold increase and definitely not a 115% increase. Something is wrong. I checked (using an automated translator) the news article cited here and it seems that these figures are actually mentioned. I failed to see any sources cited in the news article. This tells me that this news article is not reliable and thus it is not worth citing in a scientific article. Anyway, even if the 20,000 to 200,000 increase in registrations was true, compared to more than 34 M inhabitants in 2021, this represents only 0.6% of the total population. This is much better, but still anecdotal.\nAnother example. The article claims that \"after adopting a hard opt-out policy in Austria, the rate of donations quadrupled within eight years (Zink et al., 2005). On the other hand, a soft approach to the policy did not impact donation rates in Spain, which indicates that a hard opt-out policy could be more effective.\" There are several problems here. First, the reference cited with regard to Austria does not provide any evidence for the claim but cites two other sources, one of which15 makes this claim without any evidence or references provided. This claim may be true or it may not, but the reference cited here is not sufficient to support the claim. Second, with regard to Spain, the policy is soft in clinical practice but hard according to the law. Third, what did impact donation rates in Spain was not the implementation of an opt-out policy in 1979, but the creation of the National Transplant Organisation (ONT) in 1989. Fourth, it is odd to claim that a hard opt-out policy (such as in Austria) could be more effective than a soft opt-out policy (such as in Spain) considering that Spain has a much higher donation rate (49.6 pmp in 2019) than Austria (23.4 pmp in 2019) according to the GODT. Fifth, several studies, including systematic reviews, have explored the impact of presumed consent policies. They should be cited.\nOne more example. The article mentions \"a study in the Netherlands, a country that adopted a mandated choice, concluded that this system generated more registered donors than both informed and presumed consent systems (Van Dalen & Henkens, 2014).\" First, the Netherlands had not adopted a mandated choice policy but an opt-in system (as the authors of the cited study clearly state in their article). Second, the Netherlands have recently implemented an opt-out system. Third, the cited study does not assess the actual performance of a mandated choice system in the country but compares, in an experimental setting using counterfactuals, whether people would register as donors (hypothetically) if they moved to a region with presumed consent, explicit consent, or mandated choice. Fourth, the results from this study show that people would be more willing to register as donors under a mandated choice system (66%), but this result is only 4 points higher than presumed consent (62%) and many more people would also refuse to donate under a mandated choice system (34%) than under a presumed consent system (18%). In other words, mandated choice would increase donors by 4% and non-donors by 16% when compared to presumed consent.\nAre the recommendations made clear, balanced, and justified on the basis of the presented arguments?\nThe first recommendation is changing the method of obtaining consent from opt-in to mandated choice. Considering the comments above, it is not sufficiently justified. The authors may want to look at a similar recommendation made in other countries, such as a law proposal (unsuccessful) made by members of the German Parliament (see http://dip21.bundestag.de/dip21/btd/19/110/1911087.pdf, text in German), as well as the report on organ donation by the Swiss National Human Medical Ethics Commission (see https://www.nek-cne.admin.ch/inhalte/Themen/Stellungnahmen/fr/NEK-Stellungnahme_Organspende_FR.pdf, text in French).\nThe second recommendation refers to modifying the Tawakkalna App. The proposed modifications may be useful, provided that more people register their organ donation preferences in the app.\n\nThe third recommendation or part of it is sensible: \"more research dedicated to assessing the feasibility of implementing a new consent system\", as well as \"understanding the current Saudi context\" to predict [I would say, estimate] its success.\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? No\n\nIs the discussion on the implications clearly and accurately presented and does it cite the current literature? No\n\nAre the recommendations made clear, balanced, and justified on the basis of the presented arguments? Partly", "responses": [ { "c_id": "8476", "date": "04 Aug 2022", "name": "Deema AL Shawan", "role": "Author Response", "response": "Dear Dr. Molina-Pérez, We thank you for taking the time to provide constructive feedback on our policy brief. We have incorporated the suggested edits to reflect your valuable input into our resubmitted manuscript. Additionally, we have a point-by-point response below: Comment: “This second claim is based on Palmer 2012. Although this reference appears to be a good review of the literature, it has not been peer-reviewed. In addition, it is also relatively outdated (meaning that other reviews have been conducted more recently) and the studies reviewed were conducted mostly in English speaking Western countries: the United States, the United Kingdom, Australia, which means that their conclusions may not necessarily be extensible to other cultural contexts such as Saudi Arabia.” Response: We agree, and to support the claim, we have replaced the (Palmer, 2012) article with one of your suggested sources Comment: “In other words, although it may be true that lack of knowledge by the family is, in these countries, one of the main reasons for their refusal, there is no guarantee that the same conclusion holds in other countries, especially when these” “Since the argument of the article is based on the claim that family refusals are mainly caused by the family’s lack of knowledge of the potential donor wishes (which could be addressed, according to the authors, by a mandated choice policy), stronger evidence is needed to support this claim, especially in the context of Saudi Arabia. In other words, authors should provide more updated and compelling evidence that this claim is true—or, at the very least, that it may be true in their country—before proposing a policy to address it. “ Response: Due to the lack of up-to-date evidence in Saudi Arabia we have added evidence from another country as well as a survey about the Saudi publics acceptance towards this policy. Additionally, we have edited the recommendation to investigating it as a potential viable and feasible solution given the country’s culture. Comment: “There are several other means to address family refusal rates, on the one hand, and the lack of knowledge issue, on the other. These means include mass media campaigns, targeted educational campaigns, the presence of a Specialist Nurse for Organ Donation (SNOD) as it is done in the UK, extensive training of transplant coordinators for the family interview as it is done in Spain, financial incentives to donation, prioritization programmes” Response: We have acknowledged that there is a need to combine the proposed consent system with other methods to ensure it’s effectiveness to increase its effectiveness in reducing the shortage of organs Comment: “In the next paragraph, the article says: \"There are three known methods of consent when registering to become a donor upon death: informed consent (opt-in system), mandated choice and presumed consent (opt-out system).\" This wording is confusing. “ Response: Thank you for pointing that out, we have corrected the wording accordingly. Comment: “The article then states its main objective: \"This paper aims to analyze the different types of consent systems to address the issue of the high rate of family refusal. The study offers some important insights that will aid decision-makers in selecting an alternative that is more likely to reduce the shortage of organs.This objective presupposes that there is a causal relationship between the consent systems and the rates of family refusal. I would recommend the authors provide references or data to support such an assumption. I ignore whether this is the case or not and whether there is at least a correlation between the two. I am really curious about it.” Response: We appreciate the suggestion, even though we have not included a study that discusses the overall impact of consent systems on organ donation rates. We have included evidence on the effectiveness of each of the types of consent mechanisms throughout the policy brief. Comment: “Question is: first, is this the best way to increase organ donation rates and, second, how many family refusals are actually caused by lack of knowledge in Saudi Arabia?” Response: Thank you for your comment to clarify, the article does not claim that this is the best or the only approach but it is one of the main factors identified and it is also one of the most understudied. Additionally, as stated previously, we recommended the incorporation of other interventions, such as educational campaigns, since changing the method of consent alone may not be as effective (justification and evidence were included in the manuscript). As for the second question, there are no up to date published statistics on the exact number of family refusal due to the lack of knowledge. Nevertheless, we have included a study by (Kentish-Barnes et al., 2019; Walker et al., 2013) that states that one of the causes of family refusal is not knowing their loved ones’ wish to donate. Comment: “For example, the authors mention that \"According to a news article, the number of registered donors increased from 20,000 to 200,000, which is a 115% increase after the launch of the donor registration feature\". This is a ten-fold increase and definitely not a 115% increase. Something is wrong. I checked (using an automated translator) the news article cited here and it seems that these figures are actually mentioned. I failed to see any sources cited in the news article. This tells me that this news article is not reliable and thus it is not worth citing in a scientific article. Anyway, even if the 20,000 to 200,000 increase in registrations was true, compared to more than 34 M inhabitants in 2021, this represents only 0.6% of the total population. This is much better, but still anecdotal. Response: The article was replaced with on of the few reliable published sources. The information was also edited to demonstrate the rapid registrations after the launch of the app instead of the claim that the app has increased the number of donors due to the lack of evidence. This was to further support the objective of the paper which is to urge decision-makers to take the opportunity to optimize the newly launched feature in the app in the future Comment: “the reference cited with regard to Austria does not provide any evidence for the claim but cites two other sources, one of which15 makes this claim without any evidence or references provided. This claim may be true or it may not, but the reference cited here is not sufficient to support the claim. “ “Fourth, it is odd to claim that a hard opt-out policy (such as in Austria) could be more effective than a soft opt-out policy (such as in Spain) considering that Spain has a much higher donation rate (49.6 pmp in 2019) than Austria (23.4 pmp in 2019) according to the GODT. “several studies, including systematic reviews, have explored the impact of presumed consent policies. They should be cited.” Response: As recommended, the study was replaced by by a systematic review that investigated the impact of the presumed consent policy in different countries. The other other findings were also corrected as suggested. Comment: “the Netherlands had not adopted a mandated choice policy but an opt-in system “ “Third, the cited study does not assess the actual performance of a mandated choice system in the country but compares, in an experimental setting using counterfactuals, whether people would register as donors (hypothetically) if they moved to a region with presumed consent, explicit consent, or mandated choice. “ “the results from this study show that people would be more willing to register as donors under a mandated choice system (66%), but this result is only 4 points higher than presumed consent (62%) and many more people would also refuse to donate under a mandated choice system (34%) than under a presumed consent system (18%). In other words, mandated choice would increase donors by 4% and non-donors by 16% when compared to presumed consent. Response: We thank you for the corrections and suggestions, the sources were updated. We look forward to hearing from you regarding our submission and to respond to any further inquiries and comments you may have. Sincerely, Dr. Deema S. Al Shawan" } ] }, { "id": "136403", "date": "20 Jun 2022", "name": "James Stacey Taylor", "expertise": [ "Reviewer Expertise The ethics of organ procurement", "autonomy theory", "and the metaphysics of death." ], "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 nicely written paper that argues in favor of using mandated choice to increase the availability of transplant organs in Saudi Arabia. While it does not cover any new ground in its ethical discussion it provides helpful information about the ways in which new technology might be used to enhance organ procurement. However, it suffers from significant empirical and theoretical weaknesses that preclude its indexing as it stands, including inaccurate data, claims that are insufficiently supported by evidence and a poor grounding in philosophical ethics and action theory. I have provided an overview of these issues below.\nIssue 1:\n“According to a news article, the number of registered donors increased from 20,000 to 200,000, which is a 115% increase after the launch of the donor registration feature.”\nThree points are worth noting here:\nIs there a better source for these figures than a news article? Have the authors examined the original source on which this news article was based? How accurate is this claim?\n\nThe increase from 20,000 to 200,000 is not “115%” as the authors claim. This needs to be corrected.\n\nWhen the authors write “…115% increase after the launch of the donor registration feature” do they mean that this 115% increase was immediate after the launch, and then numbers further increased, or do they mean to claim that the increase to 200,000 occurred in the total time after the launch? (The former construal would be compatible with there being an initial increase of 115% and then an greater increase subsequently.)\nIssue 2:\n“As for ethical considerations, the current opt-in system respects an individual's autonomy. According to Immanuel Kant, undermining a person's autonomy is to treat that person as a mere means to an end without regard for the individual's own goals. Based on Kant's theory, organs from a deceased individual should not be harvested if the person's wish was not to be a donor, even if it intends to save others.”\nThere are three points that should be made with respect to the claims in this sentence.\nThe authors should distinguish between personal autonomy and Kantian autonomy. On a theory of personal autonomy a person is autonomous with respect to her desires and actions if they flow from her motivational set in a way that ensures that they originate from her, rather than from elsewhere (where the requirements for what counts as originating from her are spelled out in the theory of personal autonomy that one adopts). On a Kantian account of autonomy a person is autonomous if (roughly) she acts out of respect for the moral law. These are distinct accounts of autonomy, and since the former is often of primary interest in discussions of organ procurement the authors would do well to focus on it rather than its Kantian alternative.\n\nWhy couldn’t an opt-out approach to organ procurement also respect a person’s (personal) autonomy? The authors should see here Michael Gill’s “Presumed Consent, Autonomy, and Organ procurement,” Journal of Medicine and Philosophy 29, 1 (2004): 37 – 591.\n\nMerely claiming that Kant would hold that a person’s organs should not be harvested after her death if she did not agree to this is insufficient. The authors need to argue that Kant (or Kantians) are committed to holding that persons have duties to respect the wishes of the dead.\n\nIssue 3:\nThe authors should note that the differences in the effectiveness of the Austrian and Spanish systems might also be a product of differing infrastructure that is in place to secure available organs, and not merely the result of their different approaches to opt-out systems. The authors also need to provide better sources for their claims here.\nIssue 4:\n“According to a study conducted in Saudi Arabia in 2018, most participants support organ donation…” - What percentage is captured by “most”?\nIssue 5:\n“As for ethical considerations, a mandated choice system makes the two choices readily available; it increases a person's likelihood of making an autonomous choice and encourages self-determination.”\nWhy does requiring persons to make a choice between two alternatives increase her “…likelihood of making an autonomous choice and encourages self-determination”? Indeed, couldn’t requiring that a person choose between two alternatives decrease the degree to which she is autonomous with respect to her relevant choices, insofar as it removes from her the option not to choose — an option which some persons might have preferred? The authors need to do much more to support their claims here, especially since they appear prima facie implausible.\n\nDoes the paper provide a comprehensive overview of the policy and the context of its implementation in a way which is accessible to a general reader? Partly\n\nIs the discussion on the implications clearly and accurately presented and does it cite the current literature? No\n\nAre the recommendations made clear, balanced, and justified on the basis of the presented arguments? Partly", "responses": [ { "c_id": "8477", "date": "04 Aug 2022", "name": "Deema AL Shawan", "role": "Author Response", "response": "Dear Professor Taylor, Thank you for your insightful comments and suggestions. We have incorporated the edits to our manuscript. Additionally, we have a point-by-point response below. Comment: “According to a news article, the number of registered donors increased from 20,000 to 200,000, which is a 115% increase after the launch of the donor registration feature.” “Is there a better source for these figures than a news article? Have the authors examined the original source on which this news article was based? How accurate is this claim?” When the authors write “…115% increase after the launch of the donor registration feature” do they mean that this 115% increase was immediate after the launch, and then numbers further increased, or do they mean to claim that the increase to 200,000 occurred in the total time after the launch? (The former construal would be compatible with there being an initial increase of 115% and then an greater increase subsequently.) Response: This was a error on part of the news article itself, therefore, we have corrected the information and replaced it with a more reliable source. Comment: “The authors should distinguish between personal autonomy and Kantian autonomy. On a theory of personal autonomy a person is autonomous with respect to her desires and actions if they flow from her motivational set in a way that ensures that they originate from her, rather than from elsewhere (where the requirements for what counts as originating from her are spelled out in the theory of personal autonomy that one adopts). On a Kantian account of autonomy a person is autonomous if (roughly) she acts out of respect for the moral law. These are distinct accounts of autonomy, and since the former is often of primary interest in discussions of organ procurement the authors would do well to focus on it rather than its Kantian alternative. Response: We thank you for the insightful comment, we agree and we have made the suggested correction to focus on personal autonomy. We made the clarification in the background, analysis sections. Comment: “Why couldn’t an opt-out approach to organ procurement also respect a person’s (personal) autonomy? The authors should see here Michael Gill’s “Presumed Consent, Autonomy, and Organ procurement,” Journal of Medicine and Philosophy 29, 1 (2004): 37 – 591.” Response: Thank you for the insightful comment and sharing this reference. We have incorporated your suggestion into our manuscript and expressed the other potential concerns. For one thing, there is a risk that organs could be removed from bodies of individuals who did not want their organs removed. On the other hand, we do agree with (Gill, 2004) that “it is morally no worse than not removing organs from the bodies of people who did want them removed.” However, as stated in the manuscript this method is not favored by the Saudi public due to religious reasons. (Hammami et al., 2012) Which is why we recommended that decision makers support investigating mandated choice as an option, since it could be a balance between the risk of removing organs from individuals who did not wish to be donors and the risk of not harvesting organs from willing donors. The clarification was made in the manuscripts and additional references were added. Comment: “Merely claiming that Kant would hold that a person’s organs should not be harvested after her death if she did not agree to this is insufficient. The authors need to argue that Kant (or Kantians) are committed to holding that persons have duties to respect the wishes of the dead.” Response: We have updated to individual autonomy as recommended in a previous comment and provided further explanations and evidence. Comment: The authors should note that the differences in the effectiveness of the Austrian and Spanish systems might also be a product of differing infrastructure that is in place to secure available organs, and not merely the result of their different approaches to opt-out systems. The authors also need to provide better sources for their claims here. Response: The sources were updated accordingly. Comment: “According to a study conducted in Saudi Arabia in 2018, most participants support organ donation…” - What percentage is captured by “most”? Response: The percentage was added as suggested. Comment: “Why does requiring persons to make a choice between two alternatives increase her “…likelihood of making an autonomous choice and encourages self-determination”? Indeed, couldn’t requiring that a person choose between two alternatives decrease the degree to which she is autonomous with respect to her relevant choices, insofar as it removes from her the option not to choose — an option which some persons might have preferred? The authors need to do much more to support their claims here, especially since they appear prima facie implausible.” Response: That is a valid argument, however, we took into consideration that religion and culture play an important role in determining how autonomy is perceived. We made this recommendation considering the applicability to Saudi Arabia’s culture role of families, religion, public acceptance. Due to religious beliefs for organ donation to be a considered good deed there must be intent by the individual to be a donor. Due to this belief, clearly knowing the next of kin wish could influence the families to approve of the donation. Furthermore, according to a study we have added to the manuscript, mandated choice was the most favored option by the public. Lastly, due to the accessibility of the App, users have the option to opt-out at any moment. We look forward to hearing back from you and please let us know if you have any further inquiries and comments you may have. Sincerely, Dr. Deema S. Al Shawan" } ] } ]	1	https://f1000research.com/articles/11-53
https://f1000research.com/articles/11-476/v1	29 Apr 22	{ "type": "Research Article", "title": "Attitudes toward and knowledge of collaboration of dental and medical practice among medical students in Southern India: a cross-sectional questionnaire survey", "authors": [ "Harshit Atul Kumar", "Ashita Uppoor", "David Kadakampally", "B Unnikrishnan", "Prasanna Mithra", "Harshit Atul Kumar", "David Kadakampally", "B Unnikrishnan", "Prasanna Mithra" ], "abstract": "Background:\n\nEnhancing oral health care services provided through inter-professional collaboration between medical and dental practitioner is important, and even essential. The purpose of this study is to assess the attitude toward and knowledge of medical-dental collaborative practice among medical students attending colleges in Southern India. Methods:\n\nA cross sectional questionnaire survey was conducted among medical students and interns of medical colleges in coastal South India with prior information and permission. The questionnaire consisted of 11 questions to assess attitude toward and knowledge of medical-dental collaborative practice. The demographic backgrounds of participants were also recorded. Chi square test was employed for data analysis. The responses obtained were correlated with age, gender and year of study of participants using Pearson’s correlation test\nResults:\n\nA total 250 questionnaires were distributed and 234 responses were appropriately completed. Most of the students agreed that oral health was an integral part of systemic health, however participants disagreed on attending compulsory rotation in dentistry at a statistically significant level (p<0.05), moreover participants did not agree with physicians having an active role in motivating their patients for regular dental check-up. 82% of the medical students believe that dental check-up should be included in health packages under health insurance. A statistically significant (p<0.05) difference was observed among 3rd year & 4th year students and interns and also it was found that female students provided more positive responses towards medical-dental collaboration. Conclusions:\n\nEven though medical students showed fairly positive attitudes and knowledge towards dentistry, the analysis within the study groups showed that knowledge and attitudes regarding the collaborative practice worsened over the academic years among the medical students. In order to destigmatize and foster interdisciplinary collaboration which would contribute to higher resource efficiency and the standard of care, continuing education in both the disciplines would be highly beneficial.", "keywords": [ "Dental-Medical Collaboration", "Attitude and knowledge", "Medical students", "Interprofessional practice" ], "content": "Introduction\n\nOne of the commonly neglected health issues globally is oral health, and the impact of oral diseases has significant effects on individuals, communities and global health care systems.1 The evolution of professional health care education over the years is yet to compete with the demographical challenges and inequalities faced, which causes a burden on the system to fight the disease spread, and utilize the scientific knowledge and advanced technology with increasing complexity in the system. In addition to this, there is existing gap in imparting training to medical professionals about importance of oral health and its impact on general health.2,3\n\nIn order to achieve greater resource efficiency and upgrade the standard of care and comprehensiveness by reducing duplication and gaps in services, interprofessional collaboration is a key to success.4 All parties will benefit from improved professional cooperation between medical and dental practitioners and better educate the public. Overlooking underlying health problems while treating a patient is what most dentists do while they focus on the diagnosis and treatment of oral diseases. Likewise, doctors may fail to notice their patient’s oral health problems which could result in initiation of a long-lasting medical illness. Enhancing health care services through inter-professional collaboration between medical and dental practitioners is therefore essential.5 An article was published after the First Systemic Health Round Table Discussion to advocate for better medical-dental collaborative practice. Inter-professional collaboration enhances communication and decision-making, enabling a synergistic influence of grouped knowledge and skills.6 Due to limited literature and emphasis on this topic, we decided to conduct this study to improve the understanding and importance of the same.\n\nHence the purpose of this study is to evaluate the knowledge and attitudes of the medical students towards collaboration between medical and dental practice in South India to understand the shortcomings and address them with a better strategy.\n\n\nMethods\n\nApproval was obtained from the Institutional ethics committee (IEC) with protocol reference number-17020, from Manipal College of Dental Sciences, Mangalore, on 11th February 2017. Necessary permissions and the written consent of participants were obtained and all methods were in accordance with relevant guidelines and regulations for carrying out the survey.\n\nThe questionnaire survey used herein was validated in a previous study,7 which had adapted it from the questions used by other published studies.6,7 This cross-sectional self-administered questionnaire survey with a minimum calculated sample size of 180 participants was carried out among the 3rd year, 4th year students and interns (5th year) of four medical colleges in and around Mangalore, a coastal urban area in the south Indian state of Karnataka. A total of 250 medical students were invited to participate in the study by means of prior notification, and we visited their college to collect questionnaire responses in person which were filled in pen-paper format between August to December 2019.\n\nInclusion criteria:\n\n1. Undergraduate Medical Student studying in 3rd, 4th or 5th year of the college.\n\n2. Students who consent to participate in the survey\n\nExclusion criteria:\n\n1. Medical student studying in 1st or 2nd year of the college\n\n2. Students belonging to paramedical course in the same college\n\n3. Post graduate medical students\n\nThe questionnaire was subjected to face and content validation by both a medical and dental faculty member for its comprehensiveness and simplicity of understanding and each question was rated using a 5-point Likert scale to test content validity with range from very important to not important. Questionnaire was tested by 20 randomly selected medical students for the validity of the survey.\n\nAfter obtaining the written consent from the participants, questionnaire to be filled were distributed among the participants. The questionnaire had 2 components: the first component was to collect the demographic data such as age (below 20 years of age, 21-24 years, above 20 years of age), gender (male and female) and year of study (3rd year, 4th year, interns) and the second component contained 11 objective questions which were designed to assess their attitude and knowledge. Questionnaire responses were recoded using 5-point Likert scale (1-strongly disagree, 2-disagree, 3-neutral, 4-agree, 5-strongly agree).\n\nFor the study to be statistically valid and comprehensible, we calculated the mean response score for each question and conducted statistical analysis with median of scores received as measure of central tendency and evaluated the statistical significance.\n\nThe collected data were coded and analysed using statistical package of social sciences (SPSS) version 11.5. Results were expressed as proportion and summary measures (median with inter quartile range) using appropriate tables and figures. For comparison across the groups Mann Whitney U test was employed. A p value of 0.05 was considered statistically significant.\n\n\nResults\n\nA total of 250 questionnaires were distributed and 234 responses were obtained from medical students of 3rd year, 4th year and interns from medical colleges in coastal South India indicating a response rate of 93.6%. Those who returned a blank or incomplete questionnaire were excluded. The mean age of the participants was 21.5 years with 58.36% respondents being female and 41.64% male. Out of total respondents, 43.77% were 3rd years, 39.9% were 4th years and rest (17%) accounted for interns.\n\nThere was no statistically significant difference in knowledge and attitude based on gender, except that the female students were significantly more (p value-0.00) aware of interprofessional referral practice before elective medical surgeries (Table 1). Overall analysis of gender-based difference in responses indicated that females are more well informed and have increased positive attitude than males regarding the intended collaboration.\n\n* p=0.05.\n\nMost of the students agreed that oral health was an integral part of systemic health with analysis leading to median score of 5 (Table 2), but a statistically significant difference in the attitudes of medical students based on study year was seen when asked about attending compulsory rotation in dentistry with senior students showing negative attitude. The majority of participants had adequate knowledge regarding the medical-dental relationship, but almost 47% had very limited awareness about the existing relationship, which was assessed by questions 2, 3, 4 and 5. While comparing the groups based on study year there was a statistically significant difference in knowledge (Table 2) with p value of 0.003, when asked about importance of salivary bio markers. Moreover when asked about physicians’ active role in motivating their patients for regular dental check-up, there was a statistically significant difference (p value-0.013) in responses given by groups based on year of study indicating their negative attitude. However, 82% of the medical students were of the opinion that dental check-ups should be included in the health packages under health insurance.\n\n* p=0.05.\n\nMost students were aware about the necessity for interdisciplinary practice but only 61.8% agreed to the foster integral collaboration; 12.8% disagreed and the rest were unsure. Medical students (61%) gave a median score of 4, and agree that regular interaction is required with dental students to mutually exchange knowledge. Interestingly, 25% of them have replied neutrally, which again indicates a lack of interest with regards to the same.\n\nA statistically significant difference based on age was seen (Table 3) with p value of 0.014 when asked about relation of HIV patient and dental treatment. Participants belonging to 21-25 years age groups showed lesser knowledge regarding the same.\n\n* p=0.05.\n\n\nDiscussion\n\nThis study was used to evaluate the knowledge and attitudes of medical students towards the collaboration of medical and dental practice. Only medical students were involved in this survey to avoid a positive response bias from dental students as they may simply have a more positive disposition towards the study objective, as shown in a study by Zhang in 2015.7\n\nOverall, medical students showed fairly good knowledge and positive attitude towards medical and dental collaboration in congruence with the results obtained from the study by Zhang. But analysis of groups within each parameter showed a significant difference. Based on year of study, it was found that students from third and final years of study had more positive attitudes than the interns, unlike results obtained by Zhang.7 More than half the participants, particularly the interns, did not agree to attend compulsory rotation in dentistry (p value 0.017), contrary to finding in which Hendricson and Cohen concluded this rotationship was not only beneficial but essential.8\n\nAlthough nearly 50% participants had fair knowledge regarding the oral-systemic link, many participants were confused when asked if it was mandatory to undergo an oral check-up before pregnancy. Sufficient research has shown that severe periodontal disease in pregnant women predisposes them to a higher risk of delivering preterm and/or low-birth weight of the new born.9,10 Offenbacher found mothers with periodontal disease are at a risk seven times more than mothers without.11 When asked about a link between diabetes and oral health, students seemed to have limited knowledge regardless of year of study. In addition, previous investigations have established an association between either type 1 or type 2 diabetes and periodontal diseases to the extent that periodontitis has been called the “sixth complication of diabetes”.12,13 Interestingly, analysis among gender revealed a statistically significant difference with more knowledge among female participants with regard to questions about criteria to undergo treatment among HIV patients. Though it does not provide any supporting evidence to prove poor knowledge, it does indicate the need for further education among medical students about HIV patients and dental treatment.\n\nWhile assessing the attitude of the students, we found significant data that junior students advised and motivated their patients to undergo dental check-up regularly, compared to senior students who gave a more of neutral response. One of the reasons for such an attitude from senior students can be because of the concept of social hierarchy which can be due to lack of interprofessional communication and patient management.4\n\nIn the United States, utilization of oral health care services and the incidence of oral disease are strongly linked to dental insurance coverage.14 In contrast, in India the dental insurance sector is less prevalent, 40-50% of the medical students strongly feel that dental check-up and some part of treatment must be covered in general health packages.\n\nAround 60% of participants responded positively towards the integral collaboration and interprofessional communication, although 30% students were not sure and the rest disagreed with it. Analysis showed that the third and final year students were more positive than interns which is in contrast to results obtained from a study by Zhang.7 The exposure medical students undergo at clinics along with their interest in the subject affects their perception of oral health and its importance on general health. The Indian health education system, which often displays egocentric power relations among healthcare professionals, whereby medical professionals may not consider oral health as an integral part of general health due to a false perception, is threatening this interprofessional collaboration.15\n\nStudents’ attitude is associated with factors such as gender, knowledge of regular dental check-up, and curriculum. Results of a previous study reported that gender could affect a student’s attitude towards medical dental collaboration.9,16 Questions pertaining to the attitude towards collaboration such as insurance benefits for dental treatments received a more positive response from females than males. When asked about importance of interprofessional communication for exchange of knowledge and better patient care, females gave a greater positive response than males, which can be attributed to higher ego among males.15\n\nIn clinical practice, interprofessional continuing education is a useful means of regulating and stabilizing a professional’s identity and improving teamwork.4 Guidelines must be set to improve confidence in a provider’s ability with regard to cases pertaining to both fields and have access to updated knowledge about the collaboration between medical and dental practice.17,18 The existing body of medical and dental professionals play an important role since they have the ability to lay the guidelines. They can set guidelines for the indications, timing, protocols, and responsibilities of referral and consultation among physicians and dentists. Patients and the community should be made to understand the relationship between oral and systemic health by means of awareness campaigns.19 In doing so, national health goals can be achieved by reducing these kinds of healthcare disparities.\n\nIn our study we have not included dental students to avoid positive response bias. Apart from this, studies with larger sample size should be considered in future, to extrapolate the study results to a larger professional population. Even para-medical healthcare providers can be included as a part of the study to seek better understanding.\n\n\nConclusion\n\nEven though medical students showed fairly good knowledge and positive attitude towards dentistry, the analysis within the study groups showed that knowledge and attitude regarding the collaborative practice declined over the academic years among the medical students.\n\n➢ To break the stereotypes in clinical practice, continuing dental education programs is a very useful means of fostering collaboration and a two-way referral relationship, which would improve resource efficiency and the overall standard of care.\n\n➢ There is a need for improved medical curriculum for interprofessional management of patients with stress on significance of effects of oral health on general health to instil a sense of confidence and necessity of interprofessional relation among under graduates.\n\n\nData availability\n\nfigshare: HARSHIT Data MASTERCHART.xlsx. https://doi.org/10.6084/m9.figshare.19409354.v220\n\nThis project contains the following underlying data:\n\n- Data chart.xlsx\n\nfigshare: HARSHIT Data MASTERCHART.xlsx. https://doi.org/10.6084/m9.figshare.19409354.v220\n\nThis project contains the following extended data:\n\n- Data code statistical analysis.xlsx\n\n- Questionnaire with consent form.docx\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).", "appendix": "Acknowledgements\n\nAn earlier version of this article can be found on Research Square (https://doi.org/10.21203/rs.3.rs-845988/v1).\n\n\nReferences\n\nKapoor S, Sheokand V, Kaushik N, et al.: Oral Health? 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Med. 2001; 76(12): 1181–1206. Publisher Full Text\n\nZhang S, Lo ECM, Chu C-H: Attitude and awareness of medical and dental students towards collaboration between medical and dental practice in Hong Kong. BMC Oral Health. 2015; 15(1): 53. PubMed Abstract \| Publisher Full Text\n\nMigliorati CA, Madrid C: The interface between oral and systemic health: the need for more collaboration. Clin. Microbiol. Infect. 2007; 13(Suppl 4): 11–16. PubMed Abstract \| Publisher Full Text\n\nBaron-Cohen S: The Essential Difference: The Truth about the Male and Female Brain. 1st ed.Basic Books; 2003.\n\nOffenbacher S, Katz V, Fertik G, et al.: Periodontal infection as a possible risk factor for preterm low birth weight. J. Periodontol. 1996; 67(10 suppl): 1103–1113. Publisher Full Text\n\nOffenbacher S, Jared HL, O’Reilly PG, et al.: Potential pathogenic mechanisms of periodontitis associated pregnancy complications. Ann Periodontol. 1998; 3(1): 233–250. PubMed Abstract \| Publisher Full Text\n\nLöe H: Periodontal disease—the sixth complication of diabetes mellitus. Diabetes Care. 1993; 16: 329–334.\n\nEdelstein BL: Oral health services in the child health insurance program (CHIP). Children's Dental Health Project. 1998.\n\nReinhard DA, Konrath SH, Lopez WD, et al.: Expensive egos: narcissistic males have higher cortisol. PLoS One. 2012; 7(1): e30858.\n\nCarpenter J: Doctors and nurses: Stereotypes and stereotype change in interprofessional education. J. Interprof. Care. 1995; 9(2): 151–161. Publisher Full Text\n\nMaharani DA, Ariella S, Syafaaturrachma ID, et al.: Attitude toward and awareness of medical-dental collaboration among medical and dental students in a university in Indonesia. BMC Oral Health. 2019 Dec; 19(1): 1–7. Publisher Full Text\n\nMaharajan MK, Rajiah K, Khoo SP, et al.: Attitudes and readiness of students of healthcare professions towards interprofessional learning. PloS one. 2017 Jan 6; 12(1): e0168863. PubMed Abstract \| Publisher Full Text\n\nLaniado N, Cloidt M, Altonen B, et al.: Interprofessional Oral Health Collaboration: A Survey of Knowledge and Practice Behaviors of Hospital-Based Primary Care Medical Providers in New York City. Adv. Med. Educ. Pract. 2021; 12: 1211–1218. PubMed Abstract \| Publisher Full Text\n\nLuebbers J, Gurenlian J, Freudenthal J: Physicians’ perceptions of the role of the dental hygienist in interprofessional collaboration: A pilot study. J. Interprof. Care. 2021 Jan 2; 35(1): 132–135.\n\nAtul Kumar H: HARSHIT Data MASTERCHART.xlsx. figshare. [Dataset.].2022. Publisher Full Text" }	[ { "id": "136383", "date": "26 Jul 2022", "name": "Saba Kassim", "expertise": [ "Reviewer Expertise Dentistry" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for considering me to review this paper.\nMy comments are as follows:\nIf the questionnaire was validated elsewhere, why was content and face validity done? By convention reliability (Cronbach alpha) and construct validity should be tested.\n\nThe authors repeated that the students were assessed for their knowledge and attitude using a 5-point Likert scale. Please check the last two paragraphs under ‘Study and questionnaire design’.\n\nThe authors calculated the mean response score for each question and conducted the statistical analysis with the median of scores received as a measure of central tendency and evaluated the statistical significance. Why were the mean and median calculated at the same time? One of these central tendencies should be used according to the normality distribution. In addition, the authors compare the three age groups and education levels and mentioned the wrong test, Mann Whitney U test. It was appropriate to use ANOVA (if scores are normally distributed) with post hoc analysis to compare the three groups.\n\nThe authors used 'interdisciplinary' and 'interprofessional' interchangeably, consistency in using one of these terms is preferable unless there was an obvious reason(s).\n\nThis study has a number of limitations that should be mentioned in the discussion section.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "8610", "date": "05 Aug 2022", "name": "Harshit Atul Kumar", "role": "Author Response", "response": "Thank you very much for your valuable review. I appreciate your effort to review my article. I understand the points you have raised and I shall make amendments and bring more clarity to the article. Article shall be updated accordingly and resubmitted soon." }, { "c_id": "9640", "date": "15 May 2023", "name": "Harshit Atul Kumar", "role": "Author Response", "response": "I have updated the article as per reviewers suggestions to Version 1 & 2 . I kindly request the reviewers to re-review again." } ] } ]	1	https://f1000research.com/articles/11-476
https://f1000research.com/articles/12-468/v1	04 May 23	{ "type": "Method Article", "title": "Advancing posaconazole quantification analysis with a new reverse-phase HPLC method in its bulk and marketed dosage form", "authors": [ "Annamalai Rama", "Induja Govindan", "Srinivas Hebbar", "Abhishek Chaturvedi", "Usha Rani", "Anup Naha", "Annamalai Rama", "Induja Govindan", "Srinivas Hebbar", "Abhishek Chaturvedi", "Usha Rani" ], "abstract": "Introduction: Posaconazole is a widely used antifungal drug, and its accurate quantification is essential for quality control and assessment of its pharmaceutical products. This study aimed to develop and validate a reverse-phase high-performance liquid chromatography (HPLC) analytical method for quantifying Posaconazole in bulk and dosage form.\nMethods: The HPLC method was developed and validated based on International Conference on Harmonisation (ICH) guidelines. The developed method was then applied to quantify Posaconazole in a marketed tablet formulation. The method's specificity, linearity, precision, accuracy, robustness, and stability were evaluated.\nResults: The developed HPLC method showed good linearity over a 2-20 μg/mL concentration range. The percentage recovery of Posaconazole from the bulk and marketed formulations was found to be 99.01% and 99.05%, respectively. The intra-day and inter-day precisions were less than 1%, and the method was stable under different conditions. The HPLC method was successfully applied to quantify Posaconazole in the marketed formulation.\nConclusion: The developed and validated HPLC method is reliable and efficient for analyzing Posaconazole in bulk and dosage forms. The method's accuracy, precision, specificity, linearity, robustness, and stability demonstrate its effectiveness. The method can be used for the quality control and assessment of Posaconazole-containing pharmaceutical products.", "keywords": [ "Posaconazole", "HPLC", "Analytical method", "Validation", "Quality control" ], "content": "Introduction\n\nPosaconazole is an antifungal medication that inhibits the synthesis of ergosterol, a vital component of the fungal cell membrane, ultimately causing cell death. It is effective against a wide range of fungal pathogens, making it a popular treatment for various fungal infections. Accurate and precise quantification of posaconazole in dosage forms is crucial for ensuring proper dosing and therapeutic efficacy, quality control, and pharmacokinetic studies. However, existing methods for measuring posaconazole can be expensive, time-consuming, or unreliable.1–10\n\nHigh-performance liquid chromatography (HPLC) is a commonly used analytical technique for quantifying drugs in dosage forms. This study aims to develop and validate a new HPLC analytical method that is quick, sensitive, robust, cheap, and reliable for estimating posaconazole in bulk and dosage form.11–23\n\nThe HPLC method involves,\n\n▪ Preparing a solution of the active ingredient from the dosage form,\n\n▪ Injecting it into the HPLC system, and\n\n▪ Separating the different components based on their interactions with the stationary phase.\n\nPosaconazole is detected using a UV-Vis detector, which measures the absorbance of posaconazole in the eluent. The peak area or height is then correlated to the concentration of posaconazole in the sample using a standard calibration curve.24–34\n\nThe newly developed method was optimized by adjusting chromatographic conditions, including the mobile phase composition, column type, and detection wavelength. Validation was performed in accordance with International Conference on Harmonization (ICH) Q2 R1 guidelines, ensuring the method's accuracy, precision, and specificity. The method was successfully used to estimate posaconazole in its bulk and dosage forms.35–49\n\nFollowing CONSORT guidelines for reporting randomized trials increased the transparency of our study and improved the quality of our reporting, contributing to the overall usefulness of our findings. Our new analytical method has significant implications for drug delivery, including more accurate and efficient monitoring of posaconazole levels in patients, increasing overall drug efficacy and safety.\n\nOverall, this manuscript presents the development and validation of a new HPLC analytical method for estimating posaconazole in bulk and dosage form, which will provide valuable insights into analytical method development and validation for drug delivery and contribute to the ongoing efforts to improve patient outcomes.50–63\n\n\nMethods\n\nA HPLC Grade Milli-Q water (Milli Q Direct-Q 3 UV Water Purification System, Merck, United States), Analytical Weighing Balance (BSA224S-CW, Sartorius, Germany), UV Spectrophotometer (UV 1800, Shimadzu, Japan) was used in the study. Posaconazole was received as ex-gratis from Lupin Healthcare limited. Ortho-phosphoric acid (88%) was from Merck Ltd. (Mumbai, India). HPLC grade Acetonitrile (MeCN) and methanol (purity, min 99.8%), was procured from Merck Ltd. (Mumbai, India). A Nylon membrane filter of 0.45 μm was obtained from HiMedia Pvt. Ltd (Mumbai, India). Phenomenex Hyperclone C18 column (5 μm particle size, 100 Å, 250 mm × 4.6 mm id) was procured from Phenomenex (Hyderabad, India), Other reagents and solvents utilized for the method development and validation were of analytical or HPLC grade.\n\nThe Shimadzu LC-2010CHT high-performance liquid chromatography model was used in the current research investigation. The device was equipped with a dual-wavelength ultraviolet detector, a column oven, and an autosampler from Shimadzu. The data acquisition of the chromatograms produced was done using LC Solution software version 5.57. A Hyperclone C18 column (250 mm x 4.6 mm in diameter, particle size 5 microns) from Phenomenex, USA. The mobile phase was filtered through a Millipore glass filter using 0.22-micron pore-size nylon membrane filter paper and connected to a glass vacuum filtration unit. The filtered mobile phase was then sonicated in a GT Sonic Professional Ultrasonic Cleaner)GT-2013QTS, GT Sonic, China) for 10 minutes to remove any air bubbles. The pH of the buffer was determined using a pH meter and a glass electrode (μ pH System 361, Systronics, India).\n\nPosaconazole was weighed and mixed with spectroscopy grade methanol to prepare the stock solution (10 mg in 10 mL). A series of concentrations (5 μg/mL, 10 μg/mL, 15 μg/mL, 20 μg/mL, 30 μg/mL) were prepared from the stock solution, and a UV spectrophotometer determined their absorbance maxima. The absorbance maxima were then used for the HPLC method development.13,64–73\n\nChoosing the right stationary and mobile phase is critical in HPLC method development. The underlying protocol for the selection of Stationary Phase and Mobile Phase is reposited in the Protocols.io repository which can be accessed by following these references.74,75 To develop the method, the Phenomenex Hyperclone C18 column was selected as the stationary phase, and Acetonitrile and Methanol (as Organic Phase) and 10mM Phosphate buffer (pH 6.8) (Aqueous Phase) were chosen as the mobile phase. The stock solution was prepared in Acetonitrile, and an isocratic mode of elution was employed for the method. The injection volume was set to 20 microliters, and the detection wavelength was selected based on the absorbance maxima determined by UV. The stationary phase was maintained at 25°C, while the flow rate of the mobile phase varied between 0.8 and 1.2 mL per minute. From the stock solution, 1 μg/mL was prepared and used in the analysis.\n\n10 mg of Posaconazole was weighed accurately and transferred to a 10 ml volumetric flask. The volume was made up with Acetonitrile to prepare the stock solution. From the stock solution 1 μg/mL was prepared. Isocratic mode of elution was opted for the method. Injection volume was set to 20 microliters and the detection wavelength was selected based on the results of the determination of absorbance maxima by UV. Stationary phase was maintained at 25oC. Flow rate of the Mobile Phase was varied between 0.8 mL to 1.2 mL per minute.\n\nAfter the initial method development trials were conducted, an optimized trial was carried forward for analytical method validation according to ICH guidelines.76–94\n\nThe validation of an analytical method is critical for ensuring that the method is appropriate and reliable for its intended usage. In this study, the optimized analytical technique was subjected to a series of validation experiments recommended by the International Conference on Harmonization (ICH) Q2(R1) guidelines in order to evaluate its performance under various situations.53,88,89,95–125\n\nAn analytical method's capability to accurately measure the analyte despite the presence of diluents or excipients in the sample is referred to as “specificity.” To assess the specificity of the optimized analytical method, three replicates of a blank solution (diluent), Posaconazole (1 μg/mL), and a commercial formulation (equivalent to 1 μg/mL of Posaconazole) were introduced into the HPLC system. The resulting chromatograms were then examined for any interference from the diluents or excipients at the retention time of the Posaconazole.\n\nEnsuring linearity is critical to analytical method development, as it guarantees accurate analyte quantification across a broad range of concentrations. To assess linearity, a range of serial concentrations, spanning from 0.1 to 32 μg/mL, were prepared from a standard Posaconazole drug solution using the mobile phase ratio as a diluent. Quintuplicate injections were made for each concentration, and the resulting peak areas (in mV-min) were plotted against their respective concentrations (in μg/mL) to create a linear regression graph. From this graph, the intercept and slope were calculated via a linear regression equation.\n\nThe accuracy of an analytical method is determined by its ability to produce results that are close to the true or accepted value of the measured concentration. To evaluate the accuracy of the developed method, three concentrations from the linearity range (2 μg/mL, 4 μg/mL, and 8 μg/mL) were analyzed in sextuplicate. Intra-day accuracy was assessed by analyzing sextuplicate injections of all three concentrations twice on the same day (at 09:00 and 21:00 hours), while inter-day accuracy was evaluated by analyzing duplicate injections of all three concentrations over three consecutive days. The mean percentage recovery was calculated for each concentration to determine the method's accuracy.\n\nSensitivity is a crucial characteristic of an analytical method, as it determines the ability to detect small amounts of the analyte. In this study, the method's sensitivity was evaluated by determining Posaconazole's detection limit (DL) and quantitation limit (QL). The DL is defined as the lowest concentration of Posaconazole that can be detected with reliability and accuracy, while QL is the lowest concentration that can be measured with accuracy and precision. A lower DL and QL indicate a more sensitive method with the ability to detect and quantify low concentrations of the analyte.\n\nThe DL and QL are calculated based on the residual standard deviation of the regression line and its slope.\n\nThe formula is\n\nWhere, σ = residual standard deviation of the regression line\n\nS = slope of the regression line\n\nPrecision is a critical parameter in evaluating the reliability and reproducibility of an analytical method. It assesses the agreement between multiple measurements of the same homogeneous sample under the same experimental conditions. In this study, the precision of the developed analytical method was determined by analyzing four quality control concentrations of Posaconazole, including the quantitation limit, the lower quality control concentration (three times the quantitation limit), higher quality control concentration (70% of the highest concentration from the linearity concentration), and middle-quality control concentration (the mean of the lower and higher quality control concentrations). Sextuplicate injections of all quality control solutions were analyzed twice on the same day at two different times (9:00 and 21:00) to assess intra-day precision. Additionally, duplicate injections of all quality control concentrations were analyzed for inter-day precision for three consecutive days. The peak area for each concentration and the percentage relative standard deviation (%RSD) were calculated to evaluate the method's inter- and intra-day precision.\n\nRobustness is a critical factor in assessing the stability and reliability of an analytical method. It ensures that minor variations in operating conditions do not significantly affect the method's performance. In this study, the robustness of the developed analytical method was evaluated by injecting a Posaconazole concentration of 2 μg/mL three times while varying certain conditions such as the acetonitrile ratio in the mobile phase (%), column oven temperature (°C), wavelength (nm), flow rate (mL/min), injection volume (μL), and pH of the aqueous phase. The responses were monitored for any changes, and each condition's peak area and retention time were analyzed to calculate the % RSD.\n\nSystem suitability is an essential aspect of the analytical method validation that assesses the performance of the entire analytical system to ensure that it is suitable for the intended analysis. This includes the evaluation of various parameters, such as peak area and retention time (Rt). To determine system suitability for the developed analytical method, a Posaconazole concentration of 1μg/mL was injected in sextuplicate, and the peak area and Rt for each injection were analyzed. The %RSD of these parameters was calculated to assess the overall performance of the analytical system. This helps ensure that the analytical system performs consistently and reliably, which is crucial for obtaining accurate and precise analytical results.\n\nThe developed HPLC method is considered a valuable tool only after its practical application to quantify Posaconazole in dosage forms. Posaconazole was analyzed in the marketed tablet formulation (Picasa GR 100 mg, INTAS, India) to test the method's practical feasibility. The marketed formulation's standard stock solution was prepared by accurately weighing 12.6 mg (equivalent to 10 mg of Posaconazole), transferring it to a 10 mL volumetric flask, and filling the volume with the mobile phase. Further dilutions were done with the mobile phase to obtain the desired concentration (1 μg/mL). The validated method was used to analyze the desired concentration, and the Rt and peak area were measured. The amount of Posaconazole in the desired concentration was calculated by comparing the peak areas.33,126–134\n\n\nResults\n\nThe maximum absorbance was observed at 262.20 nm for all Posaconazole concentrations, leading to its selection as the optimal wavelength for subsequent HPLC analysis. This was evident with the Figure 1 which represents the UV spectrum of Posaconazole to determine its Absorption Maxima in different concentrations.\n\nThirteen different chromatograms were obtained by altering the ratios of the organic and mobile phases, as well as the flow rate, during the experimental trials. These chromatograms are depicted below.\n\nTrial No. 11 was selected as the optimized method due to its superior performance based on the obtained chromatograms from 13 different trials. The chosen conditions included a specific ratio of the organic phase and mobile phase, as well as a specific flow rate. The optimized method demonstrated excellent peak shape, a high peak area, and a suitable 5-to-8-minutes retention time. This ideal retention time range was considered to be optimal for bioanalytical method development as it allows for the elution of the drug without interference from plasma interferences that typically arise within the first 5 minutes while avoiding excessive consumption of mobile phase beyond 8 minutes, which can increase the cost of the method. Figure 2 shows the different chromatograms of initial trials of method development.\n\nStationary Phase: Phenomenex Hyperclone C18 Column\n\nMobile Phase: Acetonitrile: 10mM Phosphate Buffer pH 6.8\n\nMobile Phase Ratio: 55:45\n\nFlow Rate: 1 ml/min\n\nMode: Isocratic elution\n\nColumn Temperature: 25oC\n\nDetection Wavelength: 262 nm\n\nTotal run time of the instrument: 10 minutes\n\nThe optimized HPLC method was validated according to the ICH Q2 (R1) guidelines, which involved a range of experiments to evaluate the method's performance under different conditions. Figure 3 shows the optimized chromatogram of the Posaconazole.\n\nThe developed HPLC method exhibited high specificity in determining Posaconazole, as indicated by the absence of interferences at the retention time of 7.634 minutes for pure Posaconazole and 7.691 minutes for the Posaconazole present in the marketed formulation. This suggests that the method is capable of accurately identifying Posaconazole in the presence of other components.\n\nPosaconazole was quantified in quintuplicate for a concentration range of 0.1 to 32 μg/mL. Individual linear plots were generated for each trial, and the mean value was computed. The plotted linear regression graph showed a linear regression equation of y = 58203x-3671 for the mean value, with a coefficient of determination (R2) of 1. Notably, none of the consecutive R2 values from the five linear regression plots was less than 0.999. This indicated that the optimized method was highly linear within the Posaconazole concentration range, and further experimentation was warranted. Figure 4 represents the linearity of the method via a linear graph.\n\nIntraday and interday analyses were conducted to assess the accuracy of the optimized HPLC method for quantifying Posaconazole. In the intraday analysis, sextuplicate injections were made at three different Posaconazole concentrations ranging from 2 to 8 μg/mL, while in the inter-day analysis, duplicate injections were made at the same three concentrations. The mean percentage recovery for each concentration was calculated and found to be 91.86%, 89.22%, and 87.46% for 2 μg/mL, 4 μg/mL, and 8 μg/mL, respectively, in the intraday analysis. Similarly, the mean percentage recovery for the inter-day analysis was 94.71%, 89.15%, and 88.09% for the same concentrations. The results showed that the mean recovery percentage for both intraday and inter-day analyses of Posaconazole was within the range of 85%-115%, indicating the optimized method's accuracy and suitability for the precise quantification of Posaconazole. Data represented in the Table 1 evident the accuracy of the method.\n\nThe detection limit is an important parameter in the analytical method validation process as it determines the lowest concentration of analyte that can be detected with acceptable accuracy and precision. In this study, the detection limit of Posaconazole was calculated based on the residual standard deviation of the regression line and its slope. The limit of detection and limit of quantitation were determined to be 0.24 and 0.74 μg/mL, respectively. This suggests that the developed HPLC method is highly sensitive and can detect Posaconazole even at very low concentrations.\n\nFour quality control concentrations of Posaconazole were analyzed in duplicate during intraday and interday experiments to assess the precision of the developed analytical method. The mean peak area of the four concentrations (1.5 μg/mL, 4.5 μg/mL, 34.26 μg/mL, and 64 μg/mL) was calculated for both experiments. The results showed that the percentage relative standard deviation of the peak area for all concentrations was less than 2%, indicating the high precision of the method. This precision study confirms the suitability of the optimized method for the accurate quantification of Posaconazole. Therefore, the developed technique shows excellent potential for the precise quantification of Posaconazole, offering a reliable method for pharmaceutical research and analysis. Data represented in the Table 2 evident the precision of the method.\n\nTo assess the robustness of the developed HPLC analytical method, triplicate injections of Posaconazole at a concentration of 2 μg/mL were performed while varying the operating conditions such as the pH of the buffer, the acetonitrile ratio in the mobile phase, the column oven temperature, the wavelength, the flow rate, and the injection volume. The results showed that the mean percentage relative standard deviation (%RSD) of peak area and retention time were less than 2% for all the varied conditions. This indicates that the optimized methodology has a high degree of robustness, ensuring precise and accurate quantification of Posaconazole even in the presence of small variations in the operating conditions. Data represented in the Table 3 evident the robustness of the method.\n\nThe suitability of the analytical system for the intended application of Posaconazole quantification in its bulk and dosage forms was evaluated by injecting Posaconazole at a concentration of 1 μg/mL in sextuplicate and analyzing the retention time and mean peak area. The consistent results obtained from the sextuplicate trials indicated the system's suitability for precise and accurate quantification of Posaconazole in its various forms. Data represented in the Table 4 evident the system suitability of the method.\n\nThe analytical method developed for quantifying Posaconazole was successfully applied to the practical analysis of Posaconazole in a marketed tablet formulation (Picasa GR 100, INTAS, India). This practical application demonstrated the feasibility and accuracy of the developed HPLC method in quantifying Posaconazole in real-world samples, indicating its potential as a reliable and efficient tool for quality control and assessment of Posaconazole-containing pharmaceutical products. The results highlight the effectiveness of the developed method in analyzing Posaconazole in dosage forms, affirming its potential as a valuable analytical tool for pharmaceutical industries.\n\nThe validated HPLC method was employed to determine the concentration of Posaconazole in the marketed tablet formulation (Picasa GR 100, INTAS, India). A standard stock solution of 10 μg/mL of Posaconazole was prepared and introduced into the HPLC system for analysis. The retention time and mean peak area were carefully recorded and analyzed to determine the concentration of Posaconazole. The analysis results indicated that the mean peak area and retention time of POSA were consistent with the anticipated values, which is a strong indication of the reliability of the analytical method. Moreover, the recovery percentage obtained from the analysis was 99%, signifying high precision and accuracy. These observations demonstrate the effectiveness of the HPLC method in determining the concentration of Posaconazole in the marketed formulation with high levels of reliability, precision, and accuracy.\n\n\nConclusion\n\nIn conclusion, this study successfully developed and validated a reverse-phase HPLC analytical method for quantifying Posaconazole in bulk and dosage forms. The method showed excellent linearity, precision, accuracy, and specificity. The study adhered to the CONSORT guidelines, ensuring the validity and reproducibility of the results. This analytical method can be used for quality control and assessment of Posaconazole-containing pharmaceutical products, thereby contributing to the development of safe and effective drugs for patients.", "appendix": "Data availability\n\nFigShare. Linearity Data of Posaconazole HPLC estimation. DOI: https://doi.org/10.6084/m9.figshare.22331650\n\nThis project contains the following underlying data:\n\nLinearity Data of Posaconazole HPLC estimation\n\na. The above-mentioned dataset represents the linearity of the develop HPLC method for Posaconazole estimation.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nWe thank all the colleagues of Department of Pharmaceutics, MCOPS, MAHE for their support.\n\n\nBibliography\n\nAbou El-Alamin MM, Sultan MA, Atia MA, et al.: Novel Application of Pentabromobenzyl Column for Simultaneous Determination of Eight Antifungal Drugs Using High-performance Liquid Chromatography. Comb. Chem. High Throughput Screen. 2020; 23(10): 991–1001. PubMed Abstract \| Publisher Full Text\n\nAlffenaar JWC, Wessels AMA, van Hateren K , et al.: Method for therapeutic drug monitoring of azole antifungal drugs in human serum using LC/MS/MS. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2009; 878(1): 39–44. 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Publisher Full Text\n\nRathod RU, Navyasree KS, Bhat K: Quantification of Sofosbuvir in Human Plasma: RP-HPLC Method Development and Validation. Pharm. Chem. J. 2018; 52(7): 663–673. Publisher Full Text\n\nPhani Sekhar Reddy G, Navyasree KS, Jagadish PC, et al.: Analytical Method Development and Validation for HPLC-ECD Determination of Moxifloxacin in Marketed Formulations. Pharm. Chem. J. 2018; 52(7): 674–679. Publisher Full Text\n\nSushmitha GS, Pai G, Krishna M, et al.: Development of multiple time point stability indicating assay method and validation of nabumetone by RP-HPLC. Res J Pharm Technol. 2018; 11(11): 4813–4820. Publisher Full Text\n\nAvadhani KS, Amirthalingam M, Reddy MS, et al.: Development and validation of RP-HPLC method for estimation of epigallocatechin -3-gallate (EGCG) in lipid based nanoformulations. Res J Pharm Technol. 2016; 9(6): 725–730. Publisher Full Text\n\nWang S, Liu C, Chen Y, et al.: Aggregation of Hydroxypropyl Methylcellulose Acetate Succinate under Its Dissolving pH and the Impact on Drug Supersaturation. Mol. Pharm. 2018; 15(10): 4643–4653. PubMed Abstract \| Publisher Full Text\n\nWang M, Jiang J, Cai Y, et al.: In vitro and in vivo evaluation of a posaconazole-sulfobutyl ether-β-cyclodextrin inclusion complex. Biomed. Chromatogr. 2018; 32(12): e4364. PubMed Abstract \| Publisher Full Text\n\nVerweij-van Wissen CPWGM, Burger DM, Verweij PE, et al.: Simultaneous determination of the azoles voriconazole, posaconazole, isavuconazole, itraconazole and its metabolite hydroxy-itraconazole in human plasma by reversed phase ultra-performance liquid chromatography with ultraviolet detection. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2012; 887-888: 79–84. PubMed Abstract \| Publisher Full Text\n\nXiao Y, Xu YK, Pattengale P, et al.: A Rapid High-Performance LC-MS/MS Method for Therapeutic Drug Monitoring of Voriconazole, Posaconazole, Fluconazole, and Itraconazole in Human Serum. J. Appl. Lab. Med. 2017; 1(6): 626–636. PubMed Abstract \| Publisher Full Text\n\nYang M, Dong Z, Zhang Y, et al.: Preparation and evaluation of posaconazole-loaded enteric microparticles in rats. Drug Dev. Ind. Pharm. 2017; 43(4): 618–627. PubMed Abstract \| Publisher Full Text\n\nYang Y, Zhu X, Zhang F, et al.: Stability-indicating HPLC method development and structural elucidation of novel degradation products in posaconazole injection by LC-TOF/MS, LC-MS/MS and NMR. J. Pharm. Biomed. Anal. 2016; 125: 165–177. PubMed Abstract \| Publisher Full Text\n\nYoon SJ, Lee K, Oh J, et al.: Experience with therapeutic drug monitoring of three antifungal agents using an LC-MS/MS method in routine clinical practice. Clin. Biochem. 2019; 70: 14–17. PubMed Abstract \| Publisher Full Text\n\nZhang M, Moore GA, Barclay ML, et al.: A simple high-performance liquid chromatography method for simultaneous determination of three triazole antifungals in human plasma. Antimicrob. Agents Chemother. 2013; 57(1): 484–489. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhong W, Yang X, Tong W, et al.: Structural characterization of a novel degradant of the antifungal agent posaconazole. J. Pharm. Biomed. Anal. 2012; 66: 40–49. PubMed Abstract \| Publisher Full Text" }	[ { "id": "172003", "date": "18 May 2023", "name": "Praful Balavant Deshpande", "expertise": [ "Reviewer Expertise Pharmaceutical Research & Development" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript presents a new reverse-phase HPLC method for quantifying posaconazole in bulk and marketed dosage forms. The study was well-designed and executed, and the results demonstrate the effectiveness of the developed method in accurately quantifying posaconazole within a concentration range of 2-20 μg/mL. Overall, the manuscript is well-written and organized, with clear descriptions of the methods and results. However, there are a few minor issues that should be addressed before indexing:\nThe authors should provide more information on the validation parameters used in the study, particularly the acceptance criteria for accuracy and precision.\n\nIn Table 2, it would be helpful if the authors could provide a brief explanation of the abbreviations used for the mobile phase and detection wavelength.\n\nThe authors should consider adding a brief discussion of the advantages and limitations of the developed HPLC method compared to other methods for quantifying posaconazole.\n\nIt would be helpful if the authors could provide more information on the reproducibility of the method.\n\nFinally, there are a few minor grammatical errors and typos throughout the manuscript that should be corrected before indexing.\nI believe this study offers valuable new perspectives on posaconazole quantification and represents a significant contribution to the field of pharmaceutical analysis. With only minor revisions required, I recommend Approving the manuscript for indexing.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Yes\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes", "responses": [ { "c_id": "9794", "date": "27 Jun 2023", "name": "Annamalai Rama", "role": "Author Response", "response": "Dear Reviewer, Thank you for your thoughtful review of our manuscript titled \"Development and Validation of a Reverse-Phase HPLC Method for Quantifying Posaconazole in Bulk and Marketed Dosage Forms.\" We greatly appreciate your positive feedback and your valuable suggestions for improvement. We have carefully addressed each of your points, and we are pleased to inform you that we have made the necessary revisions. Here is our detailed response: 1. Validation Parameters: We have now provided additional information about the validation parameters used in the study, specifically the acceptance criteria for accuracy and precision. We have included this information in the discussion section, which allows readers to better understand the reliability and robustness of our developed HPLC method. 2. Explanation of Abbreviations in Table 2: We have made the required changes as per your suggestion. 3. Advantages and Limitations of the Developed HPLC Method: We have included a brief discussion in the manuscript that highlights the advantages and limitations of our developed HPLC method compared to other methods for quantifying posaconazole. This addition will help readers appreciate the unique features and potential applications of our method. 4. Reproducibility Information: We have addressed your suggestion and provided more detailed information on the reproducibility of our method in the discussion section of the manuscript. We discuss the precision and repeatability of the method and provide insights into the robustness and reliability of our results. 5. Grammar and Typographical Errors: We have meticulously reviewed the entire manuscript, correcting any grammatical errors and typographical mistakes. We utilized Grammarly Premium University Version to ensure the accuracy of the language and enhance the overall quality of the manuscript. We sincerely thank you for your positive evaluation of our study and your recommendation to approve the manuscript for indexing. We are grateful for your time and expertise in reviewing our work, and we believe that the revisions we have made have significantly improved the manuscript. Once again, we extend our gratitude for your valuable feedback and your recommendation to approve our manuscript." } ] }, { "id": "172005", "date": "24 May 2023", "name": "Vivek Dave", "expertise": [ "Reviewer Expertise Pharmaceutics", "NDDS" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript describes the development and validation of a new reverse-phase HPLC method for quantifying posaconazole in bulk and marketed dosage forms. The study was conducted following ICH guidelines, and the results demonstrate the effectiveness of the developed method in accurately quantifying posaconazole over a concentration range of 2-20 μg/mL. Overall, the manuscript is well-written and organized, with clear descriptions of the methods and results. However, there are a few minor issues that should be addressed before indexing:\nThe authors should provide more information on the sources of posaconazole used in the study, particularly the marketed tablet formulation. For example, what brand or manufacturer was used, and was the formulation within the expiration date?\n\nIt would be helpful if the authors could provide more information on the selectivity of the developed HPLC method. For example, were there any potential impurities or contaminants that could interfere with the analysis, and if so, how were they controlled for?\n\nIn Table 3, the % RSD values for precision should be expressed to two decimal places.\n\nThe authors should consider expanding the discussion section to further emphasize the significance of the study's findings.\n\nFinally, there are a few minor grammatical errors and typos throughout the manuscript that should be corrected before indexing.\nOverall, I believe this manuscript presents valuable insights into the quantification of posaconazole and provides an important contribution to the field of pharmaceutical analysis.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Yes\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes", "responses": [ { "c_id": "9793", "date": "27 Jun 2023", "name": "Annamalai Rama", "role": "Author Response", "response": "Dear Reviewer, Thank you for taking the time to review our manuscript titled \"Development and Validation of a Reverse-Phase HPLC Method for Quantifying Posaconazole in Bulk and Marketed Dosage Forms.\" We appreciate your valuable feedback and have made the necessary revisions to address your concerns. Here is a detailed response to each of your points: 1. Sources of Posaconazole: We have now provided additional information regarding the sources of posaconazole used in our study, including the brand or manufacturer of the marketed tablet formulation. We have also mentioned that the formulation used was within the expiration date. 2. Selectivity of the Developed HPLC Method: We have included a discussion section in the manuscript that provides more information on the selectivity of our developed HPLC method. 3. Precision Values in Table 3: We have revised Table 3 to express the %RSD values for precision to two decimal places, as per your suggestion. 4. Expanded Discussion Section: We have expanded the discussion section of the manuscript to further emphasize the significance of our study's findings. We have provided a more comprehensive analysis of the results and their implications, highlighting the potential applications and benefits of the developed method. 5. Grammar and Typographical Errors: We have carefully reviewed the entire manuscript, addressing any grammatical errors and typos. We utilized Grammarly Premium University Version to ensure the accuracy of the language and to enhance the overall quality of the manuscript. We would like to express our gratitude for your insightful comments and assure you that we have taken them seriously. We believe that the revisions we have made have significantly improved the manuscript. Thank you once again for your time and expertise in reviewing our manuscript." } ] } ]	1	https://f1000research.com/articles/12-468
https://f1000research.com/articles/11-1283/v1	10 Nov 22	{ "type": "Research Article", "title": "Attitude towards dengue control efforts with the potential of digital technology during COVID-19: partial least squares-structural equation modeling", "authors": [ "Sang Gede Purnama", "Dewi Susanna", "Umar Fahmi Achmadi", "Tris Eryando", "Luh Putu Lila Wulandari", "Sang Gede Purnama", "Umar Fahmi Achmadi", "Tris Eryando", "Luh Putu Lila Wulandari" ], "abstract": "Background: Dengue fever is still a public health issue in Indonesia, and during the coronavirus disease 2019 (COVID-19) pandemic, integrated digital technology will be required for its control. This study aimed to identify the factors that influence attitudes toward dengue control concerning the potential application of digital technology. Methods: This was a cross-sectional survey, with 515 people willing to fill out an online questionnaire. The analysis was conducted using Partial Least Square-Structural Equation Modelling (PLS-SEM). There were 46 indicators used to assess attitudes toward dengue control, which are organized into six variables: the need for digital information systems, perceptions of being threatened with dengue, the benefits of dengue control programs, program constraints, environmental factors and attitudes in dengue control. Results: The source of information needed for dengue control was mainly through social media. There was a positive relationship between perception of environmental factors to perception of dengue threat, perception of program constraints, perception of program benefits, and perception of digital technology needs. Perception of program benefits and threatened perception of dengue have a positive relationship with perception of digital technology needs. Conclusions: This model showed the variables perception of digital technology and perception of benefits had a positive association with attitude towards dengue control.", "keywords": [ "attitude", "dengue", "potential", "technology", "modelling dengue transmission" ], "content": "Introduction\n\nDengue hemorrhagic fever (DHF) is still a global public health problem in tropical and subtropical climates. This mosquito-borne disease has spread rapidly in the last 50 years, and WHO estimates that the annual cases reach 50–100 million DHF infections.1 Furthermore, the cases have tripled to 390 million, with more than 70% of the world’s population at risk.2\n\nThe global spread of dengue fever is influenced by urbanization, globalization, and less effective vector control. The level of dense human population in an area is also followed by the density level of the Aedes aegypti mosquito.3–5 The hemorrhagic fever can be transmitted through mosquito bites from one human to another. In addition, the development of the aviation industry in various countries increases the mobility of humans and vectors from one country to another. The lack of practical control efforts has led to dengue disease outbreaks in various regions.6\n\nMore than 70% of the population at risk of DHF live in the Southeast Asia and West Pacific region, with a global disease burden of 75%. Therefore, WHO promotes making strategic plans to quickly detect and control disease outbreaks and stop their spread to new areas.7 Sustainable vector control methods, public health policymakers, and vaccine development should receive serious attention in controlling the current and future global distribution of DHF.8\n\nIndonesia is one of the countries endemic to dengue fever. The first DHF case was reported in 1968 in Surabaya, and since then, the incidence rate has increased from 0.05 to 35-40 per 100,000 population and peaked in 2010 (IR 85).9 Based on the Ministry of Health report, until July 2020, there were 73,329 cases and 467 deaths. The regencies with the highest incidence rates in 2020 are Buleleng, Bali (2677 cases), Badung, Bali (2,138 cases), Bandung City (1,748 cases), East Jakarta (1,765 cases), and Sikka (1,715).10\n\nDuring the current coronavirus disease 2019 (COVID-19) pandemic, efforts to control DHF cannot be carried out optimally because of health protocols. These include social distancing, wearing masks, and being careful about receiving foreign guests. This makes it challenging to collect data door to door, and the condition requires a digital technology approach to conduct surveillance and health education in the community. An integrated dengue surveillance and control system is needed in the endemic areas. Data collection should be quick and easy, as well as educate the public on vector control. Therefore, it is necessary to study the potential development of digital technology in dengue control during the COVID-19 pandemic.\n\n\nMethods\n\nThe theoretical model adopts a health belief model between perceptions and dengue control behaviour.11–13 The health belief theory is then modified by adding environmental variables and the need for digital technology. The hypotheses were compared with six latent constructs related to dengue control attitudes, influenced by perceptions of the threat of dengue, program benefits, environmental factors, program constraints, and technology needs (Figure 1). The direction of the path shows the (+) and (-) effects of the relationship, and this study assessed the accuracy of the model and hypothesis with PLS-SEM.\n\nRegarding potential bias in this study, online data collection means that respondents can answer questions repeatedly. Thus, to reduce bias, data validation was carried out based on names and addresses. Incomplete answers, this is done with a re-checking system and requires answering. Respondents also only represented the Denpasar City area, not representing Indonesia.\n\nThis cross-sectional study is conducted using an online survey with 6 variables.15 These include perceptions of the need for digital information systems, dangers of DHF, benefits of DHF control programs, program constraints, and environmental factors related to attitudes toward controlling DHF. Respondents answered with a Likert scale of 1-5, where 1, 2 3, 4, and 5 represent strongly disagree, disagree, neutral, agree, and strongly agree. The questionnaire was made by discussing with experts and testing about 30 respondents to measure the validity and reliability. Respondents were selected based on inclusion criteria, aged more than 17 years, having an address in Denpasar City for more than one year, and willing to answer questions. The results of the validity and reliability tests found that 46 of the indicators were declared valid. Invalid indicators are excluded and not used. The final questionnaire can be found as Extended data.15\n\nIt was then distributed online using a google form, and data collection was carried out in the Denpasar City area, which is endemic to DHF. Table 1 shows a description of the data from the composites and indicators, as well as the definitions of attitudes towards dengue control efforts with the other five composites.\n\n* These indicators were not included in latent variables due to the multicollinearity criteria of PLS-SEM.\n\nJumantik is a volunteer recruited from each village area to inspect, monitor, and control dengue vectors. They were given the task of conducting daily inspections to visit homes. The results of their activities are reported as vector entomological surveillance. This is part of community empowerment to carry out dengue control in their area actively.\n\nThe inclusion criteria were respondents who were over 17 years old and had resided in Denpasar City for more than six months. They are willing to fill out a research approval form and receive mobile phone credit from the internet provider for two. Even though 596 respondents filled in the data, only 515 fulfilled the requirements and were complete. Sampling was carried out with non-random sampling conducted online in a limited population with the consideration that respondents could not be visited directly due to the COVID-19 pandemic in the Denpasar City area, which had previously been permitted by the Licensing Service, Health Service, Head of Public Health Center, and Village Head.\n\nThis study consists of six variables with 46 indicators using a Likert scale of 1-5, where 1, 2, 3, 4, and 5 representing strongly disagree, disagree, neutral, agree, and strongly agree. Attitudes toward prevention strategies are a dependent variable that tends to act to regulate dengue in the surrounding environment through the use of vector control activities at breeding sites for mosquitoes. Therefore, nine indicators are measured, namely willingness to carry out a weekly movement to eradicate mosquito breeding areas, close water reservoirs, clean the environment regularly, filling in data on larval density weekly independently, providing assistance to dengue control programs, supporting students’ weekly larvae care activities, willing to be sanctioned when larvae are discovered, willing to pay a fine, and making efforts to eradicate mosquito breeding areas following the officer’s advice.\n\nPerceptions of the benefits are related to the assessment of dengue control programs beneficial to the community. These consist of 7 indicators: jumantik volunteers always visit every month, the officers always provide information, the volunteers provide larvacide, the program is useful for preventing dengue cases, and students play a role for larvae, the dengue control program was supported, and the officer’s advice was followed.\n\nThe perception of being threatened with dengue is a condition that causes feelings of fear and vulnerability to outbreaks which consist of 6 variables. These include the risk of being infected with dengue fever and several families at risk of being infected. Dengue fever is a deadly, easily contagious, and dangerous disease that people are afraid of being infected.\n\nPerceptions of program constraints are obstacles in carrying out activities related to facilities and pandemic conditions in dengue control. These consist of 8 variables of limited program funding, jumantik personnel, home visit activities due to social distancing and COVID-19, visiting time, which is during working hours from 8 to 10, the information provided, the larvicides, and smartphone facilities.\n\nThe need for digital technology is a public perception of the support for implementing the systems in dengue control. These consist of 8 variables, namely being willing to use mobile phones for dengue control programs, filling in data on websites, watching digital educational videos, sharing information with family, supporting digital information system programs, having Android phones that support the program, having social media applications such as WhatsApp, Facebook, Instagram, and others, but accustomed to using WhatsApp to communicate.\n\nPerception of environmental factors is the surrounding conditions that affect the density of larvae and dengue cases, both natural and artificial. These consist of 8 variables, namely the rainy season affects the incidence of dengue, the number of water reservoirs affects the density of mosquitoes, the Aedes mosquitoes lay eggs in clean water, the bucket filled with water in bathroom containers, used bottles, tires, and vacant places have the potential to become a breeding place.\n\nThis study was analyzed using PLS-SEM with SmartPLS 3.0 software. It analyzed five variables related to attitudes towards dengue control. The PLS-SEM analysis uses two stages, and the first describes the measurement model connecting the constructs and indicators to the theory. In the second stage, the structural model determines the determinants of the relationship between the construction and the hypothetical model.\n\nThis study is part of a research carried out for the development of an integrated dengue control system. This study has been approved by the ethics committee of the Faculty of Public Health, University of Indonesia (Ket-416/UN2.F10. D11/PPM.00.02/2021). Before data collection, informants had received information about their goals, risks, and rights. In addition, a written consent form was given before the interview, and all information from participants is confidential and for this study only.\n\n\nResults\n\nTable 2 shows the socio-demographics of respondents who filled in the data for this study. There were 515 respondents, with 41.4% and 58.6% being men and women, respectively, with the highest education level being high school level with 62.3%. The respondents’ age distribution was mainly 40-44 years old (19.4%) and 17-24 years (18.6%). The type of occupation was primarily private workers (29.3%) and housewives (17.9%).\n\nMost sources of information used for dengue control are through social media such as WhatsApp, Facebook, Instagram, Tiktok, and others (37%). Most respondents find it easier to get information through social media. However, there has been a change in the sources due to the development of information technology. Another highest source of knowledge is television (23%), followed by digital educational videos (14.3%) and websites (10.6%) (Figure 2).\n\nThe types of information needed are the methods of controlling dengue, the dangers, symptoms of infection, characteristics of dengue-transmitting mosquitoes, the risk, the role of jumantik cadres, methods of eradicating mosquito breeding sites, and environmental factors. This information is needed to develop digital educational media for dengue control (Figure 3).\n\nThe percentage of the community’s efforts to seek health services in handling dengue symptoms is through hospitals (44.5%) and primary health centers (40.5%). Public awareness to conduct health checks while experiencing symptoms of DHF is high in the urban setting in which the number and proximity of health-care services are relatively close and easily accessible (Figure 4).\n\nThis section details the results obtained for the proposed study model.\n\nComposite mode A\n\nThe composite measurement model in mode A (attitude) was assessed in individual item reliability, construct reliability, convergent validity, and discriminant validity. First, the reliability of each item is analyzed through a loading factor, as seen in Figure 5.\n\nTable 3 shows the value of the measurement of validity and reliability. Cronbach’s Alpha value and composite were used to evaluate construct reliability. The values show that the construct exceeds the recommended cut-off of 0.7. Convergent validity was also proved because the construct’s extracted mean-variance (AVE) was higher than 0.500. Table 3 shows that the measurement model meets the criteria.\n\nTable 4 presents discriminant validity results through the heterotrait-monotrait (HTMT) correlation ratio. All constructs reach discriminant validity because the confidence interval does not contain a zero value. This situation means that each variable is different from one another. The data examined in the measurement model show that the attitude construct measure is reliable and valid.\n\n* Significance, the confidence interval 95% bias was corrected and performed using bootstrap procedure with 10,000 replications.\n\nComposite mode B\n\nThe composite measurement model in mode B was assessed in collinearity between the outer weights’ indicators, significance, and relevance. First, removing the indicator is carried out when the value exceeds the variance impact factor (VIF = 3). As a result of this process, only the indicators shown in Table 1 are without collinearity. Second, the relevance of the weights is analyzed, and Figure 6 shows the indicators in construction for latent variables. Finally, it is possible to start a bootstrap with 10,000 sub-samples to assess significance. Indicators with insignificant weights but significant loadings of 0.50 or higher were considered relevant (Table 5).\n\n* t statistic, and 95% bias-corrected confidence interval performed by a bootstrapping procedure with 10,000 replications.\n\nStructural model\n\nThe structural model is evaluated after verifying the correctness of the construction measurements. The path coefficients and their 10,000 resampling bootstrap significance levels are reported in Table 6 and Figure 6. Additionally, Table 6 shows that the VIF constructs range from 1,000 to 1,700, indicating no collinearity between variables. This study also assesses the quality by examining the overall predictive relevance of the model with a Q2 value above zero which indicates a fit in the prediction model. The magnitude of Q2 has a value of 0 < Q2 < 1, where the closer to 1, the better the model. The coefficient of determination (R2) also exceeds 0.1 for endogenous latent variables since the construct has an acceptable predictive power quality.\n\nFrom Table 6, there is a direct influence of Perception of Environmental Factors on the Threatened Perception of Dengue, Program Constraints, Program Benefits, and Digital Technology Needs. Perception of Program Benefits and Threatened Perception of Dengue directly influences Digital Technology Needs. In general, Perception of Digital Technology Needs and Program Benefits directly influence Attitude Towards Dengue Control. Variables Perception of Digital Technology Needs and Perception of Program Benefits positively correlate to Attitude Towards Dengue Control.\n\nVAF values above 80% indicate that the variable serves as a full mediator. The variable can be categorized as a partial mediator when the VAF value ranges from 20% to 80%. However, when the value is less than 20%, it can be concluded that there is almost no mediating effect. The value of VAF indicates that the proportion of Perception Of Digital Technology Needs from the pathway has no mediating effect (VAF<0.2 or 20%). Perception of Digital Technology Needs, Threatened Perception of Dengue, and Program Benefits can be categorized as partial mediators between Environmental Factors and Attitudes Towards Dengue Control (see the indirect effect in Table 6).\n\n\nDiscussion\n\nThe use of digital technology in dengue surveillance is currently needed, specifically during the COVID-19 pandemic. Health protocols such as social and physical distancing make direct door-to-door observation activities difficult. Therefore, there is an increase in smartphones and digital applications in conducting disease surveillance.\n\nThis study is a novelty in developing a new model that adopts the health belief model and then collaborates between digital information systems with perceptions of environmental factors, disease threats, and the obstacles related to dengue control attitudes. This study begins with a qualitative study of the potential development of digital surveillance for dengue control, which requires a digitally integrated system for reporting in real-time.16\n\nThis study aims to determine the variables that influence attitudes in dengue control related to the potential application of digital technology. It indicates a direct influence of Perception of Environmental Factors on Threatened Perception of Dengue, Program Constraints, Program Benefits, and Digital Technology needs. Perception of Program Benefits and Threatened Perception of Dengue directly Influences Digital Technology Need. Perception of Digital Technology Needs and Program Benefits directly influence Attitude Towards Dengue Control.\n\nMost sources of information needed for dengue control are through social media such as WhatsApp, Facebook, Instagram, Tiktok, and others (37%). Due to the availability of internet access and public WIFI, people have switched their sources of information, which were previously direct from health workers, television, and then using social media. In addition, teenagers use internet media for learning, specifically in urban areas, and access to information is high.17–20\n\nAttitudes in dengue control are directly influenced by the variable perception of the need for digital technology and program benefits. This is related to the source of information obtained through digital media. Perception of environmental factors is influenced by Threatened Perception of Dengue, Program Constraints, Program benefits, and Digital Technology Need.\n\nOther studies showed an increase in the use of digital technology during the pandemic for monitoring, surveillance, detection, and prevention of COVID-19.21,22 Studies in Saudi use various digital platforms such as mobile health applications, artificial intelligence, and machine learning in the pandemic surveillance.23 A digital dengue surveillance system has also been developed to predict, detect and control the threat of outbreaks.24–26 The incidence is often related to climate change, ecological and socio-demographic factors.27–31 Developing a system based on technology and the environment using spatial mapping makes it possible to predict the potential for outbreaks in an area.32,33\n\nThe strength is the development of a model that combines measurement of attitudes towards dengue control with environmental factors on the threatened perception of dengue, program constraints, program benefits, and digital technology needs. The commonly used model is the health belief, but a different approach combines the perceived need for digital technology, environmental factors, and health beliefs.\n\nThis study uses PLS-SEM analysis which was selected because it is variance-based and estimates composite components and factors.34 The PLS analysis is a multivariate statistical technique that compares several responses and explanatory variables.35–37 Through this approach, it is possible to make appropriate structural equations toward dengue control related to the perception of environmental factors on the threatened perception of dengue, program constraints, program benefits, and digital technology needs.\n\nThe use of online surveys is limited to certain areas and does not represent the whole of Indonesia, only Denpasar City. Generally, the respondents used were those with mobile phones and internet networks, and they were not randomly assigned.\n\nThe results are helpful for policymakers to promote the use of digital technology in data collection of disease cases, surveillance, monitoring, and evaluation of health programs supported by socialization through social media that can influence perceptions of the benefits of the program. The community’s attitude toward controlling the disease is also related to the source of information that affects public perception. Policies to support digital facilities such as the availability of internet networks, computer facilities, mobile phones, and data packages affect the disease reporting system and its control. In the future, it is necessary to develop an integrated digital system for reporting disease cases and collecting data on the ecological environment, specifically larval density. This system should perform spatial mapping and predict the potential for a dengue outbreak to occur. Therefore, technology can be helpful in case surveillance for quick control measures.\n\n\nConclusion\n\nDigital technology has the potential to be developed during the COVID-19 pandemic, specifically in conducting data collection, surveillance, reporting, monitoring, and evaluation. Attitudes towards dengue control directly affect the perception of digital technology needs and program benefits. Social media is a more dominant source of information about dengue disease than other forms of electronic media. The perception of environmental factors is also directly influenced by the variables of threatened perception of dengue, program constraints, program benefits, and digital technology needs.", "appendix": "Data availability\n\nDryad: Attitude towards dengue control efforts with the potential of digital technology during COVID-19: partial least squares-structural equation modelling, https://doi.org/10.5061/dryad.jdfn2z3f0. 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\nFigshare: Dengue integrated surveillance system questionnaire, https://doi.org/10.6084/m9.figshare.21300309. 15\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors are also grateful to the respondents for their participation.\n\n\nReferences\n\nWorld Health Organization: Global Strategy for Dengue Prevention and Control 2012-2020. WHP Press;2012.\n\nBhatt S, Gething PW, Brady OJ, et al.: The global distribution and burden of dengue. Nature. 2013; 496(7446): 504–507. PubMed Abstract \| Publisher Full Text\n\nIstiqamah SNA, Arsin AA, Salmah AU, et al.: Correlation study between elevation, population density, and dengue hemorrhagic fever in Kendari city in 2014–2018. Open Access Maced. J. Med. Sci. 2020; 8(T2): 63–66. Publisher Full Text\n\nPadmanabha H, Durham D, Correa F, et al.: The Interactive Roles of Aedes aegypti Super-Production and Human Density in Dengue Transmission. PLoS Negl. Trop. Dis. 2012; 6(8): e1799. PubMed Abstract \| Publisher Full Text\n\nFustec B, Phanitchat T, Hoq MI, et al.: Complex relationships between aedes vectors, socio-economics and dengue transmission— lessons learned from a case-control study in Northeastern Thailand. PLoS Negl. Trop. Dis. 2020; 14(10): e0008703–e0008725. PubMed Abstract \| Publisher Full Text\n\nGubler DJ: Dengue, Urbanization and globalization: The unholy trinity of the 21 st century. Trop. Med. Health. 2011; 39(4 SUPPL): 3–11. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization: Dengue Guidelines for Diagnosis, Treatment, Prevention and Control. WHO Press;2009. Publisher Full Text\n\nMessina JP, Brady OJ, Golding N, et al.: The current and future global distribution and population at risk of dengue. Nat. Microbiol. 2019; 4(9): 1508–1515. PubMed Abstract \| Publisher Full Text\n\nHaryanto B: Indonesia Dengue Fever: Status, Vulnerability, and Challenges. intech;2016. Publisher Full Text\n\nIndonesian Ministry of Health: Dengue Incident Report. 2020.\n\nJones CL, Jensen JD, Scherr CL, et al.: The Health Belief Model as an Explanatory Framework in Communication Research: Exploring Parallel, Serial, and Moderated Mediation. Health Commun. 2015; 30(6): 566–576. PubMed Abstract \| Publisher Full Text\n\nRaamkumar AS, Tan SG, Wee HL: Use of health belief model–based deep learning classifiers for COVID-19 social media content to examine public perceptions of physical distancing: Model development and case study. JMIR Public Heal. Surveill. 2020; 6(3): 1–8. PubMed Abstract \| Publisher Full Text\n\nZareipour MA, Ardakani MF, Moradali MR, et al.: Determinants of covid-19 prevention behavior in the elderly in urmia: Application of health belief model. Open Access Maced. J. Med. Sci. 2020; 8(T1): 646–650. Publisher Full Text\n\nPurnama SG, Susanna D, Achmadi UF, et al.: Partial Least Squares-Structural Equation Modelling for Attitude Towards Dengue Control Efforts using the Potential of Digital Technology During COVID-19. figure. 2022. Publisher Full Text\n\nPurnama SG, Susanna D: Dengue integrated surveilanceE system questionnaire. figshare J. Contrib. 2022. Publisher Full Text\n\nPurnama S, Susanna D, Achmadi UF, et al.: Potential development of digital environmental surveillance system in dengue control: A qualitative study. Open Access Maced. J. Med. Sci. 2021; 9: 1443–1453. Publisher Full Text\n\nChen J, Wang Y: Social media use for health purposes: Systematic review. J. Med. Internet Res. 2021; 23(5): e17917–e17916. PubMed Abstract \| Publisher Full Text\n\nWijayanti RP, Handayani PW, Azzahro F: Intention to seek health information on social media in Indonesia. Procedia Comput. Sci. 2021; 197(197): 118–125. Publisher Full Text\n\nFrey E, Bonfiglioli C, Brunner M, et al.: Parents’ Use of Social Media as a Health Information Source for Their Children: A Scoping Review. Acad. Pediatr. 2022; 22(4): 526–539. PubMed Abstract \| Publisher Full Text\n\nHuo J, Desai R, Hong YR, et al.: Use of Social Media in Health Communication: Findings From the Health Information National Trends Survey 2013, 2014, and 2017. Cancer Control. 2019; 26(1): 107327481984144–107327481984110. PubMed Abstract \| Publisher Full Text\n\nWang Z, Tang K: Combating COVID-19: health equity matters. Nat. Med. 2020; 26(4): 458. Publisher Full Text\n\nChen T, Wang YC: Recommending suitable smart technology applications to support mobile healthcare after the covid-19 pandemic using a fuzzy approach. Healthcare. 2021; 9(11). PubMed Abstract \| Publisher Full Text\n\nAlghamdi SM, Alsulayyim AS, Alqahtani JS, et al.: Digital health platforms in saudi arabia: Determinants from the COVID-19 pandemic experience. Healthcare. 2021; 9(11): 1–7. PubMed Abstract \| Publisher Full Text\n\nPley C, Evans M, Lowe R, et al.: Digital and technological innovation in vector-borne disease surveillance to predict, detect, and control climate-driven outbreaks. Lancet Planet. Heal. 2021; 5(10): e739–e745. PubMed Abstract \| Publisher Full Text\n\nBarde PV, Mishra N, Singh N: Timely diagnosis, use of information technology and mosquito control prevents dengue outbreaks: Experience from central India. J. Infect. Public Health. 2018; 11(5): 739–741. PubMed Abstract \| Publisher Full Text\n\nPanchapakesan C, Sheldenkar A, Wimalaratne P, et al.: Developing a digital solution for dengue through epihack: qualitative evaluation study of a five-day health hackathon in Sri Lanka. JMIR Form. Res. 2019; 3(3): e11555. PubMed Abstract \| Publisher Full Text\n\nTran BL, Tseng WC, Chen CC, et al.: Estimating the threshold effects of climate on dengue: A case study of Taiwan. Int. J. Environ. Res. Public Health. 2020; 17(4): 1–17. PubMed Abstract \| Publisher Full Text\n\nKoyadun S, Butraporn P, Kittayapong P: Ecologic and sociodemographic risk determinants for dengue transmission in urban areas in Thailand. Interdiscip Perspect. Infect. Dis. 2012; 2012. PubMed Abstract \| Publisher Full Text\n\nRahman MS, Ekalaksananan T, Zafar S, et al.: Ecological, social and other environmental determinants of dengue vector abundance in urban and rural areas of Northeastern Thailand. Int. J. Environ. Res. Public Health. 2021; 18(11). PubMed Abstract \| Publisher Full Text\n\nLi C, Wu X, Sheridan S, et al.: Interaction of climate and socio-ecological environment drives the dengue outbreak in epidemic region of China. PLoS Negl. Trop. Dis. 2021; 15(10): e0009761–e0009716. PubMed Abstract \| Publisher Full Text\n\nMatysiak A, Roess A: Interrelationship between Climatic, Ecologic, Social, and Cultural Determinants Affecting Dengue Emergence and Transmission in Puerto Rico and Their Implications for Zika Response. J. Trop. Med. 2017; 2017: 1–14. PubMed Abstract \| Publisher Full Text\n\nZafar S, Shipin O, Paul RE, et al.: Development and comparison of dengue vulnerability indices using gis-based multi-criteria decision analysis in lao pdr and Thailand. Int. J. Environ. Res. Public Health. 2021; 18(17). PubMed Abstract \| Publisher Full Text\n\nLippi CA, Stewart-Ibarra AM, Muñoz ÁG, et al.: The social and spatial ecology of dengue presence and burden during an outbreak in Guayaquil, Ecuador, 2012. Int. J. Environ. Res. Public Health. 2018; 15(4). PubMed Abstract \| Publisher Full Text\n\nValls Martínez MDC, Martín-Cervantes PA, Sánchez Pérez AM, et al.: Learning mathematics of financial operations during the covid-19 era: An assessment with partial least squares structural equation modeling. Mathematics. 2021; 9(17). Publisher Full Text\n\nSchuetz CG: Using neuroimaging to predict relapse to smoking: role of possible moderators and mediators. Int. J. Methods Psychiatr. Res. 2008; 17 Suppl 1(October 2015): S78–S82. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPurnama S, 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\n\nŠuriņa S, Martinsone K, Perepjolkina V, et al.: Factors Related to COVID-19 Preventive Behaviors: A Structural Equation Model. Front. Psychol. 2021; 12(July): 1–15. PubMed Abstract \| Publisher Full Text\n\nPurnama SG, Susanna D:Data for attitude measures towards Dengue control efforts with the potential of digital technology during COVID-19. [Dataset]. Dryad Dataset. 2022. Publisher Full Text" }	[ { "id": "156148", "date": "05 Dec 2022", "name": "Mohammad Khaleel Okour", "expertise": [ "Reviewer Expertise Technology Diffusion", "Knowledge Management", "Innovation 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 appreciate the effort that the authors did in this manuscript. However, I have some apprehensions which I have highlighted below:\nIntroduction\nThe authors mainly explained the lack of understanding of the factors that influence attitudes toward dengue control concerning the potential application of digital technology in Indonesia. It will be more beneficial if they could provide further evidences based on previous studies from the context of Southeast Asia countries; specifically, Indonesian context.\nLiterature review\nI could not find any serious attempt to write a literature review related to the variables of the study. Researchers should create a new separate section that discuss the previous conducted studies in this field of research (based on the study model).\nMethod\nAs the study is deductive in nature, the authors should clarify the rationale behind adopting the health belief theory. In its current form, there is not enough theoretical justification to propose the study hypotheses.\n\nThe authors need to make sufficient justification on how they determined the sample size?\n\nA standard PLS-SEM methodology was utilized. More evidence should be provided that the statistical assumptions of PLS-SEM have been fulfilled before using it.\n\nIn term of the study respondent characteristics, were there no respondents with master's or doctoral degrees?\n\nThe authors must write the hypotheses of the study clearly and explicitly. For better readability, I recommend the authors create a new table that includes the hypothesis statement with its result (supported / not supported).\n\nDiscussion\nBased on the study model, I don’t see a significant attempt to discuss the study findings. Authors must provide a detailed discussion that includes sufficient linkage/justification between the study findings with previous recent studies.\nImplication\n\nThe authors have focused on the practical/ managerial implications of the study. On the other hand, the authors have not given explicit discussion/ examples of theoretical implications.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "9716", "date": "27 Jun 2023", "name": "Dewi Susanna", "role": "Author Response", "response": "Thank you very much for giving any comments of our manuscript. We are very sorry for delaying posting these responses since we are highly recommended to wait for another reviewer’s report. We have discussed it to make our manuscript more understandable for readers. Here are our responses to all comments: Introduction Question: The authors mainly explained the lack of understanding of the factors that influence attitudes toward dengue control concerning the potential application of digital technology in Indonesia. It will be more beneficial if they could provide further evidences based on previous studies from the context of Southeast Asia countries; specifically, Indonesian context. Response: Additional information has been added in the text. An explanation of this has been included in the background During the COVID-19 pandemic, efforts to control dengue were hampered due to the limited door-to-door educational activities. Therefore, the use of digital technology can help carry out surveillance and education to the public. There are several studies in Indonesia regarding attitudes toward dengue control. A study in Kupang, Indonesia, explains that a significant relationship exists between knowledge, attitudes, and actions in controlling dengue11. Likewise, other studies in Indonesia show that knowledge and attitudes influence dengue prevention measures12,13. Another study in Indonesia on community perspectives on electronic-based dengue vector surveillance during the COVID-19 pandemic14. There are also studies on developing a mobile-based dengue surveillance information system as an early warning system15,16. Digital technology has developed rapidly in the health sector. Digital technology is beneficial during the Covid-19 pandemic for conducting dengue surveillance. The existence of a social restriction policy with social distancing has caused the door-to-door control program not to be implemented17, 18, 19. Attitudes in dengue control are essential because they can influence control measures. This model is needed in analyzing variables related to attitudes and the use of digital applications in conducting dengue surveillance. This study will obtain a potential model that can be used as a digital innovation for dengue control. This study aimed to identify critical indicators influencing attitudes towards DHF control related to the potential for implementing digital technology. Literature review Question: I could not find any serious attempt to write a literature review related to the variables of the study. Researchers should create a new separate section that discuss the previous conducted studies in this field of research (based on the study model). Responses: The Literature Review has been written in the paper as below: Literature review The co-epidemic trend of COVID-19 and dengue in Southeast Asia needs serious attention. These two diseases have similar clinical symptoms20, 21. The COVID-19 pandemic situation is a challenge in controlling dengue in Indonesia. The existence of a social restriction policy makes it difficult for volunteers to provide education manually door to door. The impact is increased dengue cases in several areas22. Public awareness regarding dengue control efforts still needs to be improved. Knowledge related to dengue can influence attitudes toward dengue control23, 24. A positive attitude can encourage action to control dengue25, 26. A large number of water containers is a breeding ground for mosquitoes. This is a potential mosquito breeding site that needs to be controlled. Several studies also state that interventions are needed to increase knowledge, attitudes, and actions in controlling dengue27, 28, 29. Perceptions of the threat to the disease and the benefits of the interventions also influence attitudes towards dengue control. This is in accordance with the concept of the health belief model30. Attitudes towards dengue control using digital technology need to be studied for the driving and inhibiting factors. Intervention with digital technology requires supporting facilities and infrastructure18, 17. Digital educational media that can increase public knowledge is needed during the COVID-19 pandemic. Through socialization with digital educational media, prevention activities can be carried out widely despite a social distancing policy. The development of digital technology has helped health services to provide fast and integrated services. Particularly in dengue control, digital interventions can help conduct surveillance of areas with mosquito density, larval density, and several dengue cases so that they can make a priority scale31, 32. Utilization of digital technology in conducting digital data collection and education can provide early detection and response to dengue cases in an area. Method Question: As the study is deductive in nature, the authors should clarify the rationale behind adopting the health belief theory. In its current form, there is not enough theoretical justification to propose the study hypotheses. Response: Conceptual model and hypotheses The theoretical model adopts a health belief model between perceptions and dengue control behaviour.11 – 13 The health belief theory is then modified by adding environmental variables and the need for digital technology. The hypotheses were compared with six latent constructs related to dengue control attitudes, influenced by perceptions of the threat of dengue, program benefits, environmental factors, program constraints, and technology needs (Figure 1). The direction of the path shows the (+) and (-) effects of the relationship, and this study assessed the accuracy of the model and hypothesis with PLS-SEM. Various factors influence attitudes in efforts to control dengue. During the COVID-19 pandemic, social restrictions were carried out36. Social restrictions impact dengue control programs. Based on the theory of behavior change that a person is motivated to make prevention efforts when they feel seriously threatened and feel the benefits of intervention. The use of digital technology in dengue surveillance is also encouraged by the benefits of these digital applications and their ease of use. The health belief model approach is used because it is appropriate to form a model for changing attitudes towards dengue control related to perceptions of dengue threat, benefits of dengue control programs, and perceptions of constraints37, 38. Environmental factors affect the transmission of dengue infection. Dengue is transmitted by the Aedes aegypti mosquito, which breeds in water containers. The large number of water containers in an environment can affect the density of mosquitoes. Climatic factors (temperature, humidity and rainfall), as well as population density, also increase dengue transmission39, 40. Environmental factors can increase the potential for dengue transmission in an area. The perception of environmental factors is essential to analyze. Perceived ease of use and perceived benefits influence the perceived need for technology. This is in accordance with the Technology Acceptance Model (TAM)41. Several studies on TAM are related to public acceptance of an application42, 43, 44, 45. The use of dengue surveillance applications is needed to collect data and education. Digital applications can record quickly and integrate. This study uses a combination of several theories to create a suitable model according to stakeholder needs. The determinants of these variables are by the need to develop a dengue control attitude model related to technological needs and perceptions of environmental factors. Question: The authors need to make sufficient justification on how they determined the sample size? Response: The calculation of minimum sample was calculated using a formulae and added it in the text as follow: The online survey was chosen because it was appropriate to do it during the Covid-19 pandemic. Online surveys are easier and cheaper than manual surveys using door to door. Measurement of sample size using the following formulation: S = Z2 × P × (1−P)/M2 S = (1.960)2 × 0.5 × (1−0.5)/0.052 = 3.8416 × 0.25 / 0.0025 S= 384.16 Notes: S = Sample size for infinite population P = Population proportion ( Assumed as 50% or 0.5) M = Margin of error = 5% Z = The Z-score will be 1.96 if the confidence level is 95% This means that: n = 384, z = 1.96, M = 0.05 and p = 0.5 Question: A standard PLS-SEM methodology was utilized. More evidence should be provided that the statistical assumptions of PLS-SEM have been fulfilled before using it. Response: Measurement Model Composite Mode A The composite measurement model in mode A (attitude) was assessed in individual item reliability, construct reliability, convergent validity, and discriminant validity. First, the reliability of each item is analyzed through a loading factor, as seen in Figure 5. Question: In term of the study respondent characteristics, were there no respondents with master's or doctoral degrees? Response: The selected respondents were the general public who were willing to be involved in the Denpasar area, Bali. The results of the survey showed that there were no respondents with master's and doctoral degrees. Question: The authors must write the hypotheses of the study clearly and explicitly. For better readability, I recommend the authors create a new table that includes the hypothesis statement with its result (supported / not supported). Response: Based on the literature discussed, the following hypotheses emerge to provide the scope of this study: Hypothesis 1 (H1). Perceptions of environmental factors have a positive effect on perceptions of dengue threat. Hypothesis 2 (H2). Perceptions of environmental factors have a positive effect on perceptions of program constraints. Hypothesis 3 (H3). The perception of the dengue threat positively affects the perception of the need for digital technology. Hypothesis 4 (H4). Perceptions of environmental factors have a positive effect on perceptions of digital technology needs. Hypothesis 5 (H5). Perception of dengue threat has a positive effect on perceptions of program benefits. Hypothesis 6 (H6). Perceptions of program constraints positively affect perceptions of digital technology needs. Hypothesis 7 (H7). Perceived program constraints have a positive effect on attitudes toward dengue control. Hypothesis 8 (H8). Perception of being threatened by dengue positively affects attitudes toward dengue control. Hypothesis 9 (H9). Perceived benefits of the program positively affect attitudes toward dengue control. Hypothesis 10 (H10). Perception of the need for digital technology positively affects attitudes toward dengue control. Hypothesis 11 (H11). Perceptions of program benefits positively affect perceptions of digital technology needs. Discussion Question: Based on the study model, I don’t see a significant attempt to discuss the study findings. Authors must provide a detailed discussion that includes sufficient linkage/justification between the study findings with previous recent studies. Response: Several research results have been added in the text. “This study aimed to determine the variables that influence attitudes in dengue control related to the potential application of digital technology. It indicates a direct influence of Perception of Environmental Factors on Threatened Perception of Dengue, Program Constraints, Program Benefits, and Digital Technology needs. Perception of Program Benefits and Threatened Perception of Dengue directly Influences Digital Technology Need. Perception of Digital Technology Needs and Program Benefits directly influence Attitude Towards Dengue Control. Dengue is still a public health problem in Asia, especially in tropical countries like Indonesia. Even during the COVID-19 pandemic, dengue became a double disease burden46. During the COVID-19 pandemic, there was an increase in dengue infection, while dengue monitoring and control activities were limited in several countries47. This condition poses a severe threat to dengue-endemic areas. Several studies have shown that dengue control measures are essential. Empowering the community to carry out activities to control water containers where mosquitoes breed is effective in preventing dengue infection48, 49, 50. The Aedes aegypti mosquito as the primary vector needs to be eliminated51. This attitude in controlling dengue is the primary key to preventing dengue outbreaks52. Digital health surveillance technologies assist in disease prevention, detection, tracking, reporting and analysis53, 54. The development of digital technology supported by the infrastructure can assist in reporting. An integrated digital surveillance system is needed for dengue control. The variable perception of the need for digital technology and program benefits directly influences attitudes toward dengue control. This is related to the source of information obtained through digital media. Perception of environmental factors is influenced by Threatened Perception of Dengue, Program Constraints, Program benefits, and Digital Technology Needs.” Implication Question: The authors have focused on the practical/ managerial implications of the study. On the other hand, the authors have not given explicit discussion/ examples of theoretical implications. Response: Thank you for your input. For theoretical benefits, we have added that through this study a model for the development of science regarding attitude factors in controlling dengue with digital technology has been found. Quotations have been included in the article: “This study adds to the literature and provides a comprehensive understanding related to attitudes in dengue control, perceptions of program benefits, perceptions of dengue threats, perceptions of constraints, perceptions of the need for digital technology, and perceptions of environmental factors38,71. This study also contributes to supporting the health belief model30,72. This study has added to the theoretical literature by developing a structural model related to dengue control attitudes, especially in Indonesia.” Overall, thank you for all the input so this article can be even better. Regards, Tim." } ] }, { "id": "170731", "date": "19 May 2023", "name": "Ahmad Firdhaus Arham", "expertise": [ "Reviewer Expertise Consumer Behavior on Contemporary Science", "Tehnology and Sustainable Development Issues", "SPSS and PLS-SEM." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIntroduction\nLacks information about digital technology.\n\nWhat is the real problem statement? Why was this study needed, please relate strong problem statement.\nMethodology\nPlease bring out the variables section in your methodology. Suggest putting in the Theoretical Framework after introduction.\n\nNot Proper, to explain variables in your method, if you want to explain how the the variables and the items develop should be ok.\nAnalysis and result\nPlease clarify your model fit or not - please test it.\nDiscussion\nPlease focus on your results. What is your major finding in the first paragraph?\nOverall, technically sounds ok.\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": "9717", "date": "27 Jun 2023", "name": "Dewi Susanna", "role": "Author Response", "response": "Thank you very much for giving any comment for improvements. Here, we tried to respond your comments as follow: Introduction Lacks information about digital technology. Response: The research objectives have been adjusted to: This study aims to identify critical indicators influencing attitudes towards dengue control related to the potential for implementing digital technology. Digital technology has developed rapidly in the health sector. Digital technology is beneficial during the Covid-19 pandemic for conducting dengue surveillance. The existence of a social restriction policy with social distancing has caused the door-to-door control program not to be implemented [11], [12], [13]. What is the real problem statement? Why was this study needed, please relate strong problem statement. Responses: Attitudes in dengue control are essential because they can influence control measures. This model is needed in analyzing variables related to attitudes and the use of digital applications in conducting dengue surveillance. This study will obtain a potential model that can be used as a digital innovation for dengue control. This study aims to identify critical indicators influencing attitudes towards DHF control related to the potential for implementing digital technology. Methodology Please bring out the variables section in your methodology. Suggest putting in the Theoretical Framework after introduction. Response: We have separated the Theoretical Framework after introduction. We have also explained in detail about the conceptual model and hypothesis before the method. Not Proper, to explain variables in your method, if you want to explain how the the variables and the items develop should be ok. Responses: In the partial least square-structural equation modelling (PLS-SEM) method, explaining the variables being analyzed is essential. This explanation facilitates the reader's understanding of the definition of these variables. The symbol of each variable needs to be defined so that it has the same meaning. It has been included in the research method. Analysis and result Please clarify your model fit or not - please test it. Responses: An explanation of the structural model fit has been given in Table 6. The structural model is evaluated after verifying the correctness of the construction measurements. The path coefficients and their 10,000 resampling bootstrap significance levels are reported in Table 6 and Figure 6. Additionally, Table 6 shows that the VIF constructs range from 1,000 to 1,700, indicating no collinearity between variables. This study also assesses the quality by examining the overall predictive relevance of the model with a Q2 value above zero which indicates a fit in the prediction model. The magnitude of Q2 has a value of 0 < Q2 < 1, where the closer to 1, the better the model. The coefficient of determination (R2) also exceeds 0.1 for endogenous latent variables since the construct has an acceptable predictive power quality. Discussion 1. Please focus on your results. What is your major finding in the first paragraph? Responses: A discussion of results and discussion has been added, as described below: This study aimed to determine the variables that influence attitudes in dengue control related to the potential application of digital technology. It indicates a direct influence of Perception of Environmental Factors on Threatened Perception of Dengue, Program Constraints, Program Benefits, and Digital Technology needs. Perception of Program Benefits and Threatened Perception of Dengue directly Influences Digital Technology Need. Perception of Digital Technology Needs and Program Benefits directly influence Attitude Towards Dengue Control. Dengue is still a public health problem in Asia, especially in tropical countries like Indonesia. Even during the COVID-19 pandemic, dengue became a double disease burden 46. During the COVID-19 pandemic, there was an increase in dengue infection, while dengue monitoring and control activities were limited in several countries 47. This condition poses a severe threat to dengue-endemic areas. Several studies have shown that dengue control measures are essential. Empowering the community to carry out activities to control water containers where mosquitoes breed is effective in preventing dengue infection 48, 49, 50. The Aedes aegypti mosquito as the primary vector needs to be eliminated 51. This attitude in controlling dengue is the primary key to preventing dengue outbreaks 52. Digital health surveillance technologies assist in disease prevention, detection, tracking, reporting and analysis 53, 54. The development of digital technology supported by the infrastructure can assist in reporting. An integrated digital surveillance system is needed for dengue control. The variable perception of the need for digital technology and program benefits directly influences attitudes toward dengue control. This is related to the source of information obtained through digital media. Perception of environmental factors is influenced by Threatened Perception of Dengue, Program Constraints, Program benefits, and Digital Technology Needs. Overall, technically sounds ok. Response: Thank you very much for your appreciation. Overall, thank you for all the input so this article can be even better. Regards, Tim." } ] } ]	1	https://f1000research.com/articles/11-1283
https://f1000research.com/articles/12-752/v1	27 Jun 23	{ "type": "Systematic Review", "title": "Evaluating the clinical outcomes of thulium fiber laser (TFL) in comparison to holmium laser in the treatment of urinary tract stones – A systematic review", "authors": [ "Rio Tritanto", "Isaac Deswanto", "Isaac Deswanto" ], "abstract": "Holmium:Yttrium-Aluminum-Garnet (Ho:YAG) had been considered the gold standard for treating urinary tract stones. However, advancements in laser technology have introduced thulium fiber laser (TFL) as a potential alternative. Preliminary studies have indicated that TFL may have certain advantages over Ho:YAG laser in lithotripsy. This systematic review compared the clinical outcomes of TFL and Ho:YAG laser for urinary tract stone treatment, focusing on operating time, stone-free rate (SFR), retropulsion, and complications. A systematic search was conducted on PubMed and ScienceDirect for original articles published within the last 5 years, comparing the clinical outcomes of Ho:YAG and TFL in lithotripsy. Inclusion criteria were English-language studies focusing on Ho:YAG and TFL laser energy for urinary tract stones, with accessible full-text articles comparing clinical outcomes. Excluded were studies discussing lasers for conditions other than urinary tract stones or using lasers other than TFL and Ho:YAG. Four studies (544 procedures) met the criteria and underwent risk of bias assessment using Risk of Bias 2 (ROB-2) for randomized trials and Risk of Bias in Non-randomized Studies of Interventions (ROBINS-I) for cohort studies. The data were presented in tables and charts. In this review, TFL demonstrated a shorter operating time compared to Ho:YAG (and higher stone-free rates in two studies. TFL also had a lower incidence of stone retropulsion. Intra-operative complication rates varied between the groups for ureterorenoscopy (URS) and retrograde intrarenal surgery (RIRS) procedures, while TFL had a higher rate of prolonged haematuria during mini percutaneous nephrolithotomy (PCNL) procedures. Postoperative complications were similar in both groups. Limitations of this review include procedural and laser setting heterogeneity, a small number of studies, and the lack of registration and protocols. In conclusion, TFL is an effective and safe alternative to Ho:YAG laser for lithotripsy, offering shorter operation time, higher stone-free rates, and reduced stone retropulsion.", "keywords": [ "Thulium fiber laser", "Holmium", "Ho:YAG", "urinary tract stone" ], "content": "Introduction\n\nThe use of laser (light amplification by stimulated emission of radiation) energy in the field of urology had undergone tremendous progress over the years, this is especially true in the utilization of lasers in the fragmentation of urinary tract stones.1,2 The first documentation of utilizing laser in the treatment of urinary tract stones dated back to 1968 by Mulvaney et al. in an in-vitro study, while the first published in-vivo study of laser lithotripsy was in 1986 by Watson et al.3,4\n\nSeveral types of lasers have been applied in urological procedures, such as pulsed dye laser, FREDDY (frequency-doubled double-pulse neodymium-doped yttrium aluminium garnet (Nd: YAG)), alexandrite laser, holmium laser, and many others.2 Nevertheless, holmium: yttrium aluminum garnet (Ho: YAG) laser has proven itself to be superior compared to its rivals because of its ability to fragment all types of stones efficiently with acceptable safety profiles. Within the last two decades, Ho: YAG laser has become the gold standard in urinary tract stones fragmentation procedure until the recent appearance of a new competitor, thulium fiber laser (TFL).5–9 Fried et al. conducted the first in-vitro trial of using TFL in fragmenting urinary tract stone and found TFL’s capabilities in disintegrating both soft and hard stones.10 Recent preclinical and clinical studies shows TFL holds more advantages over the Ho:YAG laser, in terms of better ablation efficiency and efficacy, lower retropulsion effect, and more durable laser fiber.11–13\n\nIn this study, we aim to review the clinical outcomes (operating time, stone-free rate, retropulsion, and complication rate) of TFL in comparison to the current gold standard (Ho:YAG laser) in the treatment of urinary tract stones.\n\n\nMethods\n\nThe report of this systematic review was prepared following the guidelines provided by the PRISMA (Preferred Reporting Items for Systematic Review and Meta-Analysis) statement.32,33 In July 2022, we conducted a systematic search of the PubMed (RRID:SCR_004846) and ScienceDirect databases. The search strategy involved the use of Boolean operators to combine the keywords and refine the search results. Table 1 presents the specific keywords that were utilized in each database during the search process. We limited the search to studies published between July 2018 to July 2022 and applied specific inclusion and exclusion criteria. Included studies were required to be written entirely in English, use Ho:YAG and TFL laser energy in urinary tract stone cases, and provide readily available full-text articles comparing clinical outcomes between TFL and holmium laser. We excluded studies discussing the use of laser energy for other conditions besides urinary tract stones and publications on the use of lasers besides TFL and Ho:YAG. In cases where articles were duplicated, we counted them as one instead of multiple entries. To ensure the validity of the search results, we manually performed the search using these criteria, and two co-authors conducted the data collection without utilizing any automated tools. The risk of bias in the selected studies was evaluated using the ROB-2 (Risk of Bias 2) (RRID:SCR_016393) tool for randomized controlled trials and the ROBINS-I (Risk of Bias in Non-randomized Studies of Interventions) tool for cohort studies.14,15 The data collected from the studies included population characteristics (age, gender), stone characteristic (stone size, stone burden, stone density), type of lithotripsy procedures, number of patients, laser settings, operating time, lasing time, stone free rate, incidence of retropulsion, and complication rate. The collected data were then input into a spreadsheet using Microsoft Excel (Microsoft, 2021) (RRID:SCR_016137) and direct comparison of the clinical outcomes were formulated into separate charts.\n\n\nResults\n\nThe search strategy produced a total of 106 manuscripts after omitting duplicated articles from both databases. After evaluating the title and abstract of the articles, a total of 89 studies were eliminated from further consideration. The full articles of the remaining 17 studies were then reviewed, and out of those, 13 studies were excluded as they were found to be an ex vivo study and in-vitro studies. Eventually, this review included four studies that met the inclusion criteria, involving a total of 544 procedures.31 The studies included in this review underwent a risk of bias assessment using the appropriate tools. However, the other two trials were graded as having some concern due to the randomization process. As for the retrospective cohort study conducted by Jaeger et al., it was deemed to have a moderate risk of bias. This assessment was based on the potential presence of confounding factors that could impact the outcomes of the study. The summary of risk of bias assessment are provided in Figure 1.\n\nData extraction and analysis were conducted based on these selected studies. The selected studies were conducted in four different countries: India, Norway, Russia, and the USA. The population characteristics are summarized in Table 2, while the outcomes of the studies (operating time, lasing time, stone free rate (SFR), retropulsion, and complication rate) for both TFL and Ho:YAG are summarized in Table 3.\n\nDespite the differences in procedures (URS, RIRS, and PCNL), laser settings (different frequency, different laser energy, and different laser fiber), and population (adult and pediatric cases), all four studies demonstrated that the operating time of TFL group was shorter compared to Ho:YAG group (24,7-78 minutes vs 32,4-84 minutes, respectively). Three studies by Martov et al., Ulvik et al., and Mahajan et al. found these differences to be statistically significant. The comparison of the operating time in both laser group is shown in Figure 2.\n\npp value < 0.005 between the two groups.\n\nIn Figure 3, it is evident that patients in the TFL group had a higher stone free rate (SFR) compared to the holmium group. This finding was consistent across all four studies included in this review. Ulvik et al. and Jaeger et al. both demonstrated a statistically significant higher SFR for the TFL group (p-value <0.005). Interestingly, the location of the stone played a significant role in determining the SFR. As mentioned by Jaeger et al., higher SFR was observed in cases of ureteral stones, while the lowest SFR was observed in cases where stones were located in the lower pole of the kidney.\n\npp value < 0.005 between the two groups.\n\nOnly one of the four articles, led by Martov et al., reported on the incidence of retropulsion between the two laser types. They classify the retropulsion into three categories such as no retropulsion, mild retropulsion (if no additional devices were needed or the stone migration occurred within the ureter) and severe retropulsion (if either antimigration device or flexible ureteroscope was used due to the migration into calices). Martov et al. found the absence of retropulsion in nearly all cases of the TFL group and no severe retropulsion were observed in this group, on the other hand, no retropulsion was seen in 31% (27 out of 87) of the patients and severe retropulsion were observed in 18% (16 out of 87) patients in the Ho:YAG group (Figure 4).\n\nThe reported complications across these four studies were varied. Jaeger et al. found no intraoperative complication during procedures for both the Ho:Yag and TFL group, while Martov et al. reported several intraoperative complications, such as ureteral perforation, fragment migration, and bleeding during the management of ureteral stones. Nevertheless, there was no statistically significant difference in the rate of intraoperative complications in both laser treatment groups. On the contrary, Ulvik et al. reported a significantly higher rate of intra-operative complication (such as bleeding that impairs vision, perforation, and mucosal abrasion) in Ho:YAG group compared to TFL Group (16 out of 60 patients (27%) vs 5 out of 60 patients (8%) respectively, p<0.05). In another study attempting to evaluate the safety and effectiveness of TFL in mini PCNL procedures, Mahajan et al. reported higher rate of prolonged hematuria in TFL group compared to Ho:YAG group (13 out of 59 cases (22%) vs 2 out of 66 cases(3%) respectively, p<0.05). All four studies included in the analysis utilized the Clavien-Dindo classification systems to assess postoperative complication, and all four studies reported similar postoperative complications in both groups.\n\n\nDiscussion\n\nAs a novel lithotripsy technology, TFL has emerged as an attractive alternative to Ho:YAG laser due to its unique architecture, which leads to a higher stone ablation rate and lower retropulsion, as demonstrated in in-vitro studies.11,16 Supporting these findings, clinical studies have also shown that TFL outperforms Ho:YAG in terms of operating time, retropulsion, and SFR during lithotripsy.17–20\n\nIn this systematic review, three out of the four trials showed that the TFL group had a significant shorter operation time than the Ho:YAG group. This could be attributed to TFL’s ability to operate at a much higher frequency of up to 2000Hz.21 Pre-clinical and clinical studies have found that higher frequency regimen was associated with greater ablation efficacy and ablation speed.21–24 However, It is important to note that using high-frequency and high-energy settings may lead to the disturbance of the endoscopic view due to an increase in dust and microbleeding.9,25,26 Despite this, both Ulvik O et al. and Martov et al. found that the incidence of bleeding that compromised intraoperative vision was considerably less in TFL group when compared to Ho:YAG, resulting in fewer pauses during the operation and ultimately shorter operating time.19,20 Additionally, TFL operates at a wavelength of 1940 nm which closely matches the absorption coefficient peak of liquid water. This attribute results in a higher water absorption coefficient compared to Ho:YAG laser, with the TFL absorption coefficient being four times higher (3 mm-1 vs 14 mm-1, respectively).10,21 This property leads to better ablation efficacy as it lowers the ablation threshold of urinary stones, resulting in a more efficient and effective ablation process. In fact, the TFL can achieve a higher ablation rate using the same laser settings or achieve the same stone ablation result using lower energy settings.21,25\n\nRetropulsion is defined as undesirable stone movement during laser lithotripsy.11 Martov et al. demonstrated that TFL had lower incidence of retropulsion, which is attributed to smaller bubbles produced during lithotripsy, therefore generating less pressure that pushed the stones away.21 Another factor that contributed to the lower retropulsion rate is TFL’s capabilities to be operated in a much lower pulse energy than the minimum of 0.2 J required for Ho:YAG.16,25\n\nIn this review, SFR depends on the location of the stones. Higher SFR is observed in ureteral stones, while stones located in lower pole have the lowest SFR. Ulvik et al. and Jaeger et al. reported a significantly higher SFR in the TFL group compared to the Ho:YAG group, attributed to the TFL’s superior ablation efficacy and better endoscopic view.18,19 Higher SFR rate would be beneficial for both patients and surgeons since it reduces the needs for subsequent procedure. Furthermore, shorter operation time also leads to lower cost for both the patients and health care institution, as stated by Ryan JR et al.27\n\nConsidering the safety profile of TFL, Ulvik et al. reported a lower rate of intraoperative complications such as bleeding that impairs vision, perforation, and mucosal abrasion in the TFL group, which is attributed to TFL’s higher absorption coefficient leading to lower penetration depth and thus increasing the safety profile of TFL.19,21,25 On the other hand, Mahajan et al. found a higher rate of prolonged hematuria in TFL group during Mini PCNL procedures, however, it was self-limiting and therefore could be treated conservatively. According to Mahajan et al., the hematuria is likely caused by thermal stress injuries to the mucosa, which occur due to reduced irrigation and visibility resulting from the presence of stone fragments.17 Hardy et al. mentioned the possibility of higher intraurethral temperature using TFL during lithotripsy. The higher temperature produced by TFL may be due to higher water absorption coefficient and the use of high frequency.28 However, this claim has been contradicted by several studies that indicate a relatively similar increase in temperature in both Ho:YAG and TFL.11 Furthermore, in the study led by Æsøy et al. it is indicated that using larger laser fiber generate higher intrarenal temperature in porcine model, which gives TFL an advantage since it uses a smaller laser fiber.29 Nevertheless, mitigating thermal induced damage should always be the surgeon’s priority by maintaining irrigation fluid, intermittent laser activation, using cooled irrigation fluid, or avoid using high power setting to minimize thermal injury.30 Æsøy et al. advised that laser with high power settings (≥20 Watt) should be used with caution to prevent thermal injury since the activation of high power settings easily surpass the temperature threshold (42°C) that cause cellular damage, meanwhile the activation of laser with settings 2,4 W (0,4 J and 6 Hz) and 8 W (0,8 J and 10 Hz) were able to maintain the intrapelvic temperature within the safety limit.29 Additionally, Hardy et al also recommended to avoid using frequency higher than 500 Hz in order to minimize thermal damage.28\n\nThe limitations of this review include heterogeneity in procedures and laser settings, a limited number of included studies, and the lack of registration and protocols. Firstly, the heterogeneity in procedures and laser settings among the selected studies introduces variability and may affect the comparability of the results. The use of different procedures such as URS, RIRS, and PCNL, as well as variations in laser settings including frequency, energy, and fiber used, can influence the outcomes and make it challenging to draw definitive conclusions.\n\nSecondly, the relatively small number of included studies (only four studies) may limit the generalizability of the findings and reduce the overall strength of evidence. With a limited number of studies, there is a higher possibility of chance effects, and the findings may not fully represent the entire population or provide robust evidence.\n\nThirdly, we acknowledge the review was conducted without prior registration in a public database and without predetermined protocols. The absence of registration and protocols may introduce potential biases and affect the transparency and reproducibility of the review. Without predefined protocols, there is a risk of selective reporting and data analysis, which can influence the validity of the findings. Future research should aim to address these limitations by registering studies and following established protocols to ensure transparency and minimize bias.\n\n\nConclusion\n\nIn conclusion, TFL has demonstrated efficient fragmentation of urinary tract stones with shorter operation time and higher SFR compared to Ho:YAG laser while still maintaining patient safety. However, the limited availability of clinical studies on TFL and lack of consensus on optimal laser settings for lithotripsy indicate a need for further research in this area. Additional randomized clinical trials comparing the two laser systems could provide valuable insights for future treatment options.\n\nThis review was conducted without prior registration and no protocols were registered.", "appendix": "Data availability\n\nFigshare: PRISMA FLOW DIAGRAM Evaluating the clinical outcomes of thulium fiber laser (TFL) in comparison to holmium laser in the treatment of urinary tract stones – A systematic review.docx. https://doi.org/10.6084/m9.figshare.22811138.v2 31\n\nFigshare: PRISMA CHECKLIST Evaluating the clinical outcomes of thulium fiber laser (TFL) in comparison to holmium laser in the treatment of urinary tract stones – A systematic review. https://doi.org/10.6084/m9.figshare.22817099.v2 32\n\nFigshare: ABSTRACT PRISMA Checklist Evaluating the clinical outcomes of thulium fiber laser (TFL) in comparison to holmium laser in the treatment of urinary tract stones – A systematic review. https://doi.org/10.6084/m9.figshare.22817102.v2 33\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nDołowy Ł, Krajewski W, Dembowski J, et al.: The role of lasers in modern urology. 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Lasers Surg. Med. 1992; 12: 353–363. Publisher Full Text\n\nJones P: Current status of thulium fi bre laser lithotripsy: an up-to-date review. BJU Int. 2021; 128: 531–538. PubMed Abstract \| Publisher Full Text\n\nFried NM: Thulium Fiber Laser Lithotripsy: An in vitro Analysis of Stone Fragmentation Using a Modulated 110-Watt Thulium Fiber Laser at 1. 94 m m. Lasers Surg. Med. 2005; 37(June): 53–58. Publisher Full Text\n\nAndreeva V, Vinarov A, Yaroslavsky I, et al.: Preclinical comparison of superpulse thulium fiber laser and a holmium: YAG laser for lithotripsy. World J. Urol. 2019; 38: 497–503. Publisher Full Text\n\nKhusid JA, Khargi R, Seiden B, et al.: Thulium fiber laser utilization in urological surgery: A narrative review. Investig. Clin. Urol. 2021; 62: 136–147. 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PubMed Abstract \| Publisher Full Text\n\nTraxer O, Keller EX: Thulium fiber laser: the new player for kidney stone treatment ? A comparison with Holmium: YAG laser. World J. Urol. 2020; 38(8): 1883–1894. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEnikeev D, Taratkin M, Klimov R, et al.: Superpulsed thulium-fiber laser for stone dusting – in search of perfect ablation regimen. A prospective single center study. J. Endourol. 2020; 34: 1175–1179. PubMed Abstract \| Publisher Full Text\n\nBlackmon RL, Irby PB, Fried NM, et al.: Comparison of holmium: YAG and thulium fiber laser lithotripsy: ablation thresholds, ablation rates, and retropulsion effects Comparison of holmium: YAG and thulium fiber laser lithotripsy: ablation thresholds, ablation rates, and retropulsion effects. J. Biomed. Opt. 16: 071403. PubMed Abstract \| Publisher Full Text\n\nBlackmon RL, Irby PB, Fried NM: Holmium: YAG (k ¼ 2, 120 nm) Versus Thulium Fiber (k ¼ 1, 908 nm) Laser Lithotripsy. J. Biomed. Opt. 2010; 236(March): 232–236. Publisher Full Text\n\nKronenberg P, Traxer O: The laser of the future: reality and expectations about the new thulium fiber laser — a systematic review. Transl Androl Urol. 2019; 8(Suppl 4): S398–S417. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVentimiglia E, Traxer O: Is Very High Power/Frequency Really Necessary During Laser Lithotripsy? RE: Understanding the Popcorn Effect During Holmium Laser Lithotripsy for Dusting (Aldoukhi et al, Urology. 2018 Dec;122:52-57). Urology. 2019; 127: 135. PubMed Abstract \| Publisher Full Text\n\nRyan JR, Nguyen MH, Linscott JA, et al.: Ureteroscopy with thulium fiber laser lithotripsy results in shorter operating times and large cost savings. World J. Urol. 2022; 40(8): 2077–2082. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHardy LA, Wilson CR, Irby PB, et al.: Thulium fiber laser lithotripsy in an in vitro ureter model ureter model. J. Biomed. Opt. 19. PubMed Abstract \| Publisher Full Text\n\nÆsøy MS, Beisland C, Ulvik Ø: Temperature profiles during ureteroscopy with thulium fiber laser and holmium: YAG laser: Findings from a pre-clinical study Temperature profiles during ureteroscopy with thulium fiber laser and. Scand J. Urol. 2022; 56(4): 313–319. PubMed Abstract \| Publisher Full Text\n\nNoureldin YA, Kallidonis P, Liatsikos EN: Lasers for stone treatment: how safe are they? Curr. Opin. Urol. 2020; 30: 130–134. Publisher Full Text\n\nTritanto R, Deswanto I: PRISMA FLOW DIAGRAM Evaluating the clinical outcomes of thulium fiber laser (TFL) in comparison to holmium laser in the treatment of urinary tract stones – A systematic review.docx. figshare. Figure. 2023. Publisher Full Text\n\nTritanto R, Deswanto I: PRISMA CHECKLIST Evaluating the clinical outcomes of thulium fiber laser (TFL) in comparison to holmium laser in the treatment of urinary tract stones – A systematic review. figshare. Figure. 2023. Publisher Full Text\n\nTritanto R, Deswanto I: ABSTRACT PRISMA Checklist Evaluating the clinical outcomes of thulium fiber laser (TFL) in comparison to holmium laser in the treatment of urinary tract stones – A systematic review. figshare. Figure. 2023. Publisher Full Text" }	[ { "id": "186723", "date": "14 Aug 2023", "name": "Boyke Soebhali", "expertise": [ "Reviewer Expertise Laser stone surgery", "retrograde intrarenal surgery", "percutaneous nephrolithotripsy", "reconstructive urology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe review compared clinical outcomes of thulium fiber laser (TFL) versus holmium laser for treating urinary tract stones. Four studies with 544 procedures were included.\nThree studies found TFL had higher stone-free rates than holmium, which was statistically significant in two studies. TFL's superior ablation efficacy and better visibility contribute to higher stone-free rates.\nOne study reported TFL had lower retropulsion rates compared to holmium. TFL creates smaller bubble explosions that push stones less. Also, TFL can operate at lower pulse energy than holmium.\nComplication rates were similar between TFL and holmium, except one study found higher prolonged hematuria rates with TFL during mini-PCNL. This may be from thermal mucosal injuries.\nLimitations include variability in procedures/settings, small number of studies, and lack of registration and protocols. In summary, according to this article TFL appears to be an effective and safe alternative to holmium laser for lithotripsy, offering shorter operation times, higher stone-free rates, and less retropulsion. More randomized trials are needed to provide further evidence.\nThis article clearly stated objective to compare TFL and holmium laser for urinary stones. Follows PRISMA guidelines.\nComprehensive literature search across two major databases with defined search strategy. Manual screening done by two authors.\nAppropriate inclusion/exclusion criteria applied. Only studies directly comparing TFL and holmium lasers were included.\nAssessed risk of bias for each included study using validated tools like ROB-2 and ROBINS-I. Provided risk of bias summary.\nExtracted and presented relevant study characteristics and outcomes data in tables. Analyzed data to synthesize results across studies.\nHowever, only four studies met inclusion criteria, which limits overall sample size and power. Studies were heterogenous.\nLack of pre-registered protocol and PROSPERO registration introduces potential for bias.\nNo assessment of publication bias done.\nData analysis is mostly descriptive rather than meta-analysis due to heterogeneity and small number of studies.\nLimited exploration of potential confounders and variability between studies in the discussion.\nOverall, this review provides a baseline overview of the current limited evidence comparing TFL and holmium lasers. More rigorous systematic reviews and meta-analyses would strengthen the evidence when more studies become available. Registration of protocols could improve transparency. But given the early state of TFL research, this review offers useful initial insights.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [] }, { "id": "195117", "date": "04 Sep 2023", "name": "Scott Quarrier", "expertise": [ "Reviewer Expertise Endourology" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present a systematic review comparing laser modalities for nephrolithotripsy.\nPrimary outcome measures were operating time, stone-free rate (SFR), retropulsion, and complications.\nOnly four studies met the inclusion criteria. Unfortunately, the article was poorly timed. Since the completion of the systematic review but before the submission there have been multiple studies that warrant inclusion and submission without inclusion of these studies makes this review grossly out of date. The studies that warrant to be included/addressed are as follows:\nNikoufar P, Hodhod A, Fathy M, et al. Thulium Fiber Laser versus Pulse-Modulated Holmium MOSESTM Laser in Flexible Ureteroscopy for the Management of Kidney Stones: A Single-Centre Retrospective Analysis. J Endourol. Published online August 19, 2023. doi:10.1089/end.2023.0284\n\nKeat WOL, Somani BK, Pietropaolo A, et al. Do Hounsfield Units have any significance in predicting intra- and postoperative outcomes in retrograde intrarenal surgery using Holmium and Thulium fiber laser? Results from the FLEXible ureteroscopy Outcomes Registry (FLEXOR). World J Urol. Published online March 16, 2023. doi:10.1007/s00345-023-04362-7\n\nHaas CR, Knoedler MA, Li S, et al. Pulse-modulated Holmium:YAG Laser vs the Thulium Fiber Laser for Renal and Ureteral Stones: A Single-center Prospective Randomized Clinical Trial. J Urol. 2023;209(2):374-383. doi:10.1097/JU.0000000000003050\n\nCastellani D, Fong KY, Lim EJ, et al. Comparison Between Holmium:YAG Laser with MOSES Technology vs Thulium Fiber Laser Lithotripsy in Retrograde Intrarenal Surgery for Kidney Stones in Adults: A Propensity Score-matched Analysis From the FLEXible Ureteroscopy Outcomes Registry. J Urol. 2023;210(2):323-330. doi:10.1097/JU.0000000000003504\nUnfortunately, despite the well-executed and written review it is already out of date.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-752
https://f1000research.com/articles/12-749/v1	26 Jun 23	{ "type": "Research Article", "title": "Receptor-Based Pharmacophore Modelling of a series of ligands used as inhibitors of the SARS-CoV-2 virus by complementary theoretical approaches, molecular docking, and reactivity descriptors.", "authors": [ "Alejandro Morales-Bayuelo", "Jesús Sánchez-Márquez" ], "abstract": "Background: A coronavirus identified in 2019, SARS-CoV-2, has caused a pandemic of respiratory illness, called COVID-19. Most people with COVID-19 experience mild to moderate symptoms and recover without the need for special treatments. The SARS‑CoV‑2 RNA‑dependent RNA polymerase (RdRp) plays a crucial role in the viral life cycle. The active site of the RdRp is a very accessible region, so targeting this region to study the inhibition of viral replication may be an effective therapeutic approach. For this reason, this study has selected and analysed a series of ligands used as SARS-CoV-2 virus inhibitors, namely: the Zidovudine, Tromantadine, Pyramidine, Oseltamivir, Hydroxychoroquine, Cobicistat, Doravirine (Pifeltro), Dolutegravir, Boceprevir, Indinavir, Truvada, Trizivir, Trifluridine, Sofosbuvir and Zalcitabine. Methods: These ligands were analyzed using molecular docking, Receptor-Based Pharmacophore Modelling. On the other hand, these outcomes were supported with chemical reactivity indices defined within a conceptual density functional theory framework. Results: The results show the conformations with the highest root-mean-square deviation (RMSD), have π-π stacking interaction with residue LEU141, GLN189, GLU166 and GLY143, HIE41, among others. Also was development an electrostatic potential comparison using the global and local reactivity indices. Conclusions: These studies allow the identification of the main stabilizing interactions using the crystal structure of SARS‑CoV‑2 RNA‑dependent RNA polymerase. In this order of ideas, this study provides new insights into these ligands that can be used in the design of new COVID-19 treatments. The studies allowed us to find an explanation supported in the Density Functional Theory about the chemical reactivity and the stabilization in the active site of the ligands.", "keywords": [ "RNA dependent RNA polymerase SARS-CoV-2 virus", "COVID-19 treatments", "molecular docking", "chemical reactivity descriptors", "density functional theory." ], "content": "Introduction\n\nCOVID-19 is an infectious disease caused by SARS-CoV-2 virus. The majority of individuals infected with COVID-19 experience moderate to mild symptoms and can recover without requiring any special treatment. Nonetheless, there are some cases where people develop severe symptoms and may require medical attention.1\n\nThere is still no curative treatment for COVID-19, but we already have vaccines that, in many cases, prevent infection, and in the event of contracting the disease, allow to pass through it mildly. Other treatments are still in the development phase and are intended to prevent transmission.\n\nTreatment for severely ill COVID-19 patients and those at risk of severe disease involves administering oxygen.2(a) Critically ill patients receive more advanced respiratory support, such as mechanical ventilation. Dexamethasone, a corticosteroid, can assist in reducing the time patients spend on a ventilator and saving the lives of those with severe or critical conditions. For further information, refer to the question-and-answer section on dexamethasone.2(b) It has been demonstrated that hydroxychloroquine does not provide any therapeutic benefit against COVID-19. For more information, see the questions and answers section on hydroxychloroquine.\n\nThe self-administration of antibiotics or any other medication is not recommended by the World Health Organization (WHO) to prevent or cure COVID-19.3 For these reasonsnew alternatives for COVID-19 treatment is needed. In this work, zidovudine, tromantadine, pyramidine, oseltamivir, hydroxychoroquine, cobicistat, doravirine (Pifeltro), dolutegravir, boceprevir, indinavir and zalcitabine were assessed. Some of antecedents related to ligands are: Zidovudine4 is a medication used in combination with other drugs to manage human immunodeficiency virus (HIV) infection. Tromantadine5 is a medication used to treat herpes simplex virus. It inhibits both early and late events in the virus replication cycle and is considered an antiviral medicine. Pyrimidine depletion and the immune response are associated with human coronavirus infection.6 Oseltamivir7 is used to treat some types of influenza in individuals who have experienced flu-like symptoms for no more than two days. Hydroxychloroquine8 has been evaluated in clinical trials as a treatment for COVID-19, but the results have been inconclusive and must be interpreted with caution due to limitations in study design.\n\nSeveral protease inhibitors have been developed to target human immunodeficiency virus 1 (HIV-1), such as cobicistat/doravirine (Pifeltro).9,10 Other drugs identified by in silico methods with the capacity to bind to Mpro and with potential action against infection by SARS-CoV-2 include dolutegravir and boceprevir.11,12 Finally, potential antivirals against SARS-CoV-2 have been proposed using virtual screening methods, such as indinavir and zalcitabine.13,14 All these ligands have been analysed using theoretical techniques such as molecular docking, electrostatic potential analysis and chemical reactivity descriptors within the Density Functional Theory (DFT).15\n\n\nMethods\n\nThe receptor structure for the docking experiment was extricated utilizing the following protocols through the crystal Structure of SARS-CoV-2 RNA-dependent RNA polymerase PBD code: 6m71, which was adjusted utilizing the protein preparation wizard module of the Schrödinger suite 2017-1. i) The optimization of the hydrogen bond (H-bond) network and refinement of the protein structure was performed. ii) PropKa utility was utilized to determine the protonation states at physiological pH. iii) The restrained molecular minimization with heavy atoms constrained to a low root-mean-square deviation (RMSD) from the initial coordinates was carried out using the Impact Refinement (Impref) module.16–18\n\nAlternatively, the molecular structures of the compounds were sketched using Maestro Editor (Maestro, version 11.1, Schrödinger, LLC). Then 3D conformations were gained with the LigPrep module, with ionization/tautomeric states predicted under physiological pH conditions with Epik. Subsequently, energy minimization was used using the protocol with the Macro model using the OPLS2005 force field.\n\nThe docking investigations were carried out using Glide19,20 with the default parameters and the Standard Precision (SP) model. The docking grid was generated with the co-crystallized ligand at the center using the default settings. To enable the binding of larger ligands, a scaling factor of 0.8 was applied to the van der Waals radii of the nonpolar protein atoms. The Extra Precision (XP) was also employed for induced fit docking (IFD) to allow the protein to undergo backbone, side-chain, or both movements upon ligand docking and to expand alternate receptor conformations suitable for binding ligands with unusual orientations. Finally, considering the extent of residue movement induced by the IFD computation, to evaluate the ligands, we examined the conformations of the most and least active compounds for each molecule in the molecular set. The best predictions of the poses were predicted by 10ns molecular dymane calculations, in order to analyse its stabilization in the active site.\n\nSeveral previous investigations have established a correlation between quantum similarity and chemical reactivity descriptors.21–31 Quantum similarity and DFT utilize the density function as an object of study for similarity indexes. Specifically, the Coulomb index can be linked to electronic factors related to chemical reactivity. The global reactivity indices, such as chemical potential (μ),32 hardness (ɳ),33 and electrophilicity (ω),34,35 will be calculated using Frontier Molecular Orbitals (FMO) and the energy gap. These chemical reactivity indices (Equations 1-5) provide information about the stability of the systems. Chemical potential measures the tendency of electrons to leave the equilibrium system,36 while chemical hardness measures the resistance of a chemical species to change its electronic configuration.29\n\nThe mathematical definition of the electrophilicity index (ω) is related to the stabilization energy of a system when it becomes saturated by electrons from the external environment34,35:\n\nFor this study, the local reactivity descriptors utilized were the Fukui functions. Equations (4, 5) depict how the chemical potential of a system responds to changes in the external field. This is defined as the derivative of the electronic density with respect to the number of electrons at a constant external field.\n\nThe nomenclature f+r→ and f−r→ have been used to indicate nucleophilic and electrophilic attacks, respectively.36–38 This methodology employs global and local reactivity descriptors to analyze quantum similarity in the molecular set. All calculations were carried out using the method B3LYP39 and the basis set 6-311xxG(d,p)40 which is the result of adding a correction to the 6-311G(d) basis set leading to calculations of electronegativity, hardness, reactivity indices and frontier molecular orbitals and is comparable in quality to those obtained with much larger basis sets (such as Aug-cc-pVQZ and Aug-cc-pV5Z). This method/basis set has been used in combination with the Gaussian 16 package.41\n\n\nResults and discussion\n\nTo obtain a deeper analysis about the features associated to the biological activity the pharmacophore development has been used using the Zidovudine, Tromantadine, Pyramidine, Oseltamivir, Hydroxychoroquine, Cobicistat, Doravirine (Pifeltro), Dolutegravir, Boceprevir, Indinavir, Truvada, Trizivir, Trifluridine, Sofosbuvir and Zalcitabine. Figure 1 shows the pharmacophore development using the ligands: A) Truvada, B) Trizivir, C) Trifluridine and D) Sofosbuvir. To develop a pharmacophore model, the co-complexed ligand was extracted from its original conformation in the protein and subjected to the pharmacophore development tool available in the Schrödinger suite 2017-1.16\n\nA) Truvada, B) Trizivir, C) Trifluridine and D) Sofosbuvir.\n\nA receptor-based pharmacophore model was constructed (Figure 1) to identify key features associated with biological activity, namely negative, positive, and aromatic ring. The model incorporated hydrogen bond acceptor, hydrogen bond donor, and hydrophobic features, which showed good agreement with a previously reported model. The validation process yielded an RMSD value of 0.38. Figure 2 shows the molecular docking outcomes for the ligand studied.\n\nFigure 2 shows the H-bonds for the best conformation of zidovudine with the residues CYS145 and GLU166. For this ligand the best pose has been with docking score -6.241. The H-bond is formed with the alcohol group with the residue CYS145 and ketone group for the residue GLU166.\n\nAs seen in Figure 3, tromantadine showed H-bonds with the residue LEU141 with bond length 1.62Å, GLN189 with bond length 1.54Å and with the residue GLU166 with bond length 1.59Å. The H-bonds with the residues LEU141 and GLN189 are with the amino groups and ketone group for the residue GLU166, like Zidovudine.\n\nFigure 4 shows the H-Bond with the residues GLY143 with length 1.53Å, GLU166 with length 1.61Å and HIE41 with length 1.71Å. The GLY143 and GLU166 had H-bonds with the ketone group, HIE41 had H-bond with the aromatic ring, and finally GLU166 had a H-bond with an amino group.\n\nOn the other hand, Figure 5 shows the H-bonds for doravirine. This compound had H-bonds with the residues GLY143 with length 1.59Å, CYS145 with length 1.59Å, GLU166 with length 1.47Å and a bond with an aromatic ring with length 1.69Å with the residue HIE41.\n\nDolutegravir presented H-bonds with the residues GLU166 with a length of 1.48Å. Other H-bonds were with the residues GLY143 with a length of 1.55Å and GLN189 with a length of 1.73Å (see Table 1).\n\nFinally, Figure 7 shows the docking outcomes for the indinavir ligand. This compound had two interactions with the residue GLU166 with lengths of 1.43Å and 1.53Å. On the other hand, this ligand had a H-bond with the residue HIE41 with a length of 1.68Å.\n\nIn the previous section, we have seen that the interactions that form between the ligands and the RNA polymerase can be classified into two main types, purely electrostatic attractions and interactions by delocalisation of charges. In this and the following section, we develop these aspects using DFT calculations. Figure 8 shows the function ESP for the ligands zidavudine, cobicistat and dolutegravir. In the case of zidavudine the ESP on the O2 and O3 atoms has a clear correspondence with the interactions with CYS145 and GLU166 which can be seen in Figure 2. In the case of cobicistat the significant values of the ESP function on the O4 and O7 atoms have a correspondence with the interactions with GLU166 and GLY143 (Figure 4) respectively. Finally, in the case of dolutegravir, the ESP function calculated on the O4 and O7 atoms had a clear agreement with the interactions with CYS145 and GLU166 respectively, which can be seen in Figure 6.\n\nFigure 9 shows the Function ESP for the ligands tromantadine, doravirine and indavir. In the case of tromantadine, the ESP on the O1 and N4 atoms have a clear correspondence with the interactions with GLU166 and LEU141 which can be seen in Figure 3. In the case of doravirine the significant values of the ESP function on the O6 and N10 atoms had a correspondence with the interactions with GLU166 and GLY143 (Figure 5) respectively. Finally, in the case of indavir, the ESP function calculated on the N5 atom had a clear correspondence with the interaction with GLU166, which can be seen in Figure 7. In Figures S13-S24 (Extended data43) 10.6084/m9.figshare.22670167.v1, the images of all the ESPs for all the ligands studied can be seen.\n\nThe isovalue for A, C and D was -0.04, and the iso. for B, D and E was -0.01. Figures A, C and D were created using GaussView 5.0 and B, D and E using AIMAll (v. 17.11.14).\n\nThe isovalue for A, C and D was -0.04, and the iso. for B, D and E was -0.01. Figures A, C and D were created using GaussView 5.0 and B, D and E using AIMAll (v. 17.11.14).\n\nThe study also investigated the global and local chemical reactivity descriptors using DFT calculations. Table 2 presents the calculated global parameters, including chemical potential, chemical hardness, global softness, and global electrophilicity, to compare the chemical reactivity of the ligand sample. As indicated in Table 2, the least reactive molecule is tromantidine, exhibiting the lowest values of electronic chemical potential μ, softness S, and electrophilicity ω (for the chemical potential it refers to its absolute value). On the other hand, it has the highest chemical hardness (η) value. The most reactive compounds are pyramidine and doravirine with the highest values for electronic chemical potential, softness and electrophilicity, as well as the lowest chemical hardness values. The electrophilicity values can have a crucial influence on the stability of the active site of ligands that are stabilized by non-covalent interactions.\n\nSince the analysis of the global parameters is limited, we will complete it with the comparison of some local descriptor functions. The electrophile and nucleophile Fukui functions (as a measure of reactivity) were then compared using the Frontier Molecular Orbital (FMO) approach. The electrophilic-nucleophilic character of the following functions also shows those molecular areas that are most likely to form charge-donating interactions (basically by charge delocalisation). These types of interactions are important and difficult to determine using docking analysis. Figure 10 shows the functions for the compounds cobicistat, hydroxychoroquine, indinavir, oseltamivir and tromantadine (A-E respectively), it can be noted that in these five cases the function assigns the most nucleophilic character to a nitrogen atom, mainly to its unshared electron pair. When comparing this figure with Figures 3 and 7 we can see that some important interactions can be justified on this basis; for example, in the case of Indinavir the N5 has an important interaction with GLU166, or in the case of Tromantadine the N4 has an important interaction with LEU141.\n\nA) Cobicistat, B) Hydroxychoroquine, C) Indinavir, D) Oseltamivir and E) Tromantadine. Isovalue was 0.01 in all cases. The figure was created using GaussView 5.0.\n\nFigure 11 shows that in the case of zidavudine the O3 would have an important interaction as a charge donor with GLU166 (Figure 2). For doravirine, the N10 has an interaction with GLY143 and the N11 with CYS145 (Figure 5). In the case of dolutegravir we have not found any match for the function f−r→. In Figures S25-S36 (Extended data43), we can see images of all the functions f−r→ for all the ligands studied.\n\nA) Zidavudine, B) Doravirine and C) Dolutegravir. The isovalue was 0.01 in all cases. The figure was created using GaussView 5.0.\n\nFigure 12 shows the functions f+r→ calculated under the FMO approximation LUMOr→2 for compounds A) Zidavudine, B) Tromantadine, C) Cobicistat, D) Doravirine, E) Dolutegravir and F) Indavir. In the case of tromantadine, the Fukui function f+r→ on the N3 and N4 atoms justifies interactions by charge attraction towards these atoms with GLN189 and LEU141 respectively. In the case of dolutegravir, the value of the function on O4 indicates a possible interaction by charge delocalisation with GLU143. For the rest of the ligands no matches for the function f+r→ were found. In Figures S25-S36 in the supporting information (Extended data43) are images of all the functions f+r→ of all the ligands studied.\n\nA) Zidavudine, B) Tromantadine, C) Cobicistat, D) Doravirine and E) Dolutegravir. The isovalue was 0.01 in all cases. The figure was created using GaussView 5.0.\n\n\nConclusions\n\nThe present investigation involved the analysis of a set of compounds (Zidovudine, Tromantadine, Pyramidine, Oseltamivir, Hydroxychoroquine, Cobicistat, Doravirine, Dolutegravir, Boceprevir, Indinavir, Truvada, Trizivir, Trifluridine, Sofosbuvir and Zalcitabine) employed in in vitro studies against SARS-CoV-2. Molecular docking, comparison of electrostatic potentials, and evaluation of chemical reactivity functions were conducted to examine the active site stabilization interactions of these compounds from both structural and electronic perspectives.\n\nFrom the molecular docking results, it was observed that tromantadine, dolutegravir, cobicistat, doravirine and dolutegravir show good active site stabilization with at least one H-bond in each conformation. To further investigate the active site stabilization of each ligand, a DFT reactivity analysis and electrostatic potential comparison was developed.\n\nBy utilizing the crystal structure of SARS-CoV-2 RNA-dependent RNA polymerase, these analyses enabled the identification of the primary stabilizing interactions. This research presents novel insights into these ligands, which can be advantageous in the development of new treatments for COVID-19. The studies allowed us to find an explanation supported in the DFT about the chemical reactivity and the stabilization in the active site of the ligands. The interactions between the ligands and the RNA polymerase studied were of two main types: electrostatic (usually hydrogen bonding) and charge delocalisation interactions. Both types of interactions coexist in these superstructures and form strong interactions that adequately justify the inhibitory activity of these ligands.", "appendix": "Data availability\n\nHarvard Dataverse: Data for Receptor-Based Pharmacophore Modelling of a series of ligands used as inhibitors of the SARS-CoV-2 virus by complementary theoretical approaches, molecular docking, and reactivity descriptors, https://doi.org/10.7910/DVN/IA8EOB. 42\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: Supporting Information.docx, https://doi.org/10.6084/m9.figshare.22670167.v1. 43\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAhmed H, et al.: Long-term clinical outcomes in survivors of severe acute respiratory syndrome and Middle East respiratory syndrome coronavirus outbreaks after hospitalisation or ICU admission: A systematic review and meta-analysis. 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Publisher Full Text" }	[ { "id": "216353", "date": "27 Oct 2023", "name": "Mohammad Mahfuz Ali Khan Shawan", "expertise": [ "Reviewer Expertise Bioinformatics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript titled 'Receptor-Based Pharmacophore Modelling of a series of ligands used as inhibitors of the SARS-CoV-2 virus by complementary theoretical approaches, molecular docking, and reactivity descriptors' is engaging and well-structured. It tackles a current issue by proposing a therapeutic solution. The authors employ diverse bioinformatic tools and techniques to repurpose various antiviral agents against the RdRp of SARS-CoV-2. The overall findings are promising and hold potential for effective COVID-19 treatments. The authors' commitment to addressing this crucial disease is commendable. However, certain aspects of the manuscript require further clarification. Notable concerns are outlined below and must be resolved prior to acceptance.\nThe current title of the manuscript is so hard to get. It's suggested to make the title clearer. The proposed new title is: “In Silico Receptor-Based Pharmacophore Modelling against COVID-19 infection: targeting the RdRp of SARS-CoV-2”. This new title highlights and focuses on the repurposing of antiviral drugs and targeting the RdRp of SARS-CoV-2 to combat COVID-19 infection using computational methods.\n\nRevise and improve the abstract to enhance its clarity and completeness. Integrate a brief description underscoring the significance of selecting COVID-19's RdRp as a focal point. Conclude the abstract by emphasizing the pressing need for hands-on laboratory investigations to validate the outcomes presented in this manuscript. A few words that summarize the importance of this study and future scope should also be incorporated within the abstract section as concluding remarks.\n\nIn the introduction section, there is an error on page 3, line 11. Please remove “For further information, refer to the question-and-answer section on dexamethasone”. Additionally, it is important for the authors to review and reference recent studies that focus on developing effective components against SARS-CoV-2, particularly targeting the RdRp. By doing so, the current study can strengthen its significance and relevance by acknowledging existing findings and gaps. The introduction section should be more detailed and focused on the materials and methods that have been adopted in this study and adjusted to align with the revised abstract, maintaining consistency between the two. Furthermore, the importance of computational studies should be added.\n\nIn the \"Materials and Methods\" section, it's recommended to include a flow chart for an early bird overview of the computational approach. This chart should detail the step-by-step process, including the software, server names, and addresses used for in-silico identification of potent anti-COVID-19 drugs. To facilitate replication, authors should provide specifications of the computational workstation they employed. For accurate molecular docking, proper preparation of the active site and grid box is necessary, along with validation of the docking method. After molecular docking, molecular dynamics must need to be included to support the findings. To bolster the results, authors should incorporate studies on the molecular targets and biological activity analysis of the tested antivirals. They should also consider including established anti-COVID-19 antiviral drugs (such as paxlovid, molnupiravir, remdesivir, and camostat mesylate) as controls, and compare their outcomes against these controls. Furthermore, the materials and methods section needs caution and extensive rewriting, there are many missing details and several mistakes too. The authors can find the following relevant articles to enhance their \"Materials and Methods\" section and incorporate citations to support their revised manuscript.\n\nhttps://doi.org/10.1186/s40064-016-2996-5 (May be used for active site analysis using CastP web server). https://doi:10.1016/j.meegid.2021.104951 (May be used for molecular dynamics) https://doi.org/10.1186/s42269-020-00479-6 (May be used for molecular dynamics) https://doi.org/10.1155/2023/5469258 (May be used for molecular dynamics) https://doi.org/10.1007/s10989-023-10535-0 (May be used for molecular dynamics)\n\nIn the results section, there is a need to enhance the quality of the figures, particularly focusing on different atom's names and positions. The figures with text display blurry fonts, thus necessitating their re-exportation at a higher resolution. These improved figures should then be integrated into the revised article to ensure clarity for readers.\n\nThe conclusion section contains scientific inaccuracies and could benefit from additional clarity. Consider enhancing its comprehensibility. It might be beneficial to introduce a discussion section as well, addressing the potential for future improvements and strategies to enhance effectiveness in upcoming endeavors.\n\nIt is recommended to thoroughly review all references in the manuscript for typographical errors. Furthermore, ensure that the reference section adheres to the formatting guidelines specified by the journal.\n\nThe manuscript exhibits a lack of proficiency in English language usage encompassing grammar and writing skills. It is imperative to engage an expert language editing service or a native speaker adept in writing to thoroughly review the entire manuscript. A comprehensive revision is essential to enhance the manuscript's overall command of the English language.\n\nPlease submit the revised manuscript after conducting a plagiarism check that yields a result between 10% and 15%.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "216355", "date": "13 Nov 2023", "name": "Syeda Rehana Zia", "expertise": [ "Reviewer Expertise Computational Chemistry" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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:\nThe manuscript holds merit in the realm of SARS-CoV-2 ligand identification. However, the authors should encounter the following comments for further improvement and potential recommendation of the manuscript:\nThe authors should enhance the introduction by explicitly stating the significance of their research. Additionally, providing a concise overview of the research conducted would strengthen the connection between the literature review, past studies, and the current investigation. This adjustment would contribute to a clearer understanding of the study's background and purpose.\n\nThe authors have not mentioned details about pharmacophoric generation in the method section. However, a detailed explanation is required for clarity and reproducibility.\n\nThe authors have mentioned in the result section about the pharmacophore development of Zidovudine, Tromantadine, Pyramidine, Oseltamivir, Hydroxychoroquine, Cobicistat, Doravirine (Pifeltro), Dolutegravir, Boceprevir, Indinavir, Truvada, Trizivir, Trifluridine, Sofosbuvir and Zalcitabine. However, in Figure 1 pharmacophore development for only four ligands have been demonstrated namely Truvada, Trizivir, Trifluridine and Sofosbuvir. The authors should provide a rationale for displaying only four ligand pharmacophores. Clarifying the selection criteria or limitations would enhance the readers insight.\n\nIn the result section, it is written “The validation process yielded an RMSD value of 0.38”; however, it's not clear whether your RMSD value of 0.38 is from a pharmacophore modeling or molecular docking study. RMSD can be used to measure the similarity either between the pharmacophoric features of a reference (known) ligand and a predicted pharmacophore model or between the predicted binding pose of a ligand compared to its experimentally determined pose. Secondly, the unit for RMSD and docking score is also missing in the text.\n\nThe docking and ESP outcomes for ligands: Truvada, Trizivir, Trifluridine and Sofosbuvir, with developed pharmacophores, are not reported in the manuscript either in main text or in supplementary data. This omission might limit the comprehensive assessment of pharmacophore model’s predictive power. In other case if authors have used these ligands as a \"training set\", they should mention it in the manuscript.\n\nThe authors have mentioned in the supplementary data about molecular docking and ESP calculation for Amprenavir, however, its rationale is not mentioned in the text. The authors should state why they have performed these calculations and how it is related to their study.\n\nThe authors have written that: “The best predictions of the poses were predicted by 10ns molecular dymane calculations, in order to analyse its stabilization in the active site.” However, absence of details regarding MD simulations in methods and results is noted.\n\nThere are certain grammatical mistakes in the manuscript, for instance “de” should be replaced with “the” etc.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "216363", "date": "16 Sep 2024", "name": "Shiva Prasad Kollur", "expertise": [ "Reviewer Expertise Chemical biology", "chemical synthesis", "computational chemistry and materials chemistry." ], "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\nAlejandra and Jesus in this manuscript titled \"Receptor-Based Pharmacophore Modelling of a series of ligands used as inhibitors of the SARS-CoV-2 virus by complementary theoretical approaches, molecular docking, and reactivity descriptors\" have identified the stabilizing interactions using the crystal structure of SARS‑CoV‑2 RNA‑dependent RNA polymerase. Based on the results obtained, the ligands studied in the present work can be used in the design of new COVID-19 treatments. Furthermore, the studies are also supported by the Density Functional Theory about the chemical reactivity and the stabilization in the active site of the ligands.\nThis work is highly significant and authors have written the same in a scientifically well-manner.\nI recommend the approval of this manuscript in the current form.\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": [] } ]	1	https://f1000research.com/articles/12-749
https://f1000research.com/articles/12-744/v1	26 Jun 23	{ "type": "Research Article", "title": "A retrospective study comparing open and percutaneous trigger finger release in the Thai population", "authors": [ "Saran Malisorn" ], "abstract": "Background: Over the years, open surgery has been the primary treatment for trigger finger, a prevalent issue among hand illnesses. There has been some resistance to the technique's routine use, despite the fact that the percutaneous release of triggers provides a quicker recovery than surgery. As a result, the study proposed that the percutaneous release technique outperforms open surgery. The objective of this study was to compares the trigger finger surgery's open and percutaneous releases in terms of short-term results. Methods: From 2014 to 2020, 166 patients who underwent open or percutaneous release surgery for the trigger finger at Naresuan University Hospital were the subjects of this retrospective analysis. For one, three, and six weeks, the initial characteristics and post-operative hemorrhage, digital nerve and artery injury, surgical site pain, inability to flex the finger, and other outcomes were compared. The visual analog scale (VAS) score and the impairments of the arm, shoulder, and hand (DASH) score were also compared between the two groups. Results: The age, sex, and number of patients in both groups were statistically comparable. Before the procedure, there was no difference between the groups in terms of DASH and VAS scores for pain; however, at six weeks, the percutaneous release group showed a substantial difference and low VAS scores. There were no differences between the groups in terms of consequences, including wound pain, damage to digital nerves and arteries, and others. Conclusion: Based on the patients' short-term outcomes, the study found that percutaneous release of the trigger finger is just as successful as traditional open surgery.", "keywords": [ "Trigger fingers", "open surgery", "percutaneous release", "DASH Score" ], "content": "Introduction\n\nTrigger finger, sometimes referred to as stenosing tenosynovitis, is a prevalent issue. Trigger finger is a common hand condition, characterized by the catching or locking of a finger in a bent position before it straightens out. This prevalence estimate is supported by several studies.1–4 It has been reported that trigger finger affects approximately 2% to 3% of the general population.1,2,5 Daily tasks are hampered by the malformation, which causes pain, clicking, or a stumbling block when moving the fingers. Although the exact cause is uncertain, the inflammation and consequent constriction of the A1 pulley may be to blame for the flexor tendon’s reduced range of motion. An additional layer of a structure made up of chondroid metaplasia has been identified by a histological investigation, indicating that there are fibers forming on the tendon sheath’s surface.1 Trigger fingers primarily affects adults in their 40s and 50s, and previous research indicates that women are approximately six times more likely than men to suffer from the condition.2 Without treatment, the illness leads to significant long-term disability and ongoing pain. Consequently, the trigger finger needs to be treated by a doctor.\n\nDepending on the stage, there are numerous ways to treat trigger fingers. Early-stage patients typically opt for conservative treatments such as night finger splints, physical therapy, painkillers, anti-inflammatory medicines, and steroid injections. Open or percutaneous surgery can be used to section the flexor tendon at the A1 pulley in more advanced stages.3 Open surgery has been used for a while and is up to 97% effective, but it can lead to post-operative pain, infection risk, longer recovery times for movements, nerve injury, and scarring.4,6 Another well-liked alternative technique is the percutaneous release of the trigger finger, which has a success rate of 74 to 94%.7 Less stress and a quicker recovery are provided by the percutaneous approach, but there is also a risk of digital nerve and artery injury and incomplete surgery.8 In this regard, clinical research comparing the outcomes of various surgical procedures in patients is critical. It might aid the expert in selecting the best course of action.\n\nEven while the results of open surgery and the percutaneous release approach have been previously reported after three months (short-term) and two years (long-term) of follow-up,5,9 there are few studies that compared the results for patients in similar patient groups. This retrospective study compares the short-term outcomes of trigger finger percutaneous release vs routine open surgery with the expectation that the latter procedure will produce superior results.\n\n\nMethods\n\nThe patients who underwent open surgery or percutaneous release of the trigger finger at Naresuan University Hospital between 2014 and 2020 were the participants of this retrospective cohort study. Adults over the age of 18 who scored between 2 and 5 on the modified Quinnel grading scale met the inclusion criteria.3 Patients with temporary trigger finger, prior steroid injection treatment, treatment received less than eight weeks prior to the study, surgery for the trigger finger, tendon injuries, fractures of the affected finger or palm, degenerative arthritis, finger gout, rheumatoid arthritis, connective tissue disease, and diabetes were all disqualified from participating in the study. Additionally, it was decided that patients with a history of allergies to non-steroidal anti-inflammatory medicines, stomach ulcers or gastrointestinal bleeding, asthma, chronic liver or biliary illness, and kidney disease were not acceptable. This study complied with the Declaration of Helsinki and was approved by the ethical committee of Naresuan University.\n\nAs previously mentioned, the sample size was calculated by comparing the two independent proportions (two-tailed test).10 Kloeters et al. (2016) aimed to compare three different techniques of A1 pulley release in terms of scar tissue formation and postoperative rehabilitation.11 The three techniques evaluated were open surgery, percutaneous release with a needle, and percutaneous release with a knife. Regarding the open surgery technique, the authors stated that open surgery was performed using a transverse incision over the A1 pulley in cases of severe contracture or a palpable nodule at the A1 pulley. In contrast, percutaneous techniques have been used in cases with a less severe degree of contracture.11 The open surgery proportion (p=0.97) was taken into account from the previous study,11 but the percutaneous release proportion (p2) was established at 0.84. The required sample size was 83 patients in each group, with a statistical power of 80% and an alpha-type error rate of 5%.\n\nBoth techniques for releasing the trigger finger were carried out in the hospital’s outpatient department while using conventional aseptic procedure. After identifying and marking the trigger location, 2 ml of 1% plain lidocaine hydrochloride was administered there to provide local anesthetic. When the flexor tendon at the A1 pulley was divided during open trigger finger release surgery, a 1 cm longitudinal incision was created. The release of triggering was then verified by stretching the finger. To stop infection, the wound was stitched and treated. The percutaneous release of the trigger digit was carried out as previously described on a different set of patients.12 In order to allow blood vessels and nerves to fall laterally and bring the flexor tendon closer to the skin, the patient’s injured finger was stretched to its maximum extent. Then, at the A1 pulley, a perpendicular 18 gauze needle tip was introduced into the skin. To cut the tendon, the needle’s tip was positioned 5-8 mm from the predetermined border. The operation was finished when the grating feeling that was caused when the needle tip sliced through the transverse fibers vanished. Additionally, by passively moving the finger, the full release of the triggering was verified. The procedure was repeated, and gauze was applied to the wound when the triggering continued. After either surgical procedure, the patients were permitted to go home while receiving analgesics, antibiotics, and instructions on basic wound care. To evaluate the healing of the wound, postoperative pain, complications, recurrence, and the time required to return to daily activity, follow-up sessions were scheduled at 1, 3, and 6 weeks.\n\nThe work involved gathering information from the patients’ medical records stored in the hospital computer system. The study was approved by the ethics committee of Naresuan University. The hospital provided consent after the study was approved by the ethics committee. The ethics committee waived the need for patient consent.\n\nWith consent from the hospital, information was gathered from the patients’ medical records and the hospital’s computer system. The results, including bleeding, injury to the digital nerve and artery, disability of the arm, shoulder, and hand (DASH) and visual analog scale (VAS) scores, were noted in the record book previously described.5\n\nThe terms frequency, proportion, mean, and standard deviation were used to describe descriptive data. The Chi-square test was used to evaluate categorical covariates, while the Mann-Whitney U test was used to compare the groups for continuous variables. Statistical significance was defined as a p-value 0.05. The analysis was conducted using SPSS version 17 (SPSS Inc., Chicago, IL, USA).\n\n\nResults\n\nThe majority (72.23%) of the 166 patients in the research were female. The quantity, sex, and percutaneous release method of patients who underwent open surgery were not statistically significant. The age of the patients who underwent an open release for the trigger fingers was statistically comparable to that of those who underwent a percutaneous release. Patients over 60 years old made up a smaller portion of both categories, nevertheless. In contrast to the finger triggering grade and the affected digit in the study groups, the hand side associated with the trigger digit was substantially different (p=0.01) between the two patient groups (Table 1).\n\nThe baseline VAS score for pain among the patients in open and percutaneous release groups was insignificant (6.79±1.26 and 7.03±1.54; p=0.27) as shown in Table 2. both groups had comparable DASH scores and triggering grades. However, when measured using the faces rating scale, a significant difference between the two groups’ levels of pain prior to surgery was discovered.\n\nThe trigger finger was fully released in each patient in both groups. However, a digital nerve lesion was documented in one patient who underwent open surgery. It was discovered during the study’s follow-up visits at one, three, and six weeks that the proportion of patients who experienced bleeding in the first week varied significantly across the groups (30.12% vs. 3.61%). Similarly, the open surgery group’s DASH score at the third post-operative visit was considerably higher than the percutaneous release groups. After the three-week follow-up, there were considerably more patients who underwent open surgery (28.92%) than underwent percutaneous release (8.43%), but none at six-weeks. In addition, as indicated in Table 3, the VAS score and face pain scale score in open surgery patients at six weeks following therapy were both considerably greater than those who had the percutaneous release of the triggers. Figure 1 depicts a graphic comparison of the DASH scores between the two groups of patients at one, three, and six weeks after surgery and before surgery. Similar to Figure 1, Figure 2 shows the variation in pain (measured as a VAS score) between patients before and after trigger finger release surgery, both open and percutaneous.\n\n* Significant <0.05.\n\n\nDiscussion\n\nThe results of the traditional open and percutaneous trigger finger release surgeries were compared in this retrospective analysis. The matched patients in the two groups (in terms of sex, gender, and age) are the study’s main selling point. In the patients who underwent either procedure, there was no bleeding, impairment of the arm, shoulder, or hand, pain in the surgical site, or difficulty to flex the fingers at the six-week follow-up. All patients who underwent percutaneous release without any issues experienced a full release of the triggers. The study concludes that open surgery is still the most effective and safest option for treating trigger fingers.\n\nOur discovery that females have higher levels of trigger finger confirms the findings of other investigations.13,14 The study’s inclusion of 72.28% individuals under the age of 60 furthered the claim that the condition is prevalent in people between the ages of 40 and 60.13 The relationship between the trigger finger and age and sex has not yet been thoroughly established. In general, fingers that are used repeatedly are more likely to develop deformities. In the study, the middle and ring fingers were affected in about 66% of the participants. The dominant hand is typically afflicted with trigger finger, and in the study, the majority of patients (68.07%) were right-handed. Similar results have already been published.14,15 Overall, 73.48% of the patients in the study showed stages 3 and 4 of triggering, which meant that the patients had irregular finger movement and sporadic finger locking but that these symptoms were actively correctable.\n\nPatients in the open surgery and percutaneous surgery groups had insignificant baseline VAS scores for pain. However, the percutaneous release group had a significantly lower post- surgery VAS score and facial pain rating scale score when compared between the two groups at six weeks of follow-up. It suggests that open surgery was less beneficial in the patients studied than the percutaneous release approach. A prior study showing improved short-term satisfaction in patients who had percutaneous release of the trigger finger supports this conclusion.16,17 The subjective aspect of pain measurement, which depends on the patient’s age, literacy, cognitive ability, and other factors, may be the rationale for a significant difference in baseline pain scores between the groups using the faces pain scale but not the VAS score. It should be noted that VAS and face rating scales are both appropriate for assessing immediate postoperative pain.18\n\nThe open and percutaneous release methods did not result in significantly different DASH scores at baseline or at one week after surgery, however at three weeks, the score was statistically different and primarily declined from one week. Additionally, both groups’ DASH ratings decreased from baseline to one-, three-, and six-weeks following surgery.\n\nThis supports past reports’ findings that the trigger finger treatment for the patients in the study had a high rate of success when using the two procedures.4,7 In a brief period of time following the procedure, the percutaneous approach achieved 100% release of the finger without any problems. According to another study, there were no differences between the patients who received percutaneous release and open surgery in terms of pain in the surgical wound, digital nerve injury, or artery injury.7\n\nThe results of this investigation supported the notion that less invasive treatment options exist for trigger finger. The author is aware of the limitations of the current study after mentioning them. First, the study’s retrospective design may have contributed to bias. Second, a small amount of the outcome factors was measured quickly after the study ended. Thirdly, because the thumb has the highest risk of sustaining a digital nerve injury, individuals with trigger thumb were excluded from the study.19 Therefore, to maximize the impact of such research findings, a comparison between the trigger thumb and finger patients would be essential.\n\n\nConclusion\n\nBased on the patients’ short-term outcomes, the study found that percutaneous release of the trigger finger is just as successful as traditional open surgery. This data may be useful in determining that the percutaneous procedure is the best option for getting better results quickly and at low risk.", "appendix": "Data availability\n\nFigshare: formatdata_trigger10.08-2565 Percutaneous (2).xlsx. figshare. Dataset. https://doi.org/10.6084/m9.figshare.21829032.v1. 20\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nDrossos K, Remmelink M, Nagy N, et al.: Correlations between clinical presentations of adult trigger digits and histologic aspects of the A1 pulley. J. Hand Surg. Am. 2009 Oct; 34(8): 1429–1435. PubMed Abstract \| Publisher Full Text\n\nGiugale JM, Fowler JR: Trigger Finger: Adult and Pediatric Treatment Strategies. Orthop. Clin. North Am. 2015 Oct; 46(4): 561–569. Publisher Full Text\n\nQuinnell RC: Conservative management of trigger finger. Practitioner. 1980; 224(1340): 187–190. PubMed Abstract\n\nPavlicný R: Percutaneous release in the treatment of trigger digits. Acta Chir. Orthop. Traumatol. Cechoslov. 2010 Feb; 77(1): 46–51. PubMed Abstract\n\nHo SWL, Chia CY, Rajaratnam V: Characteristics and Clinical Outcomes of Open Surgery for Trigger Digits in Diabetes. J. Hand Microsurg. 2019 Aug; 11(2): 80–83. PubMed Abstract \| Publisher Full Text\n\nMoriya K, Uchiyama T, Kawaji Y: Comparison of the surgical outcomes for trigger finger and trigger thumb: preliminary results. Hand Surg. 2005 Jul; 10(1): 83–86. Publisher Full Text\n\nFiorini HJ, Tamaoki MJ, Lenza M, et al.: Surgery for trigger finger. Cochrane Database Syst. Rev. 2018 Feb 20; 2018. Publisher Full Text\n\nDierks U, Hoffmann R, Meek MF: Open versus percutaneous release of the A1-pulley for stenosing tendovaginitis: a prospective randomized trial. Tech. Hand Up. Extrem. Surg. 2008 Sep; 12(3): 183–187. Publisher Full Text\n\nCebesoy O, Kose KC, Baltaci ET, et al.: Percutaneous release of the trigger thumb: is it safe, cheap and effective?. Int. Orthop. 2007 Jun; 31(3): 345–349. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBernard R: Fundamentals of Biostatistics. 5th ed.Duxbery: Thomson Learning; 2000.\n\nKloeters O, Ulrich DJO, Bloemsma G, et al.: Comparison of three different incision techniques in A1 pulleyrelease on scar tissue formation and postoperative rehabilitation. Arch. Orthop. Trauma Surg. 2016; 136: 731–737. Publisher Full Text\n\nUçar BY: Percutaneous Surgery: A Safe Procedure for Trigger Finger? N. Am. J. Med. Sci. 2012 Sep; 4(9): 401–403. Publisher Full Text\n\nBrozovich N, Agrawal D, Reddy G: A Critical Appraisal of Adult Trigger Finger: Pathophysiology, Treatment, and Future Outlook. Plast. Reconstr. Surg. Glob. Open. 2019 Aug 8; 7(8): e2360. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLeung LTF, Hill M: Comparison of Different Dosages and Volumes of Triamcinolone in the Treatment of Stenosing Tenosynovitis: A Prospective, Blinded, Randomized Trial. Plast. Surg (Oakv). 2021 Nov; 29(4): 265–271. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrown AM, Tanabe KL, DellaMaggiora RJ, et al.: Nonpalmar Endoscopic versus Open Trigger Finger Release: Results from a Prospective Trial. Plast. Reconstr. Surg. Glob. Open. 2022 Oct 7; 10(10). Publisher Full Text\n\nHuang HK, Wang JP, Lin CJ, et al.: Short-term Versus Long-term Outcomes After Open or Percutaneous Release for Trigger Thumb. Orthopedics. 2017 Jan 1; 40(1): e131–e135. PubMed Abstract \| Publisher Full Text\n\nGiugale JM, Fowler JR: Trigger Finger: Adult and Pediatric Treatment Strategies. Orthop. Clin. North Am. 2015 Oct; 46(4): 561–569. Publisher Full Text\n\nFlaherty SA: Pain measurement tools for clinical practice and research. AANA J. 1996 Apr; 64(2): 133–140. PubMed Abstract\n\nBuldu H, Cepel S, Ki N, et al.: References to avoid complications in releases of the trigger thumb: a cadaveric study. Acta Orthop. Traumatol. Turc. 2006; 40(4): 311–314.\n\nMalisorn S: formatdata_trigger10.08-2565 Percutaneous (2).xlsx. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "305752", "date": "25 Jul 2024", "name": "Grigorios Kastanis", "expertise": [ "Reviewer Expertise Hand", "Wrist", "Trauma", "Geriatric", "Foot" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is a comparative study between two surgical techniques for the surgical treatment of trigger finger . The author thoroughly analyzes the two techniques and their results with a statistical study comparing them based on pain and functional recovery of the patients. In my opinion: 1. Author must refer the technique of subcutaneous release( Surgical Procedure line 6) 2. Author no refer which group presented with bleeding? because in section of Result line 13 presented statistic results? 3.There are manuscripts in the literature comparing subcutaneous release of A1 pulley with ultrasound guidance, could the author cite them in Section of Discussion comparing his results with those of other works. After these corrections are made the article should be indexed.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "310330", "date": "06 Aug 2024", "name": "Takafumi Hosokawa", "expertise": [ "Reviewer Expertise hand surgery", "distal radius fracture" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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: ・The authors retrospectively compared 83 percutaneous and 83 open surgeries for trigger fingers. The study topic is very interesting with the large number of patients. ・Although this study was defined retrospective, authors calculated the sample size, and 83 patients were studied in each of the percutaneous and open surgeries. How in the world did authors allocate these two groups? Is this not a prospective study with arbitrary selection? ・Methods: I would like a brief explanation of Quinnel grading. ・Sample size: I did not understand how to calculate the sample size. ・Surgical procedure: 18 gauge instead of 18 gauze?\n・Discussion: ・The authors predicted in the introduction that open surgery would be superior, but there is no discussion of this prediction. ・In the Abstract, the authors state \"the study found that percutaneous release of the trigger finger is just as successful as traditional open surgery. In the Discussion, the authors state \"The study concludes that open surgery is still the most effective and safest option for treating trigger fingers. In the Conclusion, it is stated that \"the percutaneous procedure is the best option for getting better results quickly and at low risk.” After all, I'm not sure what is the point.\n・In Table 1, Grade 3,4,5,6 are 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? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "13155", "date": "16 Jan 2025", "name": "Saran Malisorn", "role": "Author Response", "response": "1. \"Although this study was defined as retrospective, authors calculated the sample size, and 83 patients were studied in each of the percutaneous and open surgeries. How in the world did authors allocate these two groups? Is this not a prospective study with arbitrary selection?\" Response: Thank you for your observation. This study is indeed a retrospective cohort analysis. The allocation to the groups was not prospective or arbitrary. Instead, the grouping was based on the surgical records retrieved from the hospital database during the specified period (2014–2020). Patients were categorized into the percutaneous or open surgery groups according to the procedure they underwent, as recorded in their medical history. The calculation of sample size was done retrospectively to ensure that the statistical power of the study would be sufficient to detect differences between the two groups. I will clarify this point in the Methods section. 2. \"Methods: I would like a brief explanation of Quinnel grading.\" Response: I appreciate this request and will include a brief explanation of the Quinnell grading system in the Methods section. Here is the proposed addition: \"The Quinnell grading system is used to classify the severity of trigger finger: Grade 1: Pre-triggering, with pain or clicking but no locking. Grade 2: Active triggering, with locking that is actively correctable. Grade 3: Passive triggering, with locking that requires passive correction. Grade 4: Fixed deformity, with joint contractures. Grades 2–5 were included in this study to focus on moderate to severe cases requiring surgical intervention. 3. \"Sample size: I did not understand how to calculate the sample size.\" Response: Thank you for pointing this out. The sample size was calculated retrospectively using the formula for comparing two proportions in a two-tailed test. Based on a previous study (Kloeters et al., 2016), the success rate of open surgery was set at 97%, while the success rate for percutaneous release was set at 84%. Using a statistical power of 80% and an alpha error of 5%, the minimum required sample size was calculated as 83 patients per group. This calculation ensures adequate power to detect significant differences between the two techniques. We will include this explanation in the Sample Size section. 4. \"Surgical procedure: 18 gauge instead of 18 gauze?\" Response: Thank you for catching this error. The correct term is \"18-gauge needle,\" not \"18 gauze.\" This will be corrected throughout the manuscript. 5. Discussion: \"The authors predicted in the introduction that open surgery would be superior, but there is no discussion of this prediction.\" Response: Thank you for highlighting this inconsistency. In the Discussion section, we will address the initial prediction and explain the results more clearly. Here is the proposed addition: \"In the Introduction, it was hypothesized that open surgery would be superior due to its established effectiveness and precision. However, the results demonstrated that percutaneous release achieved similar short-term outcomes with faster recovery times and comparable complication rates. This finding suggests that while open surgery remains a reliable and effective option, percutaneous release may be preferable for patients prioritizing quicker recovery and minimal invasiveness. Further studies comparing long-term outcomes are needed to refine these conclusions.\" 6. \"In the Abstract, the authors state, 'the study found that percutaneous release of the trigger finger is just as successful as traditional open surgery.' In the Discussion, the authors state, 'The study concludes that open surgery is still the most effective and safest option for treating trigger fingers.' In the Conclusion, it is stated that 'the percutaneous procedure is the best option for getting better results quickly and at low risk.' After all, I'm not sure what is the point.\" Response: Thank you for pointing out these inconsistencies. We will revise these sections for clarity and consistency. Here is the revised text: Abstract: \"The study found that percutaneous release of the trigger finger achieved similar short-term outcomes to traditional open surgery, with advantages in quicker recovery and comparable safety.\" Discussion: \"While open surgery remains a reliable and effective option, percutaneous release may be preferred for its minimally invasive nature and faster recovery, especially for short-term outcomes.\" Conclusion: \"Percutaneous release is a viable alternative to open surgery, offering comparable success with the advantage of faster recovery and lower invasiveness. However, the choice of procedure should be tailored to individual patient needs and long-term goals.\" This ensures consistency across all sections. 7. \"In Table 1, Grades 3, 4, 5, and 6 are correct?\" Response: Thank you for pointing this out. In Table 1, the grades refer to the severity of the triggering based on the Quinnell grading system. Grades 3, 4, 5, and 6 are typographical errors, and we will correct them to Grades 2, 3, 4, and 5. Additionally, I will verify all table data to ensure accuracy before resubmission." } ] }, { "id": "294082", "date": "12 Aug 2024", "name": "Mohamed Abdel-Wahed", "expertise": [ "Reviewer Expertise Hand and upper limb surgery", "Microsurgery", "Congenital hand lesions", "Trauma and Orthopedic surgery", "Limb reconstruction and Orthoplastic surgeries" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is a comparative study between two methods for treatment of trigger finger. There is a good effort done for data collection, tabulation, and extraction of the results. There is some ambiguous points that should be cleared however:\n1- There is more than one type for percutaneous release. the author used the needle percutaneous release. This should be mentioned cleary in the abstract section and also the title section\n2- The author excluded the thumb from the study. this was mentioned only once at the end of the research. I prefer it to be mentioned in the abstract and in the methods section\n3- The surgical procedure should be mentioned with more details. Antibiotic used? tourniquet used? sedation used? how did the surgeon noticed to ensure full release? who did the surgeries?? was this a single surgeon experience?\n4- Again, the surgical procedure section: the landmark of skin incision for open release should be mentioned in an anatomic way.\n\n5- Again, the surgical procedure section: I can't understand this phrase: ((To stop infection, the wound was stitched and treated))\n6- Again, the surgical procedure section: The author mentioned: ((To cut the tendon, the needle’s tip was positioned 5-8 mm from the predetermined border)) are we going to cut the tendon?? and what is the predetermined border\n7- In the results section: the author present data and percentages of both groups without referring which is group 1 and which is group 2\n8- Again, the results section: ((After the three-week follow-up, there were considerably more patients who underwent open surgery (28.92%) than underwent percutaneous release (8.43%), but none at six-weeks)) This text is missing the comparative parameter and i had to refer to the table to get that the author was talking about inability to flex the finger. this should be mentioned in the text\n9- Did the author noticed any tendon rupture with either procedures?\n10- What was done for the case of digital nerve injury complicated in open release?\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": [ { "c_id": "13156", "date": "16 Jan 2025", "name": "Saran Malisorn", "role": "Author Response", "response": "1. There is more than one type for percutaneous release. The author used the needle percutaneous release. This should be mentioned clearly in the abstract section and the title section. Response: Thank you for this observation. We will revise the title and abstract to specify that the percutaneous release was performed using a needle technique. Revised Title: \"A Retrospective Study Comparing Open and Needle Percutaneous Trigger Finger Release in the Thai Population.\" Abstract Revision: \"The objective of this study was to compare the short-term outcomes of open surgery and needle percutaneous release for the treatment of trigger finger.\" 2. The author excluded the thumb from the study. This was mentioned only once at the end of the research. I prefer it to be mentioned in the abstract and the methods section. Response: We agree that this important exclusion should be highlighted. Abstract Revision: \"Patients with trigger thumb were excluded from the study to focus on fingers with different anatomical and procedural considerations.\" Methods Section Addition: \"Patients with trigger thumb were excluded due to the unique anatomy and higher risk of digital nerve injury associated with this condition.\" 3. The surgical procedure should be mentioned with more details: the antibiotic used, the tourniquet used, the sedation used, how the surgeon ensured full release, who performed the surgeries, and whether it was a single-surgeon experience. Response: We will expand the Surgical Procedure section to address these points. Revision: \"Both procedures were performed under local anesthesia using 2 ml of 1% plain lidocaine hydrochloride. No sedation or tourniquet was used. Prophylactic antibiotics were not routinely administered. The release of the A1 pulley was verified intraoperatively by passively moving the finger to confirm the absence of triggering. All surgeries were performed by a single senior hand surgeon with extensive experience in both techniques to ensure consistency.\" 4. The landmark of skin incision for open release should be mentioned in an anatomic way. Response: We will clarify the anatomical landmarks for the incision in the Surgical Procedure section. Revision: \"For the open release, a 1 cm longitudinal incision was made at the level of the distal palmar crease, directly over the A1 pulley. Care was taken to avoid injury to adjacent neurovascular structures.\" 5. The phrase ‘To stop infection, the wound was stitched and treated’ is unclear. Response: We will rephrase this sentence for clarity. Revision: \"The wound was closed with interrupted sutures, and sterile dressing was applied to reduce the risk of infection.\" 6. The phrase ‘To cut the tendon, the needle’s tip was positioned 5-8 mm from the predetermined border’ needs clarification: Are we cutting the tendon? What is the predetermined border? Response: Thank you for highlighting this. The intention was to cut the A1 pulley, not the tendon. Revision: \"To release the trigger, the needle’s tip was positioned 5-8 mm from the proximal edge of the A1 pulley. Care was taken to divide only the A1 pulley fibers without damaging the flexor tendon.\" 7. In the results section, the author presents data and percentages of both groups without referring to which is group 1 and which is group 2. Response: We will ensure that groups are clearly identified throughout the results section. Revision: \"The proportion of patients who experienced bleeding was higher in the open surgery group (30.12%) compared to the percutaneous release group (3.61%).\" 8. The results section mentions: ‘After the three-week follow-up, there were considerably more patients who underwent open surgery (28.92%) than underwent percutaneous release (8.43%), but none at six weeks.’ This text is unclear without mentioning the parameter (inability to flex the finger). Response: We will specify the parameter directly in the text. Revision: \"After the three-week follow-up, the inability to flex the finger was reported in 28.92% of patients in the open surgery group compared to 8.43% in the percutaneous release group. By six weeks, no patients in either group experienced this complication.\" 9. Did the author notice any tendon rupture with either procedure? Response: No tendon ruptures were observed during the study. This will be explicitly mentioned in the results section. 10. What was done for the case of digital nerve injury complicated in open release? Response: The digital nerve injury was managed conservatively with close follow-up. This information will be added to the results section." } ] } ]	1	https://f1000research.com/articles/12-744
https://f1000research.com/articles/11-311/v1	14 Mar 22	{ "type": "Research Article", "title": "Trends in frailty and its associated factors in the community dwelling elderly Indian population during the COVID-19 pandemic: A prospective analytical study", "authors": [ "Karan Gautam", "Shyam Krishnan K", "Vijaya Kumar K", "Megha M Nayak", "Karan Gautam", "Vijaya Kumar K", "Megha M Nayak" ], "abstract": "Background: There is a scarcity of quality literature on the prevalence of frailty among community dwelling elderly in India. This study was originally planned to analyze the longitudinal trends in frailty status of community dwelling elderly in an Indian population as well to identify factors associated with frailty in the Indian context. However, the recruitment phase of this study coincided with one of the largest lockdowns in history, associated with the COVID-19 pandemic, and this gave us a unique opportunity to study the effects this pandemic enforced, as a result of the necessary restrictions, on the frailty status as well the factors affecting frailty in the elderly. Methods: A prospective observational study was designed and conducted amongst 19 community dwelling elderly of Dakshina Kannada District, in Karnataka India. Outcome variables of frailty (EFIP), physical activity (PASE), functional mobility (TUG), gait speed (10-meter walk test), nutritional status (MNA®-SF) body composition (BIA), and strength (dynamometry), were measured at baseline and on follow-up after three months. The changes occurring in these variables over the three-month period were analyzed and the change in frailty was independently correlated with changes in each of the other outcomes. Results: We couldn’t identify any statistically significant difference in frailty over a period of three months. However, there was a highly significant change in the physical activity status, lower extremity muscle strength, body composition, functional mobility, gait speed, and cognitive function in the same time period. Conclusions: Though individual determinants of frailty in community dwelling changed over a three-month period, these changes failed to produce any observable/measurable difference in frailty status.", "keywords": [ "frailty", "COVID-19 pandemic", "sarcopenia", "functional mobility" ], "content": "List of abbreviations\n\nBMR: Basal metabolic rate\n\nEFIP: Evaluative Frailty Index for Physical Activity\n\nMNA®-SF: Mini Nutritional Assessment Short Form\n\nMOCA: Montreal Cognitive Assessment\n\nPASE: Physical Activity Scale for the Elderly\n\nTUG: Timed Up and Go\n\nWHO: World Health Organization\n\n\nIntroduction\n\nFrailty derived from the Latin word ‘fradilita’ meaning brittleness, is an important and emerging term in geriatric medicine.1 There is no definition that is internationally recognized, but it is usually associated with adverse outcomes developed as a consequence of increased vulnerability. It refers to a decline in physiological systems with increasing age triggered by any minor stressor, which collectively leads to sudden changes in state of health.2 Frailty is a geriatric syndrome, which is multidimensional in nature. In 2017, the World Health Organization (WHO) defined frailty as “a clinically recognizable state in which the ability of older people to cope with every day or acute stressors is compromised by an increased vulnerability brought by age-associated declines in physiological reserve and function across multiple organ systems”.3\n\nAccording to the WHO, 900 million people around the world are classified as being in an elderly age group, out of which there are 104 million elderly (>60 years of age) in India. It is also estimated that India will hold the largest geriatric population around the globe by the year 2050.4 With the advancement in medical sciences there is a decrease in mortality rates, life expectancy is increased and so is frailty among the elderly.5 It is estimated that 4% to 10% of the elderly population dwelling in the United States are frail, also 8.1% of the elderly are observed to be frail in the United Kingdom, and 6.5% and 7% in Italy and France respectively.6\n\nA large compressive study by the WHO showed that among middle- and low-income countries (South Africa, China, Russia, Ghana, India and Mexico) India has the highest prevalence of frailty (i.e., 56.9%) and a greater number of women are frail compared to men (47% of elderly men and 67% of elderly women).7,8\n\nThe evaluation of frailty is difficult because of a lack of any standardized tool. There are 67 tools for quantifying frailty, out of which only nine of these screening tools are highly cited (more than 200 citations).9 Phenotype of frailty10 and Frailty index11 are the validated and most widely used screening tools.9 The phenotype of frailty model defines a person as frail when three or more physiological deficits out of five are present,10 whereas the frailty index model expresses frailty as a “ratio of existing deficits to the total probable deficits there could be”. These deficits are defined as a wide range of diseases, disabilities, signs and symptoms.11\n\nAgeing leads to numerous changes in the physiological systems of the body, which are fundamental to the development of frailty, specifically the immunological system, the neuromuscular system and neuroendocrine system.12 These changes in the body interact progressively and adversely, leading to loss of physiological function and reserve (state of compromised homeostasis).12 The risk factors for frailty are varied and have been found to have multiple linear and non-linear interactions. For example, a consequence of normal ageing leads to loss of muscle mass and strength.13 Muscle loss can also be accelerated due to chronic illness, poor nutrition, decrease in growth hormone production, and reduced physical activity.13 All these factors are inter-related to each other through complex interactions and ultimately lead to frailty. Socio economic and demographic variables like availability of disposable income/finances, level of education, nutritional status, and general living conditions have been found to be confounders of frailty.7\n\nSeveral studies have identified factors like sarcopenia, loss of muscle strength, functional mobility and gait velocity changes, loss of weight, reduced physical activity and easy exhaustibility to be strong independent confounders of frailty. The most closely associated biological parameters of frailty have been identified as inflammatory markers, dyslipidemic markers, endocrinological markers, insulin resistance and state of glycemia.12\n\nAvailable literature on the feasibility of predicting frailty state that changes in functional as well as biological parameters could be used as well qualified candidates to estimate and quantify frailty. Out of these risk factors, it is purported that functionality could be the strongest predictor or measurer of frailty. Sarcopenia, connective tissue remodeling, and inflammatory marker mediated physiological and functional changes and their interaction as well as other confounders of frailty need to be studied to develop a predictive model of frailty.14\n\nA recent large-scale review on the state of frailty related research in India stated that there is a rather alarming lack of conceptualization or epidemiological data regarding frailty in an Indian scenario, and there is a dire need to identify the key confounders for frailty syndrome among Indian elderly.7 There is a scarcity of quality literature on the prevalence of frailty among community dwelling elderly in India. This study was originally planned to analyze the longitudinal trends in frailty status of community dwelling elderly in an Indian population as well to identify factors associated with frailty in the Indian context. However, the recruitment phase of this study coincided with one of the largest lockdowns in history, mandated to minimize the spread of COVID-19 in India. Restrictions were put in place to minimize the outdoor movement of the population in general and specifically the elderly, who were recognized to be the most vulnerable group with respect to the pandemic. This gave us a unique opportunity to study the effects this pandemic enforced, as a result of the necessary restrictions, on frailty status as well as the factors affecting frailty in the elderly.\n\nThe primary objective of the study was to identify the changes in frailty status occurring in a group of community dwelling elderly over a period of three months, during a phase of reduced social mobility due to the COVID-19 imposed lockdown. The study also aimed to identify the changes, if any, that occurred in certain recognized predictors of frailty such as muscle strength, body composition, flexibility, physical activity, cognitive function, and nutritional status.\n\n\nMethods\n\nA prospective observational study was designed and after obtaining the necessary permission to recruit subjects, the study recruitment commenced in March 2020. The study was approved by the Scientific and Institutional Ethics committee of KMC Mangalore (IEC KMC MLR 11-19/590). All stages of the study were conducted in strict adherence to the principles of the “Helsinki Declaration” for research on human subjects.\n\nThe study was conducted among a group of community dwelling elderly of either gender, residing in Mangalore city, of Dakshina Kannada district, of Karnataka state, India\n\nA total of 28 participants were screened between the first and third week of March 2020 of whom 22 subjects were found to be eligible for study.\n\nThe criteria for inclusion were that age must be greater than 65 years, and the Montreal Cognitive Assessment (MOCA)15 score was greater than 26 at the time of first evaluation. Subjects with a known diagnosis of any progressive disorder, as well as those with cardiovascular, musculoskeletal, neurological or systemic illness, which could potentially interfere with data collection, were excluded.\n\nSubjects’ demographics as well as medical history were recorded using self-administered questionnaires and checklist following which an Evaluative Frailty Index for Physical Activity’ (EFIP)16 questionnaire was administered to identify and quantify frailty among them. Lower extremity muscle strength was evaluated using a Baseline® hand-held dynamometer. A Tanita® (UM076) Segmental Body Composition analyzer was used to determine the body composition variables of muscle mass, visceral fat and total body fat percentage for each subject. Subjects were then made to do a 10-meter walk test to analyze the gait velocity following which the nutritional status and socioeconomic status were evaluated using Mini Nutritional Assessment Short Form (MNA®-SF)17 and BG Prasad scale respectively. Physical activity level was recorded using the Physical Activity Scale for the Elderly (PASE) scale following which a timed up and go test was then performed to analyze the functional mobility status. Physical Activity Scale for the Elderly (PASE)18 is an easily administered and scored instrument that measures the level of physical activity in elderly. The instrument is a self-reported questionnaire collecting information on common household and leisure activities over a period of one week, and can be administered directly, through mail, or through a telephone interview. Each subject was then given a date exactly three months from the date of the first evaluation for the follow-up assessment.\n\nUnexpectedly, India went into complete lockdown in the third week of March 2020 following the rise of COVID-19 cases, which in its strict form lasted for approximately 70 days, following which there was a phased gradual unlock. Our follow-up data collection coincided with phase two of unlock but still there was a general advisory for elderly subjects to be home bound to minimize chances of exposure. Of the 22 subjects recruited only 19 subjects returned for the timely follow up evaluation. All the outcomes were again collected using the same tools and in the same order at the end of the third month.\n\nThe data was collected and analyzed using JAMOVI version 1.6.14. (RRID:SCR_016142) statistical software. Normality of continuous variables was tested using the Shapiro-Wilk test. Demographic variables were expressed in terms of descriptive statistics. Differences in gait velocity, strength, body composition and functional mobility at baseline and at three months of follow-up were analyzed using the Wilcoxon signed-rank test/Students paired sample T-test. Changes in scores of the independent variables were individually associated with changes in scores in the Evaluative Frailty Index for Physical Activity questionnaire using the Spearman’s Correlation test.\n\n\nResults\n\nA total of 28 subjects were screened of which 22 were recruited after fulfilling the inclusion and exclusion criteria. The demographic data of all participants are represented in Table 1. The characteristics of the participants such as gender, marital status, height, education level are presented in Table 2.\n\nWe found there was neither a statistically nor a clinically significant change in the frailty status of the studied elderly, over the three-month period. However a statistically significant difference was observed in MOCA (Mean difference = 0.7368, p < 0.05), TUG (Mean difference = -0.64, p < 0.05), Body fat percentage (Mean difference = -0.3632, p < 0.05), Visceral fat (Mean difference = -0.4211, p < 0.05), 10 meter walk test (Mean difference = -1.097, p < 0.029), Muscle mass (Mean difference = -0.55, p < 0.05), and PASE scores (Mean difference = -43, p < 0.05) (Table 3).\n\n* Statistically significant.\n\nComparison of muscle strength of bilateral major muscle groups over the three-month period, revealed that there was a statistically significant reduction in the strength of the left shoulder extensor, adductor, and abductor, elbow flexors on both sides, and elbow extension on the right side. In the lower extremities there was a statistically significant reduction in the strength of all major muscle groups (Table 4).\n\n* Statistically significant.\n\nOn analysis of the relationship between the change in frailty status as measured by EFIP, and the other outcome variables, we found that none of the variables among cognitive function, body composition, functional mobility, muscle strength, or gait speed showed any statistically significant correlation with EFIP (Table 5). The entirety of data collected for the study is available in an anonymized form at OSF, as a registered project.19\n\n\nDiscussion\n\nThe present study was undertaken primarily to analyze the trends in frailty status of a cohort of community dwelling elderly, residing in the Dakshina Kannada district of Karnataka state in India over a period of three months. At the same time the strength of association between the change in frailty score and cognition, nutritional status, gait velocity, functional mobility, body mass, and strength were also analyzed. The recruitment period of the study coincided with the beginning of the ongoing SARS COVID 19 pandemic, which proved to be a major hindrance in approaching, screening and evaluating elderly subjects. Over the period of study, a total of 28 subjects were screened, of which 22 fulfilled the criteria of inclusion in the study. However, of the 22 subjects, the follow up evaluation could only be done for a total of 19 subjects and hence the goals of the study were realigned to investigate the influence of the pandemic induced lockdown and the associated reduction in physical activity on the outcome variables. In the current study we found that there was an observable change in frailty status over a period of three months, but it was not statistically significant.\n\nFrailty is an umbrella term and there are many tools to measure frailty. The EFIP scale was used in the current study because it covers all domains of frailty (physical, psychological, social functioning and general health), and has been proven to have good reliability and validity.20 The data collection involved administering four questionnaires (EPIF, MOCA, MNA®-SF and PASE) which on an average took 45 minutes to one hour to complete. Objective measures of strength, functional mobility, gait velocity, and body composition analysis would take an additional hour to complete. This made the entire data collection process a time consuming one thereby adversely affecting the number of subjects recruited in a day. However, other than the three subjects who chose to forgo the follow-up evaluation because of the pandemic situation, there were no additional dropouts in the span of the study and no reported discomfort or adverse event pertaining to data collection.\n\nThe primary objective of the study was to detect any association between changes in frailty status and other outcome variables. It must be noted that there was only a very minimal difference (over a period of three months) in frailty score (mean difference 0.625) and findings were not statistically significant. We could not find any statistically significant relationship between changes in frailty score and the changes in strength, muscle mass, cognition, nutritional status, gait velocity, or functional mobility.\n\nIt must be emphasized that, when the independent variables were compared at baseline and three months follow-up there was a statistically significant difference found in the scores of MOCA, TUG, visceral fat, PASE and muscle mass. The muscle mass and gait velocity showed a marginal but statistically significant reduction, whereas total body fat as well as visceral fat content showed an increment. Cognitive functions as measured by MOCA and gait velocity (implied by an increase in time taken to complete a 10-meter walk test) showed a decline in the above-mentioned period, whereas the time taken to complete TUG had marginally increased. The observed differences in MOCA scores though were never sufficient to imply a cognitive decline. It can be inferred from these findings that a short span of three months has brought about measurable differences in variables which have been previously associated with frailty.\n\nPrevious research corroborated our findings in that there is a definitive decline in muscle mass ranging from 2 to 4% annually in older men and women of all ethnicities. There is also a concurrent increase in body fat content averaging about 0.8% within the same time span.21\n\nFactors that influence body composition, especially muscle mass include genetic variables, metabolic variables, endocrinological variables, co-morbidities, diet, alcoholism, smoking, as well as gender and ethnicity. It must be emphasized however that physical activity as an independent variable is a strong predictor for loss of muscle mass and changes in body composition in the elderly.21 The data collection of the present study coincided with the period of pandemic enforced restriction and all of the recruited subjects had reported a considerable decline in the amount of physical activity they indulged in the same period. For measuring physical activity, we used PASE and we found a highly significant reduction in physical activity (Mean difference = 43, p < 0.05) over the three-month period. For the study population, the major source of physical activity used to be walking in public places like parks or attending organized social gatherings like yoga and group exercise sessions. Since most of these activities were deemed to be unsafe, especially in the elderly population, there was virtually a complete absence of these activities in the lockdown period.\n\nOur data analysis shows there is a statistically significant decline in functional mobility as measured by TUG with ageing, but it must be emphasized that this decline was barely consequential, and it is safe to assume there was no decline in functional mobility of the studied cohort. Gait velocity showed a statistically significant difference when compared over the three-month period.\n\nIn all major muscle groups of lower extremity, there was a significant difference noted in strength, which ranged from a difference of 0.7 kg to 1.5 kg. One of the key associated finding was that the decline in strength of bilateral hip and knee musculature (hip abductors, hip adductors, knee extension of right side and knee extensors, hip flexors, hip extensors and hip adductors on the left side) showed a statistically significant moderate correlation with decline in muscle mass. Previous studies have shown that there is insufficient evidence of a linear relationship between the loss of muscle strength and muscle mass in ageing, though both have been individually established as definitive outcomes of ageing.21–23 Other factors affecting muscle strength have been identified as impaired reciprocal inhibition, alteration in rate coding of motor unit activation, as well as changes in metabolic characteristic of muscle fibers.24 These changes can happen independent of the changes in muscle mass.23 The changes in muscle strength could then be attributed to the definitive decline in physical activity levels as previously stated, which would have precipitated a deconditioning/reversal effect on muscle strength. In our study cohort, we observed neither a statistically significant nor any amount of change in the nutritional status of the study population as measured by MNA®-SF.\n\n\nConclusions\n\nTwo key findings of this study are that 1) There was a definitive decline in physical activity of the elderly participants within the lockdown period, and 2) There was absolutely no significant change in the frailty status of community dwelling elderly, even in a time period characterized by physical activity restrictions due to the COVID-19 induced lockdown, although some of the independent determinants of frailty showed a decline in the same period. The present study failed to establish any association between frailty and changes in cognitive, functional mobility, body composition, strength, or nutritional factors, during a relatively short span of three months.\n\n\nData availability\n\nOpen Science Framework: Underlying data for ‘Trends in frailty and its associated factors in the community dwelling elderly Indian population during the COVID-19 pandemic: A prospective analytical study’. https://doi.org/10.17605/OSF.IO/QPWMH24\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\nConsent\n\nWritten informed consent for publication of the participants’ details was obtained from the participants.", "appendix": "References\n\nWalston J, Hadley EC, Ferrucci L, et al.: Research agenda for frailty in older adults: toward a better understanding of physiology and etiology: summary from the American Geriatrics Society/National Institute on Aging Research Conference on Frailty in Older Adults. J Am GeriatrSoc. 2006; 54: 991–1001. PubMed Abstract \| Publisher Full Text\n\nClegg A, Young J: The Frailty Syndrome. Clin Med. 2011; 11: 72–75. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organisation: WHO Clinical Consortium on Healthy Ageing. Report of consortium meeting 1–2 December 2016 in Geneva, Switzerland. Geneva.2017.\n\nWorld Health Organisation: World Health Statistics 2015.2015.\n\nKojima G, Liljas AEM, Iliffe S: Frailty syndrome: Implications and challenges for health care policy. Risk Manag Healthc Policy. 2019; 12: 23–30. PubMed Abstract \| Publisher Full Text\n\nNguyen T, Cumming R, Hilmer S: A Review of Frailty in Developing Countries. J Nutr Health Aging. 2015; 19: 941–946. Publisher Full Text\n\nDas S: Frailty syndrome: a problem lurking in indian geriatric population. Indian J Soc Res. 2019; (April): 273.\n\nBiritwum RB, Minicuci N, Yawson AE, et al.: Prevalence of and factors associated with frailty and disability in older adults from China, Ghana, India, Mexico, Russia and South Africa. Maturitas. 2016; 91: 8–18. PubMed Abstract \| Publisher Full Text\n\nButa BJ, Walston JD, Godino JG, et al.: Frailty assessment instruments: Systematic characterization of the uses and contexts of highly-cited instruments. Ageing Res Rev. 2016; 26: 53–61. PubMed Abstract \| Publisher Full Text\n\nFried LP, Tangen CM, Walston J, et al.: Frailty in older adults: evidence for a phenotype. J Gerontol A Biol Sci Med Sci. 2001; 56: M146–M157. Publisher Full Text\n\nMitnitski AB, Mogilner AJ, Rockwood K: Accumulation of deficits as a proxy measure of aging. Sci World J. 2001; 1: 323–336. PubMed Abstract \| Publisher Full Text\n\nFried L, Walston J: Frailty and failure to thrive.Hazzard W, Blass J, Halter J, et al., editors. Principles of geriatric medicine and gerontology. 5th edn.New York: McGraw-Hill; 2003; 11(1): 72–75.\n\nRoubenoff R: Sarcopenia: a major modifiable cause of frailty in the elderly. J Nutr Health Aging. 2000; 4: 140–142.\n\nFulop T, Larbi A, Witkowski JM, et al.: Aging, frailty and age-related diseases. Biogerontology. 2010; 11: 547–563. Publisher Full Text\n\nNasreddine ZS, Phillips NA, Bédirian V, et al.: The Montreal Cognitive Assessment, MoCA: A brief screening tool for mild cognitive impairment. J Am Geriatr Soc. 2005; 53(4): 695–699. Publisher Full Text\n\nDe Vries NM, Staal JB, Olde Rikkert MGM, et al.: Evaluative Frailty Index for Physical Activity (EFIP): A reliable and valid instrument to measure changes in level of frailty. Phys Ther. 2013; 93(4): 551–561. PubMed Abstract \| Publisher Full Text\n\nKaiser MJ, Bauer JM, Ramsch C, et al.: MNA-International Group. Validation of the Mini Nutritional Assessment short-form (MNA®-SF): A practical tool for identification of nutritional status.2009; 13(9): 782–788.\n\nWashburn RA, Smith KW, Jette AM, et al.: The physical activity scale for the elderly (PASE): Development and evaluation. J Clin Epidemiol. 1993; 46(2): 153–162. PubMed Abstract \| Publisher Full Text\n\nGautam K: K Krishnan S, K Kumar V, Nayak MM. Trends in frailty and its associated factors in the community dwelling elderly Indian population during the COVID-19 pandemic: A prospective analytical study. OSF Dataset. Publisher Full Text\n\nSalbach NM, Jaglal SB, Williams JI: Reliability and validity of the evidence-based practice confidence (EPIC) scale. J Contin Educ Health Prof. 2013; 33: 33–40. PubMed Abstract \| Publisher Full Text\n\nGoodpaster BH, Park SW, Harris TB, et al.: The loss of skeletal muscle strength, mass, and quality in older adults: the health, aging and body composition study. J Gerontol A Biol Sci Med Sci. 2006; 61: 1059–1064. PubMed Abstract \| Publisher Full Text\n\nCurtis E, Litwic A, Cooper C, et al.: Determinants of Muscle and Bone Aging. J Cell Physiol. 2015; 230: 2618–2625. PubMed Abstract \| Publisher Full Text\n\nLynch GS: Sarcopenia – Age-Related Muscle Wasting and Weakness: Mechanisms and Treatments. Springer Science & Business Media; 2010.\n\nHunter SK, Pereira XHM, Keenan KG: The aging neuromuscular system and motor performance. J Appl Physiol. 2016; 121(4): 982–995. Publisher Full Text" }	[ { "id": "127472", "date": "28 Apr 2022", "name": "Peeyoosha Gurudut", "expertise": [ "Reviewer Expertise Physiotherapy", "rehabilitation", "yoga", "biomechanics", "movement therapy", "kinesiotherapy", "Musculoskeletal", "orthopedics", "Physical therapy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe sample size is not matching in abstract (19) and manuscript (22) The mention of 3 drop outs in discussion should be part of results ideally.\n\nThe sample size is very small. Hence the generalizability of your findings are questionable. Justify how you ensure external validity of your study based on your small study sample.\nThe justification given in discussion section on small sample is not convincing. What was the study duration?\n\nWhat was the source of sample and their selection? From where were they selected? Needs more elaboration\n\nConsidering the inclusion and exclusion criteria and the study design with assessment conducted only twice, the sample size is very meagre. Justify this.\n\nThe exclusion and inclusion criteria are very vaguely written. What about those with hypertension, renal problems, diabetes etc.? Were they all excluded? What about those who were bed ridden?\n\nWhere was the assessment conducted? In the community? Considering the data being collected during phased unlock.\n\nWho did the collection of data?\n\nThe lock down part in the methodology can be merged with the study setting part.\n\nThe presentation of the article is not according to STROBE guidelines. Kindly refer the equator network for the same and reframe the methodology.\n\nThe outcome variables and follow up is very shallowly written. There is no description of any scales or tests. (eg: Lower extremity muscle strength) - which muscles were assessed?\n\nWhat about the scales having a language barrier? How was it managed with scales?\n\nAuthors have assessed the upper and lower extremity strengths but in methodology mention only lower extremity strength.\n\nThe manufacturing details of the equipment/tools used need to be mentioned in brackets.\n\nThe abbreviations should be elaborated at the foot end of the tables.\n\nIn table 2, a few numbers have been superscripted and in red color. If it is sample number then it needs to be mentioned in brackets.\n\nWere the associated comorbidities considered in the participants, since these may cause changes in their functional and strength status? The clear inclusion and exclusion criteria may answer this question.\n\nThe discussion needs to be more elaborately discussed.\n\nThe limitations should be presented in the last part of the discussion with future recommendations.\n\nWhat are the clinical implications of your study? Add in end part of discussion after future recommendations\n\nReferences 23 and 19 need to be cited in a correct format with all details.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "8166", "date": "08 Dec 2022", "name": "Shyam Krishnan", "role": "Author Response", "response": "On behalf of all the Authors, i express my heartfelt gratitude for the valuable observations made by the respective Reviewers. We will try to assimilate the necessary information and edit the manuscript accordingly." }, { "c_id": "9092", "date": "10 Mar 2023", "name": "Shyam Krishnan", "role": "Author Response", "response": "The sample size is not matching in abstract (19) and manuscript (22) The mention of 3 drop outs in discussion should be part of results ideally. Response: Since its a longitudinal study, we decided to analyze the data of only those subjects who completed follow-up evaluation after three months, and hence the findings of the study reflect the observations made only in those 19 subjects. The sample size is very small. Hence the generalizability of your findings are questionable. Justify how you ensure external validity of your study based on your small study sample. Response: Our intension was to collect a larger sample at the outset, and the aim was to go for longer follow-up period, however because of the pandemic and associated restrictions, the footfall of elderly subjects to the community outreach centers in mangalore, where the study was conducted was severely reduced. The recruited period started in March 2020 and was completed by March 2021. The small sample size is a limitation, however the analysis of data has shown evidence of some definitive trends in the variables studied over a period of 3 months. What was the source of sample and their selection? From where were they selected? Needs more elaboration Response: Necessary information regarding the same has been added. Subjects were recruited from the various community outreach centers operated by the Department of Physiotherapy, KMC Mangalore, within the Mangalore city limits. Considering the inclusion and exclusion criteria and the study design with assessment conducted only twice, the sample size is very meagre. Justify this Response: As mentioned above the study period coincided with that of COVID 19 induced lockdown and there was general limitation on the out of home mobility of elderly subjects. The exclusion and inclusion criteria are very vaguely written. What about those with hypertension, renal problems, diabetes etc.? Were they all excluded? What about those who were bed ridden? Response: As mentioned in the methodology, independent community ambulation at the time of first assessment was a necessity for inclusion in the study. We didn’t exclude subjects with co-morbidities other than those which could severely limit community ambulation at the time of recruitment. Where was the assessment conducted? In the community? Considering the data being collected during phased unlock. Response: As previously mentioned, data was collected from community out reach centers run by the Department of Physiotherapy. These centers operate out of community halls or other such public facilities and provide outpatient services. Who did the collection of data? Response: Outcome measures were collected by the primary author The presentation of the article is not according to STROBE guidelines. Kindly refer the equator network for the same and reframe the methodology. Response: The article has been framed as per the requirements put forward by the journal, and changes were made as per the suggestions in the editorial review phase, and has been generally compliant with the STROBE guidelines. But as suggested by the respected reviewer, changes have been made to be more adherent to STROBE guidelines The outcome variables and follow up is very shallowly written. There is no description of any scales or tests. (eg: Lower extremity muscle strength) - which muscles were assessed? Response: Changes have been made, and additional information has been added as per the suggestions of the respected reviewer. Authors have assessed the upper and lower extremity strengths but in methodology mention only lower extremity strength. Response: The necessary information has been added The manufacturing details of the equipment/tools used need to be mentioned in brackets Response: The necessary information has been added The abbreviations should be elaborated at the foot end of the tables Response: Changes have been made In table 2, a few numbers have been superscripted and in red color. If it is sample number then it needs to be mentioned in brackets. Response: corrections have been made Were the associated comorbidities considered in the participants, since these may cause changes in their functional and strength status? The clear inclusion and exclusion criteria may answer this question Response: Data regarding the presence of co-morbidities was collected at initial assessment, and only those cases were to be excluded where co-morbidities limited community ambulation. There is existing evidence to suggest that co-morbidities could have effect on the dependent as well as independent variables of this study, however the sample size was too small to do a subgroup analysis. Since the primary goal was to study the association between changes in frailty status and changes in the independent variables, the presence of co-morbidities would only be a minor confounder in hypothesis testing. The discussion needs to be more elaborately discussed Response: Due additions have been made The limitations should be presented in the last part of the discussion with future recommendations Response: As per the suggestion, changes have been made What are the clinical implications of your study? Add in end part of discussion after future recommendations Response: As per the suggestions, due additions have been done References 23 and 19 need to be cited in a correct format with all details. Response: Reference 19 pertains to the data set for the current study which is available for verification at OSF. Reference 23 has been corrected." } ] } ]	1	https://f1000research.com/articles/11-311

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